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% Please edit documentation in R/utils.R
\docType{import}
\name{reexports}
\alias{reexports}
\alias{scale_color_viridis}
\alias{scale_fill_viridis}
\title{Objects exported from other packages}
\keyword{internal}
\description{
These objects are imported from other packages. Follow the links
below to see their documentation.
\describe{
\item{viridis}{\code{\link[viridis]{scale_color_viridis}}, \code{\link[viridis]{scale_fill_viridis}}}
}}
ggraph/man/geom_edge_link.Rd 0000644 0001762 0000144 00000020451 13617226162 015524 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/geom_edge_link.R
\name{geom_edge_link}
\alias{geom_edge_link}
\alias{geom_edge_link2}
\alias{geom_edge_link0}
\title{Draw edges as straight lines between nodes}
\usage{
geom_edge_link(
mapping = NULL,
data = get_edges("short"),
position = "identity",
arrow = NULL,
n = 100,
lineend = "butt",
linejoin = "round",
linemitre = 1,
label_colour = "black",
label_alpha = 1,
label_parse = FALSE,
check_overlap = FALSE,
angle_calc = "rot",
force_flip = TRUE,
label_dodge = NULL,
label_push = NULL,
show.legend = NA,
...
)
geom_edge_link2(
mapping = NULL,
data = get_edges("long"),
position = "identity",
arrow = NULL,
n = 100,
lineend = "butt",
linejoin = "round",
linemitre = 1,
label_colour = "black",
label_alpha = 1,
label_parse = FALSE,
check_overlap = FALSE,
angle_calc = "rot",
force_flip = TRUE,
label_dodge = NULL,
label_push = NULL,
show.legend = NA,
...
)
geom_edge_link0(
mapping = NULL,
data = get_edges(),
position = "identity",
arrow = NULL,
lineend = "butt",
show.legend = NA,
...
)
}
\arguments{
\item{mapping}{Set of aesthetic mappings created by \code{\link[ggplot2:aes]{ggplot2::aes()}}
or \code{\link[ggplot2:aes_]{ggplot2::aes_()}}. By default x, y, xend, yend, group and
circular are mapped to x, y, xend, yend, edge.id and circular in the edge
data.}
\item{data}{The return of a call to \code{get_edges()} or a data.frame
giving edges in correct format (see details for for guidance on the format).
See \code{\link[=get_edges]{get_edges()}} for more details on edge extraction.}
\item{position}{Position adjustment, either as a string, or the result of
a call to a position adjustment function.}
\item{arrow}{Arrow specification, as created by \code{\link[grid:arrow]{grid::arrow()}}.}
\item{n}{The number of points to create along the path.}
\item{lineend}{Line end style (round, butt, square).}
\item{linejoin}{Line join style (round, mitre, bevel).}
\item{linemitre}{Line mitre limit (number greater than 1).}
\item{label_colour}{The colour of the edge label. If \code{NA} it will use
the colour of the edge.}
\item{label_alpha}{The opacity of the edge label. If \code{NA} it will use
the opacity of the edge.}
\item{label_parse}{If \code{TRUE}, the labels will be parsed into expressions
and displayed as described in \code{\link[grDevices:plotmath]{grDevices::plotmath()}}.}
\item{check_overlap}{If \code{TRUE}, text that overlaps previous text in the
same layer will not be plotted.}
\item{angle_calc}{Either 'none', 'along', or 'across'. If 'none' the label will
use the angle aesthetic of the geom. If 'along' The label will be written
along the edge direction. If 'across' the label will be written across the
edge direction.}
\item{force_flip}{Logical. If \code{angle_calc} is either 'along' or 'across'
should the label be flipped if it is on it's head. Default to \code{TRUE}.}
\item{label_dodge}{A \code{\link[grid:unit]{grid::unit()}} giving a fixed vertical shift
to add to the label in case of \code{angle_calc} is either 'along' or 'across'}
\item{label_push}{A \code{\link[grid:unit]{grid::unit()}} giving a fixed horizontal shift
to add to the label in case of \code{angle_calc} is either 'along' or 'across'}
\item{show.legend}{logical. Should this layer be included in the legends?
\code{NA}, the default, includes if any aesthetics are mapped.
\code{FALSE} never includes, and \code{TRUE} always includes.
It can also be a named logical vector to finely select the aesthetics to
display.}
\item{...}{Other arguments passed on to \code{\link[ggplot2:layer]{layer()}}. These are
often aesthetics, used to set an aesthetic to a fixed value, like
\code{colour = "red"} or \code{size = 3}. They may also be parameters
to the paired geom/stat.}
}
\description{
This geom draws edges in the simplest way - as straight lines between the
start and end nodes. Not much more to say about that...
}
\section{Edge variants}{
Many geom_edge_* layers comes in 3 flavors depending on the level of control
needed over the drawing. The default (no numeric postfix) generate a number
of points (\code{n}) along the edge and draws it as a path. Each point along
the line has a numeric value associated with it giving the position along the
path, and it is therefore possible to show the direction of the edge by
mapping to this e.g. \code{colour = stat(index)}. The version postfixed with a
"2" uses the "long" edge format (see \code{\link[=get_edges]{get_edges()}}) and makes it
possible to interpolate node parameter between the start and end node along
the edge. It is considerable less performant so should only be used if this
is needed. The version postfixed with a "0" draws the edge in the most
performant way, often directly using an appropriate grob from the grid
package, but does not allow for gradients along the edge.
Often it is beneficial to stop the drawing of the edge before it reaches the
node, for instance in cases where an arrow should be drawn and the arrowhead
shouldn't lay on top or below the node point. geom_edge_* and geom_edge_*2
supports this through the start_cap and end_cap aesthetics that takes a
\code{\link[=geometry]{geometry()}} specification and dynamically caps the termini of the
edges based on the given specifications. This means that if
\code{end_cap = circle(1, 'cm')} the edges will end at a distance of 1cm even
during resizing of the plot window.
All \verb{geom_edge_*} and \code{geom_edge_*2} have the ability to draw a
label along the edge. The reason this is not a separate geom is that in order
for the label to know the location of the edge it needs to know the edge type
etc. Labels are drawn by providing a label aesthetic. The label_pos can be
used to specify where along the edge it should be drawn by supplying a number
between 0 and 1. The label_size aesthetic can be used to control the size of
the label. Often it is needed to have the label written along the direction
of the edge, but since the actual angle is dependent on the plot dimensions
this cannot be calculated beforehand. Using the angle_calc argument allows
you to specify whether to use the supplied angle aesthetic or whether to draw
the label along or across the edge.
}
\section{Edge aesthetic name expansion}{
In order to avoid excessive typing edge aesthetic names are
automatically expanded. Because of this it is not necessary to write
\code{edge_colour} within the \code{aes()} call as \code{colour} will
automatically be renamed appropriately.
}
\section{Aesthetics}{
\code{geom_edge_link} and \code{geom_edge_link0} understand the following
aesthetics. Bold aesthetics are automatically set, but can be overridden.
\itemize{
\item \strong{x}
\item \strong{y}
\item \strong{xend}
\item \strong{yend}
\item edge_colour
\item edge_width
\item edge_linetype
\item edge_alpha
\item filter
}
\code{geom_edge_link2} understand the following aesthetics. Bold aesthetics are
automatically set, but can be overridden.
\itemize{
\item \strong{x}
\item \strong{y}
\item \strong{group}
\item edge_colour
\item edge_width
\item edge_linetype
\item edge_alpha
\item filter
}
\code{geom_edge_link} and \code{geom_edge_link2} furthermore takes the following
aesthetics.
\itemize{
\item start_cap
\item end_cap
\item label
\item label_pos
\item label_size
\item angle
\item hjust
\item vjust
\item family
\item fontface
\item lineheight
}
}
\section{Computed variables}{
\describe{
\item{index}{The position along the path (not computed for the *0 version)}
}
}
\examples{
require(tidygraph)
gr <- create_notable('bull') \%>\%
mutate(class = sample(letters[1:3], n(), replace = TRUE)) \%>\%
activate(edges) \%>\%
mutate(class = sample(letters[1:3], n(), replace = TRUE))
ggraph(gr, 'stress') +
geom_edge_link(aes(alpha = stat(index)))
ggraph(gr, 'stress') +
geom_edge_link2(aes(colour = node.class))
ggraph(gr, 'stress') +
geom_edge_link0(aes(colour = class))
}
\seealso{
Other geom_edge_*:
\code{\link{geom_edge_arc}()},
\code{\link{geom_edge_bend}()},
\code{\link{geom_edge_density}()},
\code{\link{geom_edge_diagonal}()},
\code{\link{geom_edge_elbow}()},
\code{\link{geom_edge_fan}()},
\code{\link{geom_edge_hive}()},
\code{\link{geom_edge_loop}()},
\code{\link{geom_edge_parallel}()},
\code{\link{geom_edge_point}()},
\code{\link{geom_edge_span}()},
\code{\link{geom_edge_tile}()}
}
\author{
Thomas Lin Pedersen
}
\concept{geom_edge_*}
ggraph/man/geom_node_voronoi.Rd 0000644 0001762 0000144 00000011765 13617226162 016313 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/geom_node_voronoi.R
\name{geom_node_voronoi}
\alias{geom_node_voronoi}
\title{Show nodes as voronoi tiles}
\usage{
geom_node_voronoi(
mapping = NULL,
data = NULL,
position = "identity",
show.legend = NA,
bound = NULL,
eps = 1e-09,
max.radius = NULL,
normalize = FALSE,
asp.ratio = 1,
expand = 0,
radius = 0,
...
)
}
\arguments{
\item{mapping}{Set of aesthetic mappings created by \code{\link[ggplot2:aes]{ggplot2::aes()}}
or \code{\link[ggplot2:aes_]{ggplot2::aes_()}}. By default x and y are mapped to x and y in
the node data and group set to \code{-1}.}
\item{data}{The data to be displayed in this layer. There are three
options:
If \code{NULL}, the default, the data is inherited from the plot
data as specified in the call to \code{\link[=ggplot]{ggplot()}}.
A \code{data.frame}, or other object, will override the plot
data. All objects will be fortified to produce a data frame. See
\code{\link[=fortify]{fortify()}} for which variables will be created.
A \code{function} will be called with a single argument,
the plot data. The return value must be a \code{data.frame}, and
will be used as the layer data. A \code{function} can be created
from a \code{formula} (e.g. \code{~ head(.x, 10)}).}
\item{position}{Position adjustment, either as a string, or the result of
a call to a position adjustment function.}
\item{show.legend}{logical. Should this layer be included in the legends?
\code{NA}, the default, includes if any aesthetics are mapped.
\code{FALSE} never includes, and \code{TRUE} always includes.
It can also be a named logical vector to finely select the aesthetics to
display.}
\item{bound}{The bounding rectangle for the tesselation or a custom polygon
to clip the tesselation to. Defaults to \code{NULL} which creates a rectangle
expanded 10\% in all directions. If supplied as a bounding box it should be a
vector giving the bounds in the following order: xmin, xmax, ymin, ymax. If
supplied as a polygon it should either be a 2-column matrix or a data.frame
containing an \code{x} and \code{y} column.}
\item{eps}{A value of epsilon used in testing whether a quantity is zero,
mainly in the context of whether points are collinear. If anomalous errors
arise, it is possible that these may averted by adjusting the value of eps
upward or downward.}
\item{max.radius}{The maximum distance a tile can extend from the point of
origin. Will in effect clip each tile to a circle centered at the point with
the given radius. If \code{normalize = TRUE} the radius will be given relative to
the normalized values}
\item{normalize}{Should coordinates be normalized prior to calculations. If
\code{x} and \code{y} are in wildly different ranges it can lead to
tesselation and triangulation that seems off when plotted without
\code{\link[ggplot2:coord_fixed]{ggplot2::coord_fixed()}}. Normalization of coordinates solves this.
The coordinates are transformed back after calculations.}
\item{asp.ratio}{If \code{normalize = TRUE} the x values will be multiplied by this
amount after normalization.}
\item{expand}{A numeric or unit vector of length one, specifying the
expansion amount. Negative values will result in contraction instead. If the
value is given as a numeric it will be understood as a proportion of the
plot area width.}
\item{radius}{As \code{expand} but specifying the corner radius.}
\item{...}{Other arguments passed on to \code{\link[=layer]{layer()}}. These are
often aesthetics, used to set an aesthetic to a fixed value, like
\code{colour = "red"} or \code{size = 3}. They may also be parameters
to the paired geom/stat.}
}
\description{
This geom is equivalent in functionality to \code{\link[ggforce:geom_voronoi_tile]{ggforce::geom_voronoi_tile()}}
and allows for plotting of nodes as tiles from a voronoi tesselation. As with
\code{\link[ggforce:geom_voronoi_tile]{ggforce::geom_voronoi_tile()}} it is possible to restrict the size of the
tile to a fixed radius, as well as round corners and expand/contract the
tile.
}
\section{Aesthetics}{
\code{geom_node_voronoi} understand the following aesthetics. Bold aesthetics are
automatically set, but can be overridden.
\itemize{
\item \strong{x}
\item \strong{y}
\item alpha
\item colour
\item fill
\item shape
\item size
\item stroke
\item filter
}
}
\examples{
require(tidygraph)
gr <- create_notable('meredith') \%>\%
mutate(group = sample(letters[1:4], n(), TRUE))
ggraph(gr) +
geom_node_voronoi(aes(fill = group, colour = group), alpha = 0.3) +
geom_edge_link(alpha = 0.3) +
geom_node_point()
# Use max.radius to make the tesselation more "node"-like
ggraph(gr) +
geom_node_voronoi(aes(fill = group, colour = group), alpha = 0.3, max.radius = 1) +
geom_edge_link(alpha = 0.3) +
geom_node_point()
}
\seealso{
Other geom_node_*:
\code{\link{geom_node_arc_bar}()},
\code{\link{geom_node_circle}()},
\code{\link{geom_node_point}()},
\code{\link{geom_node_range}()},
\code{\link{geom_node_text}()},
\code{\link{geom_node_tile}()}
}
\author{
Thomas Lin Pedersen
}
\concept{geom_node_*}
ggraph/man/whigs.Rd 0000644 0001762 0000144 00000001706 13050776432 013720 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data_whigs.R
\docType{data}
\name{whigs}
\alias{whigs}
\title{Membership network of American Whigs}
\format{The data is stored as an incidence matrix with persons as rows and
organizations as columns. A 0 means no membership while a one means
membership.}
\source{
\url{https://github.com/kjhealy/revere/blob/master/data/PaulRevereAppD.csv}
adapted from:
Fischer, David H. (1995) \emph{Paul Revere's Ride}. Oxford University Press
}
\usage{
whigs
}
\description{
This dataset shows the membership of 136 colonial Americans in 5 whig
organization and is a bipartite graph. The data appeared in the appendix to
David Hackett Fischer's \emph{Paul Revere's Ride} (Oxford University Press,
1995) and compiled by Kieran Healy for the blog post
\href{http://kieranhealy.org/blog/archives/2013/06/09/using-metadata-to-find-paul-revere/}{Using Metadata to Find Paul Revere}.
}
\keyword{datasets}
ggraph/man/autograph.Rd 0000644 0001762 0000144 00000003343 13617214151 014562 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/autograph.R
\name{autograph}
\alias{autograph}
\alias{autograph.default}
\title{Quickplot wrapper for networks}
\usage{
autograph(graph, ...)
\method{autograph}{default}(
graph,
...,
node_colour = NULL,
edge_colour = NULL,
node_size = NULL,
edge_width = NULL,
node_label = NULL,
edge_label = NULL
)
}
\arguments{
\item{graph}{An object coercible to a tbl_graph}
\item{...}{arguments passed on to methods}
\item{node_colour, edge_colour}{Colour mapping for nodes and edges}
\item{node_size, edge_width}{Size/width mapping for nodes and edges}
\item{node_label, edge_label}{Label mapping for nodes and edges}
}
\description{
This function is intended to quickly show an overview of your network data.
While it returns a ggraph object that layers etc can be added to it is
limited in use and should not be used as a foundation for more complicated
plots. It allows colour, labeling and sizing of nodes and edges, and the
exact combination of layout and layers will depend on these as well as the
features of the network. The output of this function may be fine-tuned at any
release and should not be considered stable. If a plot should be reproducible
it should be created manually.
}
\examples{
library(tidygraph)
gr <- create_notable('herschel') \%>\%
mutate(class = sample(letters[1:3], n(), TRUE)) \%E>\%
mutate(weight = runif(n()))
# Standard graph
autograph(gr)
# Adding node labels will cap edges
autograph(gr, node_label = class)
# Use tidygraph calls for mapping
autograph(gr, node_size = centrality_pagerank())
# Trees are plotted as dendrograms
iris_tree <- hclust(dist(iris[1:4], method = 'euclidean'), method = 'ward.D2')
autograph(iris_tree)
}
ggraph/man/layout_tbl_graph_eigen.Rd 0000644 0001762 0000144 00000003457 13617226162 017311 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/layout_eigen.R
\name{layout_tbl_graph_eigen}
\alias{layout_tbl_graph_eigen}
\title{Place nodes according to their eigenvalues}
\usage{
layout_tbl_graph_eigen(
graph,
type = "laplacian",
eigenvector = "smallest",
circular = FALSE
)
}
\arguments{
\item{graph}{A tbl_graph object}
\item{type}{The type of matrix to extract the eigenvectors from. Either
\code{'laplacian'} or \code{'adjacency'}}
\item{eigenvector}{The eigenvector to use for coordinates. Either \code{'smallest'}
or \code{'largest'}}
\item{circular}{ignored}
}
\value{
A data.frame with the columns \code{x}, \code{y}, \code{circular} as
well as any information stored as node variables in the tbl_graph object.
}
\description{
This layout is based on the idea of spectral layouts where node coordinates
are calculated directly by decomposing a matrix representation of the graph
and extracting the eigenvectors.
}
\seealso{
Other layout_tbl_graph_*:
\code{\link{layout_tbl_graph_auto}()},
\code{\link{layout_tbl_graph_backbone}()},
\code{\link{layout_tbl_graph_centrality}()},
\code{\link{layout_tbl_graph_circlepack}()},
\code{\link{layout_tbl_graph_dendrogram}()},
\code{\link{layout_tbl_graph_fabric}()},
\code{\link{layout_tbl_graph_focus}()},
\code{\link{layout_tbl_graph_hive}()},
\code{\link{layout_tbl_graph_igraph}()},
\code{\link{layout_tbl_graph_linear}()},
\code{\link{layout_tbl_graph_manual}()},
\code{\link{layout_tbl_graph_matrix}()},
\code{\link{layout_tbl_graph_partition}()},
\code{\link{layout_tbl_graph_pmds}()},
\code{\link{layout_tbl_graph_stress}()},
\code{\link{layout_tbl_graph_treemap}()},
\code{\link{layout_tbl_graph_unrooted}()}
}
\author{
The underlying algorithm is implemented in the graphlayouts package
by David Schoch
}
\concept{layout_tbl_graph_*}
ggraph/man/qgraph.Rd 0000644 0001762 0000144 00000000372 13617226162 014056 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/autograph.R
\name{qgraph}
\alias{qgraph}
\title{Deprecated autograph predecessor}
\usage{
qgraph(...)
}
\description{
Deprecated autograph predecessor
}
\keyword{internal}
ggraph/man/geom_edge_loop.Rd 0000644 0001762 0000144 00000017723 13617226162 015550 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/geom_edge_loop.R
\name{geom_edge_loop}
\alias{geom_edge_loop}
\alias{geom_edge_loop0}
\title{Draw edges as diagonals}
\usage{
geom_edge_loop(
mapping = NULL,
data = get_edges(),
position = "identity",
arrow = NULL,
n = 100,
lineend = "butt",
linejoin = "round",
linemitre = 1,
label_colour = "black",
label_alpha = 1,
label_parse = FALSE,
check_overlap = FALSE,
angle_calc = "rot",
force_flip = TRUE,
label_dodge = NULL,
label_push = NULL,
show.legend = NA,
...
)
geom_edge_loop0(
mapping = NULL,
data = get_edges(),
position = "identity",
arrow = NULL,
lineend = "butt",
show.legend = NA,
...
)
}
\arguments{
\item{mapping}{Set of aesthetic mappings created by \code{\link[ggplot2:aes]{ggplot2::aes()}}
or \code{\link[ggplot2:aes_]{ggplot2::aes_()}}. By default x, y, xend, yend, group and
circular are mapped to x, y, xend, yend, edge.id and circular in the edge
data.}
\item{data}{The return of a call to \code{get_edges()} or a data.frame
giving edges in correct format (see details for for guidance on the format).
See \code{\link[=get_edges]{get_edges()}} for more details on edge extraction.}
\item{position}{Position adjustment, either as a string, or the result of
a call to a position adjustment function.}
\item{arrow}{Arrow specification, as created by \code{\link[grid:arrow]{grid::arrow()}}.}
\item{n}{The number of points to create along the path.}
\item{lineend}{Line end style (round, butt, square).}
\item{linejoin}{Line join style (round, mitre, bevel).}
\item{linemitre}{Line mitre limit (number greater than 1).}
\item{label_colour}{The colour of the edge label. If \code{NA} it will use
the colour of the edge.}
\item{label_alpha}{The opacity of the edge label. If \code{NA} it will use
the opacity of the edge.}
\item{label_parse}{If \code{TRUE}, the labels will be parsed into expressions
and displayed as described in \code{\link[grDevices:plotmath]{grDevices::plotmath()}}.}
\item{check_overlap}{If \code{TRUE}, text that overlaps previous text in the
same layer will not be plotted.}
\item{angle_calc}{Either 'none', 'along', or 'across'. If 'none' the label will
use the angle aesthetic of the geom. If 'along' The label will be written
along the edge direction. If 'across' the label will be written across the
edge direction.}
\item{force_flip}{Logical. If \code{angle_calc} is either 'along' or 'across'
should the label be flipped if it is on it's head. Default to \code{TRUE}.}
\item{label_dodge}{A \code{\link[grid:unit]{grid::unit()}} giving a fixed vertical shift
to add to the label in case of \code{angle_calc} is either 'along' or 'across'}
\item{label_push}{A \code{\link[grid:unit]{grid::unit()}} giving a fixed horizontal shift
to add to the label in case of \code{angle_calc} is either 'along' or 'across'}
\item{show.legend}{logical. Should this layer be included in the legends?
\code{NA}, the default, includes if any aesthetics are mapped.
\code{FALSE} never includes, and \code{TRUE} always includes.
It can also be a named logical vector to finely select the aesthetics to
display.}
\item{...}{Other arguments passed on to \code{\link[ggplot2:layer]{layer()}}. These are
often aesthetics, used to set an aesthetic to a fixed value, like
\code{colour = "red"} or \code{size = 3}. They may also be parameters
to the paired geom/stat.}
}
\description{
This geom draws edge loops (edges starting and ending at the same node).
Loops are drawn as bezier curves starting and ending at the position of the
node and with control points protruding at an angle and in a direction
specified in the call. As the start and end node is always the same no *2
method is provided. Loops can severely clutter up your visualization which is
why they are decoupled from the other edge drawings. Only plot them if they
are of importance. If the graph doesn't contain any loops the geom adds
nothing silently.
}
\section{Aesthetics}{
\code{geom_edge_loop} and \code{geom_edge_loop0} understand the following
aesthetics. Bold aesthetics are automatically set, but can be overridden.
\itemize{
\item \strong{x}
\item \strong{y}
\item \strong{from}
\item \strong{to}
\item \strong{span} \emph{90}
\item \strong{direction} \emph{45}
\item \strong{strength} \emph{1}
\item edge_colour
\item edge_width
\item edge_linetype
\item edge_alpha
\item filter
}
\code{geom_edge_loop} furthermore takes the following aesthetics.
\itemize{
\item start_cap
\item end_cap
\item label
\item label_pos
\item label_size
\item angle
\item hjust
\item vjust
\item family
\item fontface
\item lineheight
}
}
\section{Computed variables}{
\describe{
\item{index}{The position along the path (not computed for the *0 version)}
}
}
\section{Edge variants}{
Many geom_edge_* layers comes in 3 flavors depending on the level of control
needed over the drawing. The default (no numeric postfix) generate a number
of points (\code{n}) along the edge and draws it as a path. Each point along
the line has a numeric value associated with it giving the position along the
path, and it is therefore possible to show the direction of the edge by
mapping to this e.g. \code{colour = stat(index)}. The version postfixed with a
"2" uses the "long" edge format (see \code{\link[=get_edges]{get_edges()}}) and makes it
possible to interpolate node parameter between the start and end node along
the edge. It is considerable less performant so should only be used if this
is needed. The version postfixed with a "0" draws the edge in the most
performant way, often directly using an appropriate grob from the grid
package, but does not allow for gradients along the edge.
Often it is beneficial to stop the drawing of the edge before it reaches the
node, for instance in cases where an arrow should be drawn and the arrowhead
shouldn't lay on top or below the node point. geom_edge_* and geom_edge_*2
supports this through the start_cap and end_cap aesthetics that takes a
\code{\link[=geometry]{geometry()}} specification and dynamically caps the termini of the
edges based on the given specifications. This means that if
\code{end_cap = circle(1, 'cm')} the edges will end at a distance of 1cm even
during resizing of the plot window.
All \verb{geom_edge_*} and \code{geom_edge_*2} have the ability to draw a
label along the edge. The reason this is not a separate geom is that in order
for the label to know the location of the edge it needs to know the edge type
etc. Labels are drawn by providing a label aesthetic. The label_pos can be
used to specify where along the edge it should be drawn by supplying a number
between 0 and 1. The label_size aesthetic can be used to control the size of
the label. Often it is needed to have the label written along the direction
of the edge, but since the actual angle is dependent on the plot dimensions
this cannot be calculated beforehand. Using the angle_calc argument allows
you to specify whether to use the supplied angle aesthetic or whether to draw
the label along or across the edge.
}
\section{Edge aesthetic name expansion}{
In order to avoid excessive typing edge aesthetic names are
automatically expanded. Because of this it is not necessary to write
\code{edge_colour} within the \code{aes()} call as \code{colour} will
automatically be renamed appropriately.
}
\examples{
require(tidygraph)
gr <- as_tbl_graph(
data.frame(from = c(1, 1, 2, 2, 3, 3, 3), to = c(1, 2, 2, 3, 3, 1, 2))
)
ggraph(gr, 'stress') +
geom_edge_loop(aes(alpha = stat(index))) +
geom_edge_fan(aes(alpha = stat(index)))
ggraph(gr, 'stress') +
geom_edge_loop0() +
geom_edge_fan0()
}
\seealso{
Other geom_edge_*:
\code{\link{geom_edge_arc}()},
\code{\link{geom_edge_bend}()},
\code{\link{geom_edge_density}()},
\code{\link{geom_edge_diagonal}()},
\code{\link{geom_edge_elbow}()},
\code{\link{geom_edge_fan}()},
\code{\link{geom_edge_hive}()},
\code{\link{geom_edge_link}()},
\code{\link{geom_edge_parallel}()},
\code{\link{geom_edge_point}()},
\code{\link{geom_edge_span}()},
\code{\link{geom_edge_tile}()}
}
\author{
Thomas Lin Pedersen
}
\concept{geom_edge_*}
ggraph/man/highschool.Rd 0000644 0001762 0000144 00000001553 13276561316 014731 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data_highschool.R
\docType{data}
\name{highschool}
\alias{highschool}
\title{Friendship among high school boys}
\format{The graph is stored as an unnamed edgelist with a year attribute.
\describe{
\item{from}{The boy answering the question}
\item{to}{The boy being the answer to the question}
\item{year}{The year the friendship was reported}
}}
\source{
Coleman, J. S. \emph{Introduction to Mathematical Sociology}. New York: Free
Press, pp.450-451.
}
\usage{
highschool
}
\description{
This dataset shows the friendship among high school boys as assessed by the
question: "What fellows here in school do you go around with most often?".
The question was posed twice, with one year in between (1957 and 1958) and
shows the evolution in friendship between the two timepoints.
}
\keyword{datasets}
ggraph/man/scale_edge_fill.Rd 0000644 0001762 0000144 00000015767 13617226162 015673 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/scale_edge_fill.R
\name{scale_edge_fill}
\alias{scale_edge_fill}
\alias{scale_edge_fill_hue}
\alias{scale_edge_fill_brewer}
\alias{scale_edge_fill_distiller}
\alias{scale_edge_fill_gradient}
\alias{scale_edge_fill_gradient2}
\alias{scale_edge_fill_gradientn}
\alias{scale_edge_fill_grey}
\alias{scale_edge_fill_identity}
\alias{scale_edge_fill_manual}
\alias{scale_edge_fill_viridis}
\alias{scale_edge_fill_continuous}
\alias{scale_edge_fill_discrete}
\title{Edge fill scales}
\usage{
scale_edge_fill_hue(
...,
h = c(0, 360) + 15,
c = 100,
l = 65,
h.start = 0,
direction = 1,
na.value = "grey50"
)
scale_edge_fill_brewer(..., type = "seq", palette = 1, direction = 1)
scale_edge_fill_distiller(
...,
type = "seq",
palette = 1,
direction = -1,
values = NULL,
space = "Lab",
na.value = "grey50",
guide = "edge_colourbar"
)
scale_edge_fill_gradient(
...,
low = "#132B43",
high = "#56B1F7",
space = "Lab",
na.value = "grey50",
guide = "edge_colourbar"
)
scale_edge_fill_gradient2(
...,
low = muted("red"),
mid = "white",
high = muted("blue"),
midpoint = 0,
space = "Lab",
na.value = "grey50",
guide = "edge_colourbar"
)
scale_edge_fill_gradientn(
...,
colours,
values = NULL,
space = "Lab",
na.value = "grey50",
guide = "edge_colourbar",
colors
)
scale_edge_fill_grey(..., start = 0.2, end = 0.8, na.value = "red")
scale_edge_fill_identity(..., guide = "none")
scale_edge_fill_manual(..., values)
scale_edge_fill_viridis(
...,
alpha = 1,
begin = 0,
end = 1,
discrete = FALSE,
option = "D",
direction = 1
)
scale_edge_fill_continuous(
...,
low = "#132B43",
high = "#56B1F7",
space = "Lab",
na.value = "grey50",
guide = "edge_colourbar"
)
scale_edge_fill_discrete(
...,
h = c(0, 360) + 15,
c = 100,
l = 65,
h.start = 0,
direction = 1,
na.value = "grey50"
)
}
\arguments{
\item{...}{Arguments passed on to \code{discrete_scale}
\describe{
\item{palette}{A palette function that when called with a single integer
argument (the number of levels in the scale) returns the values that
they should take.}
\item{breaks}{One of:
\itemize{
\item \code{NULL} for no breaks
\item \code{waiver()} for the default breaks computed by the
transformation object
\item A character vector of breaks
\item A function that takes the limits as input and returns breaks
as output
}}
\item{limits}{A character vector that defines possible values of the scale
and their order.}
\item{drop}{Should unused factor levels be omitted from the scale?
The default, \code{TRUE}, uses the levels that appear in the data;
\code{FALSE} uses all the levels in the factor.}
\item{na.translate}{Unlike continuous scales, discrete scales can easily show
missing values, and do so by default. If you want to remove missing values
from a discrete scale, specify \code{na.translate = FALSE}.}
\item{na.value}{If \code{na.translate = TRUE}, what value aesthetic
value should missing be displayed as? Does not apply to position scales
where \code{NA} is always placed at the far right.}
\item{scale_name}{The name of the scale}
\item{name}{The name of the scale. Used as the axis or legend title. If
\code{waiver()}, the default, the name of the scale is taken from the first
mapping used for that aesthetic. If \code{NULL}, the legend title will be
omitted.}
\item{labels}{One of:
\itemize{
\item \code{NULL} for no labels
\item \code{waiver()} for the default labels computed by the
transformation object
\item A character vector giving labels (must be same length as \code{breaks})
\item A function that takes the breaks as input and returns labels
as output
}}
\item{expand}{Vector of range expansion constants used to add some
padding around the data, to ensure that they are placed some distance
away from the axes. Use the convenience function \code{\link[ggplot2:expand_scale]{expand_scale()}}
to generate the values for the \code{expand} argument. The defaults are to
expand the scale by 5\% on each side for continuous variables, and by
0.6 units on each side for discrete variables.}
\item{guide}{A function used to create a guide or its name. See
\code{\link[ggplot2:guides]{guides()}} for more info.}
\item{position}{The position of the axis. "left" or "right" for vertical
scales, "top" or "bottom" for horizontal scales}
\item{super}{The super class to use for the constructed scale}
}}
\item{h}{range of hues to use, in [0, 360]}
\item{c}{chroma (intensity of colour), maximum value varies depending on
combination of hue and luminance.}
\item{l}{luminance (lightness), in [0, 100]}
\item{h.start}{hue to start at}
\item{direction}{direction to travel around the colour wheel,
1 = clockwise, -1 = counter-clockwise}
\item{na.value}{Colour to use for missing values}
\item{type}{One of seq (sequential), div (diverging) or qual (qualitative)}
\item{palette}{If a string, will use that named palette. If a number, will
index into the list of palettes of appropriate \code{type}}
\item{values}{if colours should not be evenly positioned along the gradient
this vector gives the position (between 0 and 1) for each colour in the
\code{colours} vector. See \code{\link[=rescale]{rescale()}} for a convenience function
to map an arbitrary range to between 0 and 1.}
\item{space}{colour space in which to calculate gradient. Must be "Lab" -
other values are deprecated.}
\item{guide}{Type of legend. Use \code{"colourbar"} for continuous
colour bar, or \code{"legend"} for discrete colour legend.}
\item{low, high}{Colours for low and high ends of the gradient.}
\item{mid}{colour for mid point}
\item{midpoint}{The midpoint (in data value) of the diverging scale.
Defaults to 0.}
\item{colours, colors}{Vector of colours to use for n-colour gradient.}
\item{start}{grey value at low end of palette}
\item{end}{grey value at high end of palette}
\item{alpha}{pass through parameter to \code{viridis}}
\item{begin}{The (corrected) hue in [0,1] at which the viridis colormap begins.}
\item{discrete}{generate a discrete palette? (default: \code{FALSE} - generate continuous palette)}
\item{option}{A character string indicating the colormap option to use. Four
options are available: "magma" (or "A"), "inferno" (or "B"), "plasma" (or "C"),
"viridis" (or "D", the default option) and "cividis" (or "E").}
}
\value{
A ggproto object inheriting from \code{Scale}
}
\description{
This set of scales defines new fill scales for edge geoms equivalent to the
ones already defined by ggplot2. The parameters are equivalent to the ones
from ggplot2 so there is nothing new under the sun. The different geoms will
know whether to use edge scales or the standard scales so it is not necessary
to write \code{edge_fill} in the call to the geom - just use \code{fill}.
}
\seealso{
Other scale_edge_*:
\code{\link{scale_edge_alpha}()},
\code{\link{scale_edge_colour}},
\code{\link{scale_edge_linetype}()},
\code{\link{scale_edge_shape}()},
\code{\link{scale_edge_size}()},
\code{\link{scale_edge_width}()},
\code{\link{scale_label_size}()}
}
\concept{scale_edge_*}
ggraph/man/geometry.Rd 0000644 0001762 0000144 00000004633 13617226162 014433 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/geometry.R
\name{geometry}
\alias{geometry}
\alias{circle}
\alias{square}
\alias{ellipsis}
\alias{rectangle}
\alias{label_rect}
\alias{is.geometry}
\title{Define simple shapes for line capping}
\usage{
geometry(
type = "circle",
width = 1,
height = width,
width_unit = "cm",
height_unit = width_unit
)
circle(radius = 1, unit = "cm")
square(length = 1, unit = "cm")
ellipsis(a = 1, b = 1, a_unit = "cm", b_unit = a_unit)
rectangle(width = 1, height = 1, width_unit = "cm", height_unit = width_unit)
label_rect(label, padding = margin(1, 1, 1.5, 1, "mm"), ...)
is.geometry(x)
}
\arguments{
\item{type}{The type of geometry to use. Currently \code{'circle'} and
\code{'rect'} is supported.}
\item{width, height, length, radius, a, b}{The dimensions of the shape.}
\item{unit, width_unit, height_unit, a_unit, b_unit}{The unit for the numbers
given.}
\item{label}{The text to be enclosed}
\item{padding}{extra size to be added around the text using the
\code{\link[ggplot2:margin]{ggplot2::margin()}} function}
\item{...}{Passed on to \code{\link[grid:gpar]{grid::gpar()}}}
\item{x}{An object to test for geometry inheritance}
}
\value{
A geometry object encoding the specified shape.
}
\description{
This set of functions makes it easy to define shapes at the terminal points
of edges that are used to shorten the edges. The shapes themselves are not
drawn, but the edges will end at the boundary of the shape rather than at
the node position. This is especially relevant when drawing arrows at the
edges as the arrows will be partly obscured by the node unless the edge is
shortened. Edge shortening is dynamic and will update as the plot is resized,
making sure that the capping remains at an absolute distance to the end
point.
}
\details{
\code{geometry} is the base constructor, while the rest are helpers to save
typing. \code{circle} creates circles width a given radius, \code{square}
creates squares at a given side length, \code{ellipsis} creates ellipses with
given a and b values (width and height radii), and \code{rectangle} makes
rectangles of a given width and height. label_rect is a helper that, given
a list of strings and potentially formatting options creates a rectangle that
encloses the string.
}
\examples{
geometry(c('circle', 'rect', 'rect'), 1:3, 3:1)
circle(1:4, 'mm')
label_rect(c('some', 'different', 'words'), fontsize = 18)
}
ggraph/man/layout_tbl_graph_dendrogram.Rd 0000644 0001762 0000144 00000005400 13617226162 020332 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/layout_dendrogram.R
\name{layout_tbl_graph_dendrogram}
\alias{layout_tbl_graph_dendrogram}
\title{Apply a dendrogram layout to layout_tbl_graph}
\usage{
layout_tbl_graph_dendrogram(
graph,
circular = FALSE,
offset = pi/2,
height = NULL,
length = NULL,
repel = FALSE,
ratio = 1,
direction = "out"
)
}
\arguments{
\item{graph}{A \code{tbl_graph} object}
\item{circular}{Logical. Should the layout be transformed to a circular
representation. Defaults to \code{FALSE}.}
\item{offset}{If \code{circular = TRUE}, where should it begin. Defaults to
\code{pi/2} which is equivalent to 12 o'clock.}
\item{height}{The node variable holding the height of each node in the
dendrogram. If \code{NULL} it will be calculated as the maximal distance to a
leaf.}
\item{length}{An edge parameter giving the length of each edge. The node
height will be calculated from the maximal length to the root node (ignored
if \code{height} does not evaluate to \code{NULL})}
\item{repel}{Should leafs repel each other relative to the height of their
common ancestor. Will emphasize clusters}
\item{ratio}{The strength of repulsion if \code{repel = TRUE}. Higher values will
give more defined clusters}
\item{direction}{The direction to the leaves. Defaults to 'out'}
}
\value{
A data.frame with the columns \code{x}, \code{y}, \code{circular}, \code{depth} and
\code{leaf} as well as any information stored as node variables on the
tbl_graph
}
\description{
This layout mimics the \code{\link[igraph:layout_as_tree]{igraph::layout_as_tree()}} algorithm
supplied by igraph, but puts all leaves at 0 and builds it up from there,
instead of starting from the root and building it from there. The height of
branch points are related to the maximum distance to an edge from the branch
node, or read from a node variable.
}
\note{
This function is not intended to be used directly but by setting
\code{layout = 'dendrogram'} in \code{\link[=create_layout]{create_layout()}}
}
\seealso{
Other layout_tbl_graph_*:
\code{\link{layout_tbl_graph_auto}()},
\code{\link{layout_tbl_graph_backbone}()},
\code{\link{layout_tbl_graph_centrality}()},
\code{\link{layout_tbl_graph_circlepack}()},
\code{\link{layout_tbl_graph_eigen}()},
\code{\link{layout_tbl_graph_fabric}()},
\code{\link{layout_tbl_graph_focus}()},
\code{\link{layout_tbl_graph_hive}()},
\code{\link{layout_tbl_graph_igraph}()},
\code{\link{layout_tbl_graph_linear}()},
\code{\link{layout_tbl_graph_manual}()},
\code{\link{layout_tbl_graph_matrix}()},
\code{\link{layout_tbl_graph_partition}()},
\code{\link{layout_tbl_graph_pmds}()},
\code{\link{layout_tbl_graph_stress}()},
\code{\link{layout_tbl_graph_treemap}()},
\code{\link{layout_tbl_graph_unrooted}()}
}
\concept{layout_tbl_graph_*}
ggraph/man/geom_edge_hive.Rd 0000644 0001762 0000144 00000022003 13617226162 015515 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/geom_edge_hive.R
\name{geom_edge_hive}
\alias{geom_edge_hive}
\alias{geom_edge_hive2}
\alias{geom_edge_hive0}
\title{Draw edges in hive plots}
\usage{
geom_edge_hive(
mapping = NULL,
data = get_edges(),
position = "identity",
arrow = NULL,
strength = 1,
n = 100,
lineend = "butt",
linejoin = "round",
linemitre = 1,
label_colour = "black",
label_alpha = 1,
label_parse = FALSE,
check_overlap = FALSE,
angle_calc = "rot",
force_flip = TRUE,
label_dodge = NULL,
label_push = NULL,
show.legend = NA,
...,
curvature
)
geom_edge_hive2(
mapping = NULL,
data = get_edges("long"),
position = "identity",
arrow = NULL,
strength = 1,
n = 100,
lineend = "butt",
linejoin = "round",
linemitre = 1,
label_colour = "black",
label_alpha = 1,
label_parse = FALSE,
check_overlap = FALSE,
angle_calc = "rot",
force_flip = TRUE,
label_dodge = NULL,
label_push = NULL,
show.legend = NA,
...,
curvature
)
geom_edge_hive0(
mapping = NULL,
data = get_edges(),
position = "identity",
arrow = NULL,
strength = 1,
lineend = "butt",
show.legend = NA,
...,
curvature
)
}
\arguments{
\item{mapping}{Set of aesthetic mappings created by \code{\link[ggplot2:aes]{ggplot2::aes()}}
or \code{\link[ggplot2:aes_]{ggplot2::aes_()}}. By default x, y, xend, yend, group and
circular are mapped to x, y, xend, yend, edge.id and circular in the edge
data.}
\item{data}{The return of a call to \code{get_edges()} or a data.frame
giving edges in correct format (see details for for guidance on the format).
See \code{\link[=get_edges]{get_edges()}} for more details on edge extraction.}
\item{position}{Position adjustment, either as a string, or the result of
a call to a position adjustment function.}
\item{arrow}{Arrow specification, as created by \code{\link[grid:arrow]{grid::arrow()}}.}
\item{strength}{The curvature of the bezier. Defines the distance from the
control points to the midpoint between the start and end node. 1 means the
control points are positioned halfway between the nodes and the middle of the
two axes, while 0 means it coincide with the nodes (resulting in straight
lines)}
\item{n}{The number of points to create along the path.}
\item{lineend}{Line end style (round, butt, square).}
\item{linejoin}{Line join style (round, mitre, bevel).}
\item{linemitre}{Line mitre limit (number greater than 1).}
\item{label_colour}{The colour of the edge label. If \code{NA} it will use
the colour of the edge.}
\item{label_alpha}{The opacity of the edge label. If \code{NA} it will use
the opacity of the edge.}
\item{label_parse}{If \code{TRUE}, the labels will be parsed into expressions
and displayed as described in \code{\link[grDevices:plotmath]{grDevices::plotmath()}}.}
\item{check_overlap}{If \code{TRUE}, text that overlaps previous text in the
same layer will not be plotted.}
\item{angle_calc}{Either 'none', 'along', or 'across'. If 'none' the label will
use the angle aesthetic of the geom. If 'along' The label will be written
along the edge direction. If 'across' the label will be written across the
edge direction.}
\item{force_flip}{Logical. If \code{angle_calc} is either 'along' or 'across'
should the label be flipped if it is on it's head. Default to \code{TRUE}.}
\item{label_dodge}{A \code{\link[grid:unit]{grid::unit()}} giving a fixed vertical shift
to add to the label in case of \code{angle_calc} is either 'along' or 'across'}
\item{label_push}{A \code{\link[grid:unit]{grid::unit()}} giving a fixed horizontal shift
to add to the label in case of \code{angle_calc} is either 'along' or 'across'}
\item{show.legend}{logical. Should this layer be included in the legends?
\code{NA}, the default, includes if any aesthetics are mapped.
\code{FALSE} never includes, and \code{TRUE} always includes.
It can also be a named logical vector to finely select the aesthetics to
display.}
\item{...}{Other arguments passed on to \code{\link[ggplot2:layer]{layer()}}. These are
often aesthetics, used to set an aesthetic to a fixed value, like
\code{colour = "red"} or \code{size = 3}. They may also be parameters
to the paired geom/stat.}
\item{curvature}{Deprecated. Use \code{strength} instead.}
}
\description{
This geom is only intended for use together with the hive layout. It draws
edges between nodes as bezier curves, with the control points positioned at
the same radii as the start or end point, and at a distance defined by the
curvature argument.
}
\section{Aesthetics}{
\code{geom_edge_hive} and \code{geom_edge_hive0} understand the following
aesthetics. Bold aesthetics are automatically set, but can be overridden.
\itemize{
\item \strong{x}
\item \strong{y}
\item \strong{xend}
\item \strong{yend}
\item edge_colour
\item edge_width
\item edge_linetype
\item edge_alpha
\item filter
}
\code{geom_edge_hive2} understand the following aesthetics. Bold aesthetics are
automatically set, but can be overridden.
\itemize{
\item \strong{x}
\item \strong{y}
\item \strong{group}
\item edge_colour
\item edge_width
\item edge_linetype
\item edge_alpha
\item filter
}
\code{geom_edge_hive} and \code{geom_edge_hive2} furthermore takes the following
aesthetics.
\itemize{
\item start_cap
\item end_cap
\item label
\item label_pos
\item label_size
\item angle
\item hjust
\item vjust
\item family
\item fontface
\item lineheight
}
}
\section{Computed variables}{
\describe{
\item{index}{The position along the path (not computed for the *0 version)}
}
}
\section{Edge variants}{
Many geom_edge_* layers comes in 3 flavors depending on the level of control
needed over the drawing. The default (no numeric postfix) generate a number
of points (\code{n}) along the edge and draws it as a path. Each point along
the line has a numeric value associated with it giving the position along the
path, and it is therefore possible to show the direction of the edge by
mapping to this e.g. \code{colour = stat(index)}. The version postfixed with a
"2" uses the "long" edge format (see \code{\link[=get_edges]{get_edges()}}) and makes it
possible to interpolate node parameter between the start and end node along
the edge. It is considerable less performant so should only be used if this
is needed. The version postfixed with a "0" draws the edge in the most
performant way, often directly using an appropriate grob from the grid
package, but does not allow for gradients along the edge.
Often it is beneficial to stop the drawing of the edge before it reaches the
node, for instance in cases where an arrow should be drawn and the arrowhead
shouldn't lay on top or below the node point. geom_edge_* and geom_edge_*2
supports this through the start_cap and end_cap aesthetics that takes a
\code{\link[=geometry]{geometry()}} specification and dynamically caps the termini of the
edges based on the given specifications. This means that if
\code{end_cap = circle(1, 'cm')} the edges will end at a distance of 1cm even
during resizing of the plot window.
All \verb{geom_edge_*} and \code{geom_edge_*2} have the ability to draw a
label along the edge. The reason this is not a separate geom is that in order
for the label to know the location of the edge it needs to know the edge type
etc. Labels are drawn by providing a label aesthetic. The label_pos can be
used to specify where along the edge it should be drawn by supplying a number
between 0 and 1. The label_size aesthetic can be used to control the size of
the label. Often it is needed to have the label written along the direction
of the edge, but since the actual angle is dependent on the plot dimensions
this cannot be calculated beforehand. Using the angle_calc argument allows
you to specify whether to use the supplied angle aesthetic or whether to draw
the label along or across the edge.
}
\section{Edge aesthetic name expansion}{
In order to avoid excessive typing edge aesthetic names are
automatically expanded. Because of this it is not necessary to write
\code{edge_colour} within the \code{aes()} call as \code{colour} will
automatically be renamed appropriately.
}
\examples{
# Plot the flare import graph as a hive plot
library(tidygraph)
flareGr <- as_tbl_graph(flare$imports) \%>\%
mutate(
type = dplyr::case_when(
centrality_degree(mode = 'in') == 0 ~ 'Source',
centrality_degree(mode = 'out') == 0 ~ 'Sink',
TRUE ~ 'Both'
)
) \%>\%
activate(edges) \%>\%
mutate(
type = dplyr::case_when(
grepl('flare.analytics', paste(.N()$name[from], .N()$name[to])) ~ 'Analytics',
TRUE ~ 'Other'
)
)
ggraph(flareGr, 'hive', axis = type) +
geom_edge_hive(aes(colour = type), edge_alpha = 0.1) +
coord_fixed()
}
\seealso{
Other geom_edge_*:
\code{\link{geom_edge_arc}()},
\code{\link{geom_edge_bend}()},
\code{\link{geom_edge_density}()},
\code{\link{geom_edge_diagonal}()},
\code{\link{geom_edge_elbow}()},
\code{\link{geom_edge_fan}()},
\code{\link{geom_edge_link}()},
\code{\link{geom_edge_loop}()},
\code{\link{geom_edge_parallel}()},
\code{\link{geom_edge_point}()},
\code{\link{geom_edge_span}()},
\code{\link{geom_edge_tile}()}
}
\author{
Thomas Lin Pedersen
}
\concept{geom_edge_*}
ggraph/man/layout_tbl_graph_stress.Rd 0000644 0001762 0000144 00000005612 13617226162 017540 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/layout_stress.R
\name{layout_tbl_graph_stress}
\alias{layout_tbl_graph_stress}
\alias{layout_tbl_graph_sparse_stress}
\title{Place nodes using stress majorisation}
\usage{
layout_tbl_graph_stress(
graph,
weights = NULL,
niter = 500,
tolerance = 1e-04,
mds = TRUE,
bbox = 50,
circular = FALSE
)
layout_tbl_graph_sparse_stress(
graph,
pivots,
weights = NULL,
niter = 500,
circular = FALSE
)
}
\arguments{
\item{graph}{a tbl_graph object}
\item{weights}{An expression evaluated on the edge data to provide edge
weights for the layout. Currently ignored for the sparse version}
\item{niter}{number of iterations during stress optimization}
\item{tolerance}{stopping criterion for stress optimization}
\item{mds}{should an MDS layout be used as initial layout (default: TRUE)}
\item{bbox}{constrain dimension of output. Only relevant to determine the
placement of disconnected graphs.}
\item{circular}{ignored}
\item{pivots}{The number of pivot nodes.}
}
\value{
A data.frame with the columns \code{x}, \code{y}, \code{circular} as
well as any information stored as node variables in the tbl_graph object.
}
\description{
This layout is related to the stress-minimization algorithm known as
Kamada-Kawai (available as the 'kk' layout), but uses another optimization
strategy. It generally have better runtime, quality, and stability compared
to the Kamada-Kawai layout and is thus generally preferred. The sparse
version of the layout have better performance (especially on larger networks)
at the expense of layout quality, but will generally outperform many other
algorithms for large graphs in both runtime and quality (e.g. the 'drl'
layout from igraph).
}
\references{
Gansner, E. R., Koren, Y., & North, S. (2004). \emph{Graph drawing by stress
majorization.} In International Symposium on Graph Drawing (pp. 239-250). Springer, Berlin, Heidelberg.
Ortmann, M. and Klimenta, M. and Brandes, U. (2016). \emph{A Sparse Stress Model.} https://arxiv.org/pdf/1608.08909.pdf
}
\seealso{
Other layout_tbl_graph_*:
\code{\link{layout_tbl_graph_auto}()},
\code{\link{layout_tbl_graph_backbone}()},
\code{\link{layout_tbl_graph_centrality}()},
\code{\link{layout_tbl_graph_circlepack}()},
\code{\link{layout_tbl_graph_dendrogram}()},
\code{\link{layout_tbl_graph_eigen}()},
\code{\link{layout_tbl_graph_fabric}()},
\code{\link{layout_tbl_graph_focus}()},
\code{\link{layout_tbl_graph_hive}()},
\code{\link{layout_tbl_graph_igraph}()},
\code{\link{layout_tbl_graph_linear}()},
\code{\link{layout_tbl_graph_manual}()},
\code{\link{layout_tbl_graph_matrix}()},
\code{\link{layout_tbl_graph_partition}()},
\code{\link{layout_tbl_graph_pmds}()},
\code{\link{layout_tbl_graph_treemap}()},
\code{\link{layout_tbl_graph_unrooted}()}
}
\author{
The underlying algorithm is implemented in the graphlayouts package
by David Schoch
}
\concept{layout_tbl_graph_*}
ggraph/man/scale_edge_width.Rd 0000644 0001762 0000144 00000012001 13617226162 016036 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/scale_edge_width.R
\name{scale_edge_width}
\alias{scale_edge_width}
\alias{scale_edge_width_continuous}
\alias{scale_edge_width_discrete}
\alias{scale_edge_width_manual}
\alias{scale_edge_width_identity}
\title{Edge width scales}
\usage{
scale_edge_width_continuous(..., range = c(1, 6))
scale_edge_width(..., range = c(1, 6))
scale_edge_width_discrete(..., range = c(2, 6))
scale_edge_width_manual(..., values)
scale_edge_width_identity(..., guide = "none")
}
\arguments{
\item{...}{Arguments passed on to \code{continuous_scale}
\describe{
\item{name}{The name of the scale. Used as the axis or legend title. If
\code{waiver()}, the default, the name of the scale is taken from the first
mapping used for that aesthetic. If \code{NULL}, the legend title will be
omitted.}
\item{breaks}{One of:
\itemize{
\item \code{NULL} for no breaks
\item \code{waiver()} for the default breaks computed by the
transformation object
\item A numeric vector of positions
\item A function that takes the limits as input and returns breaks
as output
}}
\item{minor_breaks}{One of:
\itemize{
\item \code{NULL} for no minor breaks
\item \code{waiver()} for the default breaks (one minor break between
each major break)
\item A numeric vector of positions
\item A function that given the limits returns a vector of minor breaks.
}}
\item{labels}{One of:
\itemize{
\item \code{NULL} for no labels
\item \code{waiver()} for the default labels computed by the
transformation object
\item A character vector giving labels (must be same length as \code{breaks})
\item A function that takes the breaks as input and returns labels
as output
}}
\item{limits}{One of:
\itemize{
\item \code{NULL} to use the default scale range
\item A numeric vector of length two providing limits of the scale.
Use \code{NA} to refer to the existing minimum or maximum
\item A function that accepts the existing (automatic) limits and returns
new limits
}}
\item{oob}{Function that handles limits outside of the scale limits
(out of bounds). The default replaces out of bounds values with \code{NA}.}
\item{na.value}{Missing values will be replaced with this value.}
\item{trans}{Either the name of a transformation object, or the
object itself. Built-in transformations include "asn", "atanh",
"boxcox", "date", "exp", "hms", "identity", "log", "log10", "log1p", "log2",
"logit", "modulus", "probability", "probit", "pseudo_log", "reciprocal",
"reverse", "sqrt" and "time".
A transformation object bundles together a transform, its inverse,
and methods for generating breaks and labels. Transformation objects
are defined in the scales package, and are called \code{name_trans}, e.g.
\code{\link[scales:boxcox_trans]{scales::boxcox_trans()}}. You can create your own
transformation with \code{\link[scales:trans_new]{scales::trans_new()}}.}
\item{guide}{A function used to create a guide or its name. See
\code{\link[ggplot2:guides]{guides()}} for more info.}
\item{position}{The position of the axis. "left" or "right" for vertical
scales, "top" or "bottom" for horizontal scales}
\item{super}{The super class to use for the constructed scale}
\item{expand}{Vector of range expansion constants used to add some
padding around the data, to ensure that they are placed some distance
away from the axes. Use the convenience function \code{\link[ggplot2:expand_scale]{expand_scale()}}
to generate the values for the \code{expand} argument. The defaults are to
expand the scale by 5\% on each side for continuous variables, and by
0.6 units on each side for discrete variables.}
}}
\item{range}{a numeric vector of length 2 that specifies the minimum and
maximum size of the plotting symbol after transformation.}
\item{values}{a set of aesthetic values to map data values to. If this
is a named vector, then the values will be matched based on the names.
If unnamed, values will be matched in order (usually alphabetical) with
the limits of the scale. Any data values that don't match will be
given \code{na.value}.}
\item{guide}{A function used to create a guide or its name. See
\code{\link[ggplot2:guides]{guides()}} for more info.}
}
\value{
A ggproto object inheriting from \code{Scale}
}
\description{
This set of scales defines width scales for edge geoms. Of all the new edge
scales defined in ggraph, this is the only one not having an equivalent in
ggplot2. In essence it mimics the use of size in
\code{\link[ggplot2:geom_line]{ggplot2::geom_line()}} and related. As almost all edge
representations are lines of some sort, edge_width will be used much more
often than edge_size. It is not necessary to spell out that it is an edge
scale as the geom knows if it is drawing an edge. Just write \code{width} and
not \code{edge_width} in the call to geoms.
}
\seealso{
Other scale_edge_*:
\code{\link{scale_edge_alpha}()},
\code{\link{scale_edge_colour}},
\code{\link{scale_edge_fill}},
\code{\link{scale_edge_linetype}()},
\code{\link{scale_edge_shape}()},
\code{\link{scale_edge_size}()},
\code{\link{scale_label_size}()}
}
\concept{scale_edge_*}
ggraph/man/guide_edge_direction.Rd 0000644 0001762 0000144 00000006374 13617226162 016725 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/edge_direction.R
\name{guide_edge_direction}
\alias{guide_edge_direction}
\title{Edge direction guide}
\usage{
guide_edge_direction(
title = waiver(),
title.position = NULL,
title.theme = NULL,
title.hjust = NULL,
title.vjust = NULL,
arrow = TRUE,
arrow.position = NULL,
barwidth = NULL,
barheight = NULL,
nbin = 500,
direction = NULL,
default.unit = "line",
reverse = FALSE,
order = 0,
override.aes = list(),
...
)
}
\arguments{
\item{title}{A character string or expression indicating a title of guide.
If \code{NULL}, the title is not shown. By default
(\code{\link[ggplot2:waiver]{waiver()}}), the name of the scale object or the name
specified in \code{\link[ggplot2:labs]{labs()}} is used for the title.}
\item{title.position}{A character string indicating the position of a
title. One of "top" (default for a vertical guide), "bottom", "left"
(default for a horizontal guide), or "right."}
\item{title.theme}{A theme object for rendering the title text. Usually the
object of \code{\link[ggplot2:element_text]{element_text()}} is expected. By default, the theme is
specified by \code{legend.title} in \code{\link[ggplot2:theme]{theme()}} or theme.}
\item{title.hjust}{A number specifying horizontal justification of the
title text.}
\item{title.vjust}{A number specifying vertical justification of the title
text.}
\item{arrow}{Logical. Should an arrow be drawn to illustrate the direction.
Defaults to \code{TRUE}}
\item{arrow.position}{The position of the arrow relative to the example edge.}
\item{barwidth}{A numeric or a \code{\link[grid:unit]{grid::unit()}} object specifying
the width of the colourbar. Default value is \code{legend.key.width} or
\code{legend.key.size} in \code{\link[ggplot2:theme]{theme()}} or theme.}
\item{barheight}{A numeric or a \code{\link[grid:unit]{grid::unit()}} object specifying
the height of the colourbar. Default value is \code{legend.key.height} or
\code{legend.key.size} in \code{\link[ggplot2:theme]{theme()}} or theme.}
\item{nbin}{A numeric specifying the number of bins for drawing the
colourbar. A smoother colourbar results from a larger value.}
\item{direction}{A character string indicating the direction of the guide.
One of "horizontal" or "vertical."}
\item{default.unit}{A character string indicating \code{\link[grid:unit]{grid::unit()}}
for \code{barwidth} and \code{barheight}.}
\item{reverse}{logical. If \code{TRUE} the colourbar is reversed. By default,
the highest value is on the top and the lowest value is on the bottom}
\item{order}{positive integer less than 99 that specifies the order of
this guide among multiple guides. This controls the order in which
multiple guides are displayed, not the contents of the guide itself.
If 0 (default), the order is determined by a secret algorithm.}
\item{override.aes}{A list specifying aesthetic parameters of legend key.}
\item{...}{ignored.}
}
\description{
This guide is intended to show the direction of edges based on the aesthetics
mapped to its progression, such as changing width, colour and opacity.
}
\examples{
gr <- tidygraph::as_tbl_graph(highschool)
ggraph(gr, layout = 'kk') +
geom_edge_fan(aes(alpha = stat(index))) +
guides(edge_alpha = guide_edge_direction())
}
ggraph/man/layout_tbl_graph_unrooted.Rd 0000644 0001762 0000144 00000005601 13617226162 020052 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/layout_unrooted.R
\name{layout_tbl_graph_unrooted}
\alias{layout_tbl_graph_unrooted}
\title{Create an unrooted layout using equal-angle or equal-daylight}
\usage{
layout_tbl_graph_unrooted(
graph,
daylight = TRUE,
length = NULL,
tolerance = 0.05,
rotation_mod = 1,
maxiter = 100,
circular = FALSE
)
}
\arguments{
\item{graph}{A tbl_graph object}
\item{daylight}{Should equal-daylight adjustments be made}
\item{length}{An expression evaluating to the branch length of each edge}
\item{tolerance}{The threshold for mean angular adjustment before terminating
the daylight adjustment}
\item{rotation_mod}{A modifier for the angular adjustment of each branch. Set
it below 1 to let the daylight adjustment progress more slowly}
\item{maxiter}{The maximum number of iterations in the the daylight
adjustment}
\item{circular}{ignored}
}
\value{
A data.frame with the columns \code{x}, \code{y}, \code{circular}, \code{leaf} as well as
any information stored as node variables in the tbl_graph object.
}
\description{
When drawing unrooted trees the standard dendrogram layout is a bad fit as it
implicitly creates a visual root node. Instead it is possible to spread the
leafs out on the plane without putting any special emphasis on a particular
node using an unrooted layout. The standard algorithm is the equal angle
algorithm, but it can struggle with optimising the leaf distribution for
large trees trees with very uneven branch length. The equal daylight
algorithm modifies the output of the equal angle algorithm to better disperse
the leaves, at the cost of higher computational cost and the possibility of
edge crossings for very large unbalanced trees. For standard sized trees the
daylight algorithm is far superior and not too heavy so it is the default.
}
\note{
Unrooted is a layout intended for undirected trees, that is, graphs with no
cycles. If the provided graph does not fit this format an attempt to convert
it to such a format will be made.
}
\references{
Felsenstein, J. (2004) \emph{Drawing Trees}, in Inferring Phylogenies. Sinauer
Assoc., pp 573-584
}
\seealso{
Other layout_tbl_graph_*:
\code{\link{layout_tbl_graph_auto}()},
\code{\link{layout_tbl_graph_backbone}()},
\code{\link{layout_tbl_graph_centrality}()},
\code{\link{layout_tbl_graph_circlepack}()},
\code{\link{layout_tbl_graph_dendrogram}()},
\code{\link{layout_tbl_graph_eigen}()},
\code{\link{layout_tbl_graph_fabric}()},
\code{\link{layout_tbl_graph_focus}()},
\code{\link{layout_tbl_graph_hive}()},
\code{\link{layout_tbl_graph_igraph}()},
\code{\link{layout_tbl_graph_linear}()},
\code{\link{layout_tbl_graph_manual}()},
\code{\link{layout_tbl_graph_matrix}()},
\code{\link{layout_tbl_graph_partition}()},
\code{\link{layout_tbl_graph_pmds}()},
\code{\link{layout_tbl_graph_stress}()},
\code{\link{layout_tbl_graph_treemap}()}
}
\concept{layout_tbl_graph_*}
ggraph/man/scale_edge_shape.Rd 0000644 0001762 0000144 00000007225 13617226162 016033 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/scale_edge_shape.R
\name{scale_edge_shape}
\alias{scale_edge_shape}
\alias{scale_edge_shape_discrete}
\alias{scale_edge_shape_continuous}
\alias{scale_edge_shape_manual}
\alias{scale_edge_shape_identity}
\title{Edge shape scales}
\usage{
scale_edge_shape(..., solid = TRUE)
scale_edge_shape_discrete(..., solid = TRUE)
scale_edge_shape_continuous(...)
scale_edge_shape_manual(..., values)
scale_edge_shape_identity(..., guide = "none")
}
\arguments{
\item{...}{Arguments passed on to \code{discrete_scale}
\describe{
\item{palette}{A palette function that when called with a single integer
argument (the number of levels in the scale) returns the values that
they should take.}
\item{breaks}{One of:
\itemize{
\item \code{NULL} for no breaks
\item \code{waiver()} for the default breaks computed by the
transformation object
\item A character vector of breaks
\item A function that takes the limits as input and returns breaks
as output
}}
\item{limits}{A character vector that defines possible values of the scale
and their order.}
\item{drop}{Should unused factor levels be omitted from the scale?
The default, \code{TRUE}, uses the levels that appear in the data;
\code{FALSE} uses all the levels in the factor.}
\item{na.translate}{Unlike continuous scales, discrete scales can easily show
missing values, and do so by default. If you want to remove missing values
from a discrete scale, specify \code{na.translate = FALSE}.}
\item{na.value}{If \code{na.translate = TRUE}, what value aesthetic
value should missing be displayed as? Does not apply to position scales
where \code{NA} is always placed at the far right.}
\item{aesthetics}{The names of the aesthetics that this scale works with}
\item{scale_name}{The name of the scale}
\item{name}{The name of the scale. Used as the axis or legend title. If
\code{waiver()}, the default, the name of the scale is taken from the first
mapping used for that aesthetic. If \code{NULL}, the legend title will be
omitted.}
\item{labels}{One of:
\itemize{
\item \code{NULL} for no labels
\item \code{waiver()} for the default labels computed by the
transformation object
\item A character vector giving labels (must be same length as \code{breaks})
\item A function that takes the breaks as input and returns labels
as output
}}
\item{guide}{A function used to create a guide or its name. See
\code{\link[ggplot2:guides]{guides()}} for more info.}
\item{super}{The super class to use for the constructed scale}
}}
\item{solid}{Should the shapes be solid, \code{TRUE}, or hollow,
\code{FALSE}?}
\item{values}{a set of aesthetic values to map data values to. If this
is a named vector, then the values will be matched based on the names.
If unnamed, values will be matched in order (usually alphabetical) with
the limits of the scale. Any data values that don't match will be
given \code{na.value}.}
\item{guide}{Guide to use for this scale.}
}
\value{
A ggproto object inheriting from \code{Scale}
}
\description{
This set of scales defines new shape scales for edge geoms equivalent to the
ones already defined by ggplot2. See \code{\link[ggplot2:scale_shape]{ggplot2::scale_shape()}} for
more information. The different geoms will know whether to use edge scales or
the standard scales so it is not necessary to write \code{edge_shape} in
the call to the geom - just use \code{shape}.
}
\seealso{
Other scale_edge_*:
\code{\link{scale_edge_alpha}()},
\code{\link{scale_edge_colour}},
\code{\link{scale_edge_fill}},
\code{\link{scale_edge_linetype}()},
\code{\link{scale_edge_size}()},
\code{\link{scale_edge_width}()},
\code{\link{scale_label_size}()}
}
\concept{scale_edge_*}
ggraph/man/layout_tbl_graph_backbone.Rd 0000644 0001762 0000144 00000004314 13617226162 017757 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/layout_backbone.R
\name{layout_tbl_graph_backbone}
\alias{layout_tbl_graph_backbone}
\title{Place node to emphasize group structure}
\usage{
layout_tbl_graph_backbone(graph, keep = 0.2, circular = FALSE)
}
\arguments{
\item{graph}{A tbl_graph object}
\item{keep}{The fraction of edges to use for creating the backbone}
\item{circular}{ignored}
}
\value{
A data.frame with the columns \code{x}, \code{y}, \code{circular} as
well as any information stored as node variables in the tbl_graph object.
Further an edge attribute called \code{backbone} is added giving whether the edge
was selected as backbone.
}
\description{
This layout is optimised for drawing small-world types of graphs often found
in social networks, where distinct groups are still highly connected to the
remaining graph. Typical layouts struggle with this as they attempt to
minimise the edge length of all edges equally. The backbone layout is based
on weighing edges based on how well they hold together communities. The end
result is that communities tend to stick together despite high
interconnectivity.
}
\references{
Nocaj, A., Ortmann, M., & Brandes, U. (2015). \emph{Untangling the hairballs of
multi-centered, small-world online social media networks.} Journal of Graph
Algorithms and Applications: JGAA, 19(2), 595-618.
}
\seealso{
Other layout_tbl_graph_*:
\code{\link{layout_tbl_graph_auto}()},
\code{\link{layout_tbl_graph_centrality}()},
\code{\link{layout_tbl_graph_circlepack}()},
\code{\link{layout_tbl_graph_dendrogram}()},
\code{\link{layout_tbl_graph_eigen}()},
\code{\link{layout_tbl_graph_fabric}()},
\code{\link{layout_tbl_graph_focus}()},
\code{\link{layout_tbl_graph_hive}()},
\code{\link{layout_tbl_graph_igraph}()},
\code{\link{layout_tbl_graph_linear}()},
\code{\link{layout_tbl_graph_manual}()},
\code{\link{layout_tbl_graph_matrix}()},
\code{\link{layout_tbl_graph_partition}()},
\code{\link{layout_tbl_graph_pmds}()},
\code{\link{layout_tbl_graph_stress}()},
\code{\link{layout_tbl_graph_treemap}()},
\code{\link{layout_tbl_graph_unrooted}()}
}
\author{
The underlying algorithm is implemented in the graphlayouts package
by David Schoch
}
\concept{layout_tbl_graph_*}
ggraph/man/geom_node_point.Rd 0000644 0001762 0000144 00000005271 13617226162 015744 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/geom_node_point.R
\name{geom_node_point}
\alias{geom_node_point}
\title{Show nodes as points}
\usage{
geom_node_point(
mapping = NULL,
data = NULL,
position = "identity",
show.legend = NA,
...
)
}
\arguments{
\item{mapping}{Set of aesthetic mappings created by \code{\link[ggplot2:aes]{ggplot2::aes()}}
or \code{\link[ggplot2:aes_]{ggplot2::aes_()}}. By default x and y are mapped to x and y in
the node data.}
\item{data}{The data to be displayed in this layer. There are three
options:
If \code{NULL}, the default, the data is inherited from the plot
data as specified in the call to \code{\link[ggplot2:ggplot]{ggplot()}}.
A \code{data.frame}, or other object, will override the plot
data. All objects will be fortified to produce a data frame. See
\code{\link[ggplot2:fortify]{fortify()}} for which variables will be created.
A \code{function} will be called with a single argument,
the plot data. The return value must be a \code{data.frame}, and
will be used as the layer data. A \code{function} can be created
from a \code{formula} (e.g. \code{~ head(.x, 10)}).}
\item{position}{Position adjustment, either as a string, or the result of
a call to a position adjustment function.}
\item{show.legend}{logical. Should this layer be included in the legends?
\code{NA}, the default, includes if any aesthetics are mapped.
\code{FALSE} never includes, and \code{TRUE} always includes.
It can also be a named logical vector to finely select the aesthetics to
display.}
\item{...}{Other arguments passed on to \code{\link[ggplot2:layer]{layer()}}. These are
often aesthetics, used to set an aesthetic to a fixed value, like
\code{colour = "red"} or \code{size = 3}. They may also be parameters
to the paired geom/stat.}
}
\description{
This geom is equivalent in functionality to \code{\link[ggplot2:geom_point]{ggplot2::geom_point()}}
and allows for simple plotting of nodes in different shapes, colours and sizes.
}
\section{Aesthetics}{
\code{geom_node_point} understand the following aesthetics. Bold aesthetics are
automatically set, but can be overridden.
\itemize{
\item \strong{x}
\item \strong{y}
\item alpha
\item colour
\item fill
\item shape
\item size
\item stroke
\item filter
}
}
\examples{
require(tidygraph)
gr <- create_notable('bull') \%>\%
mutate(class = sample(letters[1:3], n(), replace = TRUE))
ggraph(gr, 'stress') + geom_node_point()
}
\seealso{
Other geom_node_*:
\code{\link{geom_node_arc_bar}()},
\code{\link{geom_node_circle}()},
\code{\link{geom_node_range}()},
\code{\link{geom_node_text}()},
\code{\link{geom_node_tile}()},
\code{\link{geom_node_voronoi}()}
}
\author{
Thomas Lin Pedersen
}
\concept{geom_node_*}
ggraph/man/get_con.Rd 0000644 0001762 0000144 00000003652 13617226162 014216 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/connections.R
\name{get_con}
\alias{get_con}
\title{Create a connection extractor function}
\usage{
get_con(
from = integer(),
to = integer(),
paths = NULL,
...,
weight = NULL,
mode = "all"
)
}
\arguments{
\item{from, to}{The index of the start and end nodes for the connections}
\item{paths}{A list of integer vectors giving the index of nodes defining
connections}
\item{...}{Additional information to be added to the final data output}
\item{weight}{An expression to be evaluated on the edge data to provide
weights for the shortest path calculations}
\item{mode}{Character constant, gives whether the shortest paths to or from
the given vertices should be calculated for directed graphs. If \code{out}
then the shortest paths \emph{from} the vertex, if \code{in} then \emph{to}
it will be considered. If \code{all}, the default, then the corresponding
undirected graph will be used, ie. not directed paths are searched. This
argument is ignored for undirected graphs.}
}
\value{
A function that takes a layout_ggraph object and returns the given
connections
}
\description{
Connections within the ggraph terminology are links between nodes that are
not part of the network structure itself. In that sense connections do not
affect the layout calculation in any way and will not be drawn by the
standard \verb{geom_edge_*} functions. A connection does not need to only be
defined by a start and end node, but can include intermediary nodes.
\code{get_con} helps in creating connection data by letting you specify start
and end nodes and automatically finds the shortest path within the graph
structure that connects the given points. If this is not what is needed it is
also possible to supply a list of vectors giving node indices that define a
connection.
}
\seealso{
Other extractors:
\code{\link{get_edges}()},
\code{\link{get_nodes}()}
}
\concept{extractors}
ggraph/man/facet_nodes.Rd 0000644 0001762 0000144 00000006521 13617226162 015050 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/facet_nodes.R
\name{facet_nodes}
\alias{facet_nodes}
\title{Create small multiples based on node attributes}
\usage{
facet_nodes(
facets,
nrow = NULL,
ncol = NULL,
scales = "fixed",
shrink = TRUE,
labeller = "label_value",
as.table = TRUE,
switch = NULL,
drop = TRUE,
dir = "h",
strip.position = "top"
)
}
\arguments{
\item{facets}{A set of variables or expressions quoted by \code{\link[ggplot2:vars]{vars()}}
and defining faceting groups on the rows or columns dimension.
The variables can be named (the names are passed to \code{labeller}).
For compatibility with the classic interface, can also be a
formula or character vector. Use either a one sided formula, \code{~a + b},
or a character vector, \code{c("a", "b")}.}
\item{nrow}{Number of rows and columns.}
\item{ncol}{Number of rows and columns.}
\item{scales}{Should scales be fixed (\code{"fixed"}, the default),
free (\code{"free"}), or free in one dimension (\code{"free_x"},
\code{"free_y"})?}
\item{shrink}{If \code{TRUE}, will shrink scales to fit output of
statistics, not raw data. If \code{FALSE}, will be range of raw data
before statistical summary.}
\item{labeller}{A function that takes one data frame of labels and
returns a list or data frame of character vectors. Each input
column corresponds to one factor. Thus there will be more than
one with formulae of the type \code{~cyl + am}. Each output
column gets displayed as one separate line in the strip
label. This function should inherit from the "labeller" S3 class
for compatibility with \code{\link[ggplot2:labeller]{labeller()}}. See
\code{\link[ggplot2:label_value]{label_value()}} for more details and pointers to other
options.}
\item{as.table}{If \code{TRUE}, the default, the facets are laid out like
a table with highest values at the bottom-right. If \code{FALSE}, the
facets are laid out like a plot with the highest value at the top-right.}
\item{switch}{By default, the labels are displayed on the top and
right of the plot. If \code{"x"}, the top labels will be
displayed to the bottom. If \code{"y"}, the right-hand side
labels will be displayed to the left. Can also be set to
\code{"both"}.}
\item{drop}{If \code{TRUE}, the default, all factor levels not used in the
data will automatically be dropped. If \code{FALSE}, all factor levels
will be shown, regardless of whether or not they appear in the data.}
\item{dir}{Direction: either \code{"h"} for horizontal, the default, or \code{"v"},
for vertical.}
\item{strip.position}{By default, the labels are displayed on the top of
the plot. Using \code{strip.position} it is possible to place the labels on
either of the four sides by setting \code{strip.position = c("top",
"bottom", "left", "right")}}
}
\description{
This function is equivalent to \code{\link[ggplot2:facet_wrap]{ggplot2::facet_wrap()}} but only
facets nodes. Edges are drawn if their terminal nodes are both present in a
panel.
}
\examples{
library(tidygraph)
gr <- as_tbl_graph(highschool) \%>\%
mutate(popularity = as.character(cut(centrality_degree(mode = 'in'),
breaks = 3,
labels = c('low', 'medium', 'high')
)))
ggraph(gr) +
geom_edge_link() +
geom_node_point() +
facet_nodes(~popularity)
}
\seealso{
Other ggraph-facets:
\code{\link{facet_edges}()},
\code{\link{facet_graph}()}
}
\concept{ggraph-facets}
ggraph/man/get_nodes.Rd 0000644 0001762 0000144 00000002037 13617226162 014543 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/nodes.R
\name{get_nodes}
\alias{get_nodes}
\title{Create a node extractor function}
\usage{
get_nodes(...)
}
\arguments{
\item{...}{Additional data that should be cbind'ed together with the node
data.}
}
\value{
A data.frame with the node data as well of any additional data
supplied through \code{...}
}
\description{
This function returns another function that can extract nodes from a
ggraph_layout object. As a ggraph_layout object is essentially a data.frame
of nodes it might seem useless to provide this function, but since the node
data is not necessarily available until after the \code{ggraph()} call it
can be beneficial to be able to add information to the node data on a
per-layer basis. Unlike \code{\link[=get_edges]{get_edges()}} the use of \code{get_nodes} is not
mandatory and is only required if additional data should be added to selected
node layers.
}
\seealso{
Other extractors:
\code{\link{get_con}()},
\code{\link{get_edges}()}
}
\concept{extractors}
ggraph/man/facet_graph.Rd 0000644 0001762 0000144 00000010341 13617226162 015034 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/facet_graph.R
\name{facet_graph}
\alias{facet_graph}
\title{Create a grid of small multiples by node and/or edge attributes}
\usage{
facet_graph(
facets,
row_type = "edge",
col_type = "node",
margins = FALSE,
scales = "fixed",
space = "fixed",
shrink = TRUE,
labeller = "label_value",
as.table = TRUE,
switch = NULL,
drop = TRUE
)
}
\arguments{
\item{facets}{This argument is soft-deprecated, please use \code{rows}
and \code{cols} instead.}
\item{row_type, col_type}{Either \code{'node'} or \code{'edge'}. Which data
type is being facetted in the rows and columns. Default is to facet on nodes
column wise and on edges row wise.}
\item{margins}{Either a logical value or a character
vector. Margins are additional facets which contain all the data
for each of the possible values of the faceting variables. If
\code{FALSE}, no additional facets are included (the
default). If \code{TRUE}, margins are included for all faceting
variables. If specified as a character vector, it is the names of
variables for which margins are to be created.}
\item{scales}{Are scales shared across all facets (the default,
\code{"fixed"}), or do they vary across rows (\code{"free_x"}),
columns (\code{"free_y"}), or both rows and columns (\code{"free"})?}
\item{space}{If \code{"fixed"}, the default, all panels have the same size.
If \code{"free_y"} their height will be proportional to the length of the
y scale; if \code{"free_x"} their width will be proportional to the
length of the x scale; or if \code{"free"} both height and width will
vary. This setting has no effect unless the appropriate scales also vary.}
\item{shrink}{If \code{TRUE}, will shrink scales to fit output of
statistics, not raw data. If \code{FALSE}, will be range of raw data
before statistical summary.}
\item{labeller}{A function that takes one data frame of labels and
returns a list or data frame of character vectors. Each input
column corresponds to one factor. Thus there will be more than
one with formulae of the type \code{~cyl + am}. Each output
column gets displayed as one separate line in the strip
label. This function should inherit from the "labeller" S3 class
for compatibility with \code{\link[ggplot2:labeller]{labeller()}}. See
\code{\link[ggplot2:label_value]{label_value()}} for more details and pointers to other
options.}
\item{as.table}{If \code{TRUE}, the default, the facets are laid out like
a table with highest values at the bottom-right. If \code{FALSE}, the
facets are laid out like a plot with the highest value at the top-right.}
\item{switch}{By default, the labels are displayed on the top and
right of the plot. If \code{"x"}, the top labels will be
displayed to the bottom. If \code{"y"}, the right-hand side
labels will be displayed to the left. Can also be set to
\code{"both"}.}
\item{drop}{If \code{TRUE}, the default, all factor levels not used in the
data will automatically be dropped. If \code{FALSE}, all factor levels
will be shown, regardless of whether or not they appear in the data.}
}
\description{
This function is equivalent to \code{\link[ggplot2:facet_grid]{ggplot2::facet_grid()}} in that it
allows for building a grid of small multiples where rows and columns
correspond to a specific data value. While \code{\link[ggplot2:facet_grid]{ggplot2::facet_grid()}}
could be used it would lead to unexpected results as it is not possible to
specify whether you are referring to a node or an edge attribute. Furthermore
\code{\link[ggplot2:facet_grid]{ggplot2::facet_grid()}} will draw edges in panels even though the
panel does not contain both terminal nodes. \code{facet_graph} takes care of
all of these issues, allowing you to define which data type the rows and
columns are referencing as well as filtering the edges based on the nodes in
each panel (even when nodes are not drawn).
}
\examples{
library(tidygraph)
gr <- as_tbl_graph(highschool) \%>\%
mutate(popularity = as.character(cut(centrality_degree(mode = 'in'),
breaks = 3,
labels = c('low', 'medium', 'high')
)))
ggraph(gr) +
geom_edge_link() +
geom_node_point() +
facet_graph(year ~ popularity)
}
\seealso{
Other ggraph-facets:
\code{\link{facet_edges}()},
\code{\link{facet_nodes}()}
}
\concept{ggraph-facets}
ggraph/man/ggraph.Rd 0000644 0001762 0000144 00000015076 13524253234 014050 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/ggraph.R, R/layout.R, R/tbl_graph.R
\name{ggraph}
\alias{ggraph}
\alias{create_layout}
\alias{layout_ggraph}
\alias{create_layout.default}
\alias{create_layout.layout_ggraph}
\alias{create_layout.tbl_graph}
\alias{layout_tbl_graph}
\title{Create a ggraph plot}
\usage{
ggraph(graph, layout = "auto", ...)
create_layout(graph, layout, circular, ...)
\method{create_layout}{default}(graph, layout, ...)
\method{create_layout}{layout_ggraph}(graph, ...)
\method{create_layout}{tbl_graph}(graph, layout, circular = FALSE, ...)
}
\arguments{
\item{graph}{The object containing the graph. See \emph{Details} for a list
of supported classes. Or a \code{layout_ggraph} object as returned from
\code{create_layout} in which case all subsequent arguments is ignored.}
\item{layout}{The type of layout to create. Either a valid string, a
function, a matrix, or a data.frame (see Details)}
\item{...}{Arguments passed on to the layout function.}
\item{circular}{Should the layout be transformed into a radial
representation. Only possible for some layouts. Defaults to \code{FALSE}}
}
\value{
For \code{ggraph()} an object of class gg onto which layers, scales,
etc. can be added. For \code{create_layout()} an object inheriting from
\code{layout_ggraph}. \code{layout_ggraph} itself inherits from
\code{data.frame} and can be considered as such. The data.frame contains
the node positions in the \code{x} and \code{y} column along with
additional columns generated by the specific layout, as well as node
parameters inherited from the graph. Additional information is stored as
attributes to the data.frame. The original graph object is stored in the
\code{graph} attribute and the \code{circular} attribute contains a logical
indicating whether the layout has been transformed to a circular
representation.
}
\description{
This function is the equivalent of \code{\link[ggplot2:ggplot]{ggplot2::ggplot()}} in ggplot2.
It takes care of setting up the plot object along with creating the layout
for the plot based on the graph and the specification passed in.
Alternatively a layout can be prepared in advance using
\code{create_layout} and passed as the data argument. See \emph{Details} for
a description of all available layouts.
}
\details{
Following is a short description of the different layout types available in
ggraph. Each layout is further described in its own help pages. Any type of
regular graph/network data can be represented as a tbl_graph object. Because
of this the different layouts that can be applied to tbl_graph
objects are quite diverse, but not all layouts makes sense to all types of
graphs. It is up to the user to understand their data and choose an
appropriate layout. For standard node-edge diagrams igraph defines a
long range of different layout functions that are all available through the
\code{igraph} layout where the specific layout is specified using the
\code{algorithm} argument. In order to minimize typing all igraph algorithms
can also be passed directly into the \code{layout} argument.
Any object that has an appropriate \code{as_tbl_graph} method can be passed
into \code{ggraph()} and will automatically be converted underneath.
\describe{
\item{\code{auto}}{The default layout. See \code{\link[=layout_tbl_graph_auto]{layout_tbl_graph_auto()}} for further
details}
\item{\code{igraph}}{Use one of the internal igraph layout algorithms.
The algorithm is specified using the \code{algorithm} argument. All strings
accepted by the \code{algorithm} argument can also be supplied directly
into \code{layout}. See \code{\link[=layout_tbl_graph_igraph]{layout_tbl_graph_igraph()}} for further
details}
\item{\code{dendrogram}}{Lays out the nodes in a tree-like graph as a
dendrogram with leaves set at 0 and parents 1 unit above its tallest child.
See \code{\link[=layout_tbl_graph_dendrogram]{layout_tbl_graph_dendrogram()}} for further details}
\item{\code{manual}}{Lets the user manually specify the location of each
node. See \code{\link[=layout_tbl_graph_manual]{layout_tbl_graph_manual()}} for further details}
\item{\code{linear}}{Arranges the nodes linearly or circularly in order to
make an arc diagram. See \code{\link[=layout_tbl_graph_linear]{layout_tbl_graph_linear()}} for further
details}
\item{\code{matrix}}{Arranges nodes on a diagonal thus preparing it for use with
\code{\link[=geom_edge_point]{geom_edge_point()}} to make a matrix plot. See \code{\link[=layout_tbl_graph_matrix]{layout_tbl_graph_matrix()}}
for further details}
\item{\code{treemap}}{Creates a treemap from the graph, that is, a
space-filing subdivision of rectangles showing a weighted hierarchy. See
\code{\link[=layout_tbl_graph_treemap]{layout_tbl_graph_treemap()}} for further details}
\item{\code{circlepack}}{Creates a layout showing a hierarchy as circles
within circles. Conceptually equal to treemaps. See
\code{\link[=layout_tbl_graph_circlepack]{layout_tbl_graph_circlepack()}} for further details}
\item{\code{partition}}{Create icicle or sunburst charts, where each layer
subdivides the division given by the preceding layer. See
\code{\link[=layout_tbl_graph_partition]{layout_tbl_graph_partition()}} for further details}
\item{\code{hive}}{Positions nodes on axes spreading out from the center
based on node attributes. See \code{\link[=layout_tbl_graph_hive]{layout_tbl_graph_hive()}} for further
details}
}
Alternatively a matrix or a data.frame can be provided to the \code{layout}
argument. In the former case the first column will be used as x coordinates
and the second column will by used as y coordinates, further columns are
dropped. In the latter case the data.frame is used as the layout table and
must thus contain a numeric x and y column.
Lastly a function can be provided to the \code{layout} argument. It will be called
with the graph object as its first argument and any additional argument
passed into \code{ggraph()}/\code{create_layout()}. The function must return either a
data.frame or an object coercible to one and have an \code{x} and \code{y} column, or
an object coercible to a \code{tbl_graph}. In the latter case the node data is
extracted and used as layout (and must thus contain an \code{x} and \code{y} column)
and the graph will be added as the \code{graph} attribute.
}
\examples{
require(tidygraph)
gr <- create_notable('bull')
layout <- create_layout(gr, layout = 'igraph', algorithm = 'kk')
}
\seealso{
\code{\link[=get_edges]{get_edges()}} for extracting edge information from the
layout and \code{\link[=get_con]{get_con()}} for extracting path information.
}
\keyword{graph}
\keyword{hierarchy}
\keyword{layout}
\keyword{network}
\keyword{visualisation}
ggraph/man/flare.Rd 0000644 0001762 0000144 00000002740 13276561316 013672 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data_flare.R
\docType{data}
\name{flare}
\alias{flare}
\title{The class hierarchy of the flare visualization library}
\format{A list of three data.frames describing the software structure of
flare:
\describe{
\item{edges}{This data.frame maps the hierarchical structure of the class
hierarchy as an edgelist, with the class in \code{from} being the superclass
of the class in \code{to}.}
\item{vertices}{This data.frame gives additional information on the classes.
It contains the full name, size and short name of each class.}
\item{imports}{This data.frame contains the class imports for each class
implementation. The \code{from} column gives the importing class and the
\code{to} column gives the import.}
}}
\source{
The data have been adapted from the JSON downloaded from
\url{https://gist.github.com/mbostock/1044242#file-readme-flare-imports-json}
courtesy of Mike Bostock. The Flare framework is the work of the
\href{http://vis.berkeley.edu/}{UC Berkeley Visualization Lab}.
}
\usage{
flare
}
\description{
This dataset contains the graph that describes the class hierarchy for the
\href{http://flare.prefuse.org}{Flare} ActionScript visualization library. It
contains both the class hierarchy as well as the import connections between
classes. This dataset has been used extensively in the D3.js documentation
and examples and are included here to make it easy to redo the examples in
ggraph.
}
\keyword{datasets}
ggraph/man/layout_tbl_graph_fabric.Rd 0000644 0001762 0000144 00000005427 13617226162 017447 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/layout_fabric.R
\name{layout_tbl_graph_fabric}
\alias{layout_tbl_graph_fabric}
\alias{node_rank_fabric}
\title{Create a fabric layout}
\usage{
layout_tbl_graph_fabric(
graph,
circular = FALSE,
sort.by = NULL,
shadow.edges = FALSE
)
node_rank_fabric()
}
\arguments{
\item{graph}{An \code{tbl_graph} object}
\item{circular}{Ignored}
\item{sort.by}{An expression providing the sorting of the nodes. If \code{NULL}
the nodes will be ordered by their index in the graph.}
\item{shadow.edges}{Should shadow edges be shown.}
}
\value{
A data.frame with the columns \code{x}, \code{xmin}, \code{xmax}, \code{y}, \code{circular} as
well as any information stored as node variables in the tbl_graph object.
Further, the edges of the graph will gain a \code{edge_x} variable giving the
horizontal position of the edge as well as a \code{shadow_edge} variable denoting
whether the edge is a shadow edge added by the layout.
}
\description{
This layout is a bit unusual in that it shows nodes as horizontal line ranges
end edges as evenly spaced vertical spans connecting the nodes. As with the
matrix layout the strength comes from better scalability but its use require
some experience recognising the patterns that different connectivity features
gives rise to. As with matrix layouts the ordering of nodes have huge power
over the look of the plot. The \code{node_rank_fabric()} mimics the default
ordering from the original BioFabric implementation, but other ranking
algorithms from tidygraph can be used with the \code{sort.by} argument as well.
Fabric layouts tend to become quite wide as the graph grows which is
something that should be handled with care - e.g. by only zooming in on a
specific region.
}
\references{
BioFabric website: \url{http://www.biofabric.org}
Longabaugh, William J.R. (2012).
\emph{Combing the hairball with BioFabric: a new approach for visualization of large networks}.
BMC Bioinformatics, 13: 275. \url{https://doi.org/10.1186/1471-2105-13-275}
}
\seealso{
Other layout_tbl_graph_*:
\code{\link{layout_tbl_graph_auto}()},
\code{\link{layout_tbl_graph_backbone}()},
\code{\link{layout_tbl_graph_centrality}()},
\code{\link{layout_tbl_graph_circlepack}()},
\code{\link{layout_tbl_graph_dendrogram}()},
\code{\link{layout_tbl_graph_eigen}()},
\code{\link{layout_tbl_graph_focus}()},
\code{\link{layout_tbl_graph_hive}()},
\code{\link{layout_tbl_graph_igraph}()},
\code{\link{layout_tbl_graph_linear}()},
\code{\link{layout_tbl_graph_manual}()},
\code{\link{layout_tbl_graph_matrix}()},
\code{\link{layout_tbl_graph_partition}()},
\code{\link{layout_tbl_graph_pmds}()},
\code{\link{layout_tbl_graph_stress}()},
\code{\link{layout_tbl_graph_treemap}()},
\code{\link{layout_tbl_graph_unrooted}()}
}
\concept{layout_tbl_graph_*}
ggraph/man/layout_tbl_graph_auto.Rd 0000644 0001762 0000144 00000004050 13617226162 017160 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/layout_auto.R
\name{layout_tbl_graph_auto}
\alias{layout_tbl_graph_auto}
\title{Automatically pick a layout based on graph type}
\usage{
layout_tbl_graph_auto(graph, circular, ...)
}
\arguments{
\item{graph}{A tbl_graph object}
\item{circular}{Logical. Should the layout be transformed to a circular
representation. Defaults to \code{FALSE}. Only applicable if the graph is a tree
structure}
\item{...}{Arguments passed on to the chosen layout}
}
\value{
A data.frame with the columns \code{x}, \code{y}, \code{circular} as
well as any information stored as node variables in the tbl_graph object.
}
\description{
This function infers the layout from the graph structure and is the default
when calling \code{\link[=ggraph]{ggraph()}}. If an \code{x} and \code{y} argument is passed along, the
manual layout is chosen. Otherwise if the graph is either a rooted tree or a
rooted forest the layout will be \code{dendrogram} if the nodes contains a height
variable or \code{tree} if not. If the tree is unrooted the \code{unrooted} layout will
be used. If the tree is a DAG the \code{sygiyama} layout will be used. Otherwise
the \code{stress} layout will be used (or \code{sparse_tree} if the graph contains more
than 2000 nodes).
}
\seealso{
Other layout_tbl_graph_*:
\code{\link{layout_tbl_graph_backbone}()},
\code{\link{layout_tbl_graph_centrality}()},
\code{\link{layout_tbl_graph_circlepack}()},
\code{\link{layout_tbl_graph_dendrogram}()},
\code{\link{layout_tbl_graph_eigen}()},
\code{\link{layout_tbl_graph_fabric}()},
\code{\link{layout_tbl_graph_focus}()},
\code{\link{layout_tbl_graph_hive}()},
\code{\link{layout_tbl_graph_igraph}()},
\code{\link{layout_tbl_graph_linear}()},
\code{\link{layout_tbl_graph_manual}()},
\code{\link{layout_tbl_graph_matrix}()},
\code{\link{layout_tbl_graph_partition}()},
\code{\link{layout_tbl_graph_pmds}()},
\code{\link{layout_tbl_graph_stress}()},
\code{\link{layout_tbl_graph_treemap}()},
\code{\link{layout_tbl_graph_unrooted}()}
}
\concept{layout_tbl_graph_*}
ggraph/man/guide-helpers.Rd 0000644 0001762 0000144 00000001354 13276373323 015335 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/edge_colourbar.R, R/edge_direction.R
\name{guide_train.edge_colourbar}
\alias{guide_train.edge_colourbar}
\alias{guide_train.edge_direction}
\alias{guide_merge.edge_direction}
\alias{guide_geom.edge_direction}
\alias{guide_gengrob.edge_direction}
\title{Helper methods for guides}
\usage{
\method{guide_train}{edge_colourbar}(guide, scale, aesthetic = NULL)
\method{guide_train}{edge_direction}(guide, scale, aesthetic = NULL)
\method{guide_merge}{edge_direction}(guide, new_guide)
\method{guide_geom}{edge_direction}(guide, layers, default_mapping)
\method{guide_gengrob}{edge_direction}(guide, theme)
}
\description{
Helper methods for guides
}
\keyword{internal}
ggraph/man/geom_edge_elbow.Rd 0000644 0001762 0000144 00000022370 13617226162 015701 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/geom_edge_elbow.R
\name{geom_edge_elbow}
\alias{geom_edge_elbow}
\alias{geom_edge_elbow2}
\alias{geom_edge_elbow0}
\title{Draw edges as elbows}
\usage{
geom_edge_elbow(
mapping = NULL,
data = get_edges(),
position = "identity",
arrow = NULL,
strength = 1,
flipped = FALSE,
n = 100,
lineend = "butt",
linejoin = "round",
linemitre = 1,
label_colour = "black",
label_alpha = 1,
label_parse = FALSE,
check_overlap = FALSE,
angle_calc = "rot",
force_flip = TRUE,
label_dodge = NULL,
label_push = NULL,
show.legend = NA,
...
)
geom_edge_elbow2(
mapping = NULL,
data = get_edges("long"),
position = "identity",
arrow = NULL,
strength = 1,
flipped = FALSE,
n = 100,
lineend = "butt",
linejoin = "round",
linemitre = 1,
label_colour = "black",
label_alpha = 1,
label_parse = FALSE,
check_overlap = FALSE,
angle_calc = "rot",
force_flip = TRUE,
label_dodge = NULL,
label_push = NULL,
show.legend = NA,
...
)
geom_edge_elbow0(
mapping = NULL,
data = get_edges(),
position = "identity",
arrow = NULL,
flipped = FALSE,
lineend = "butt",
show.legend = NA,
...
)
}
\arguments{
\item{mapping}{Set of aesthetic mappings created by \code{\link[ggplot2:aes]{ggplot2::aes()}}
or \code{\link[ggplot2:aes_]{ggplot2::aes_()}}. By default x, y, xend, yend, group and
circular are mapped to x, y, xend, yend, edge.id and circular in the edge
data.}
\item{data}{The return of a call to \code{get_edges()} or a data.frame
giving edges in correct format (see details for for guidance on the format).
See \code{\link[=get_edges]{get_edges()}} for more details on edge extraction.}
\item{position}{Position adjustment, either as a string, or the result of
a call to a position adjustment function.}
\item{arrow}{Arrow specification, as created by \code{\link[grid:arrow]{grid::arrow()}}.}
\item{strength}{How bend the elbow should be. 1 will give a right angle,
while \code{0} will give a straight line. Ignored for circular layouts}
\item{flipped}{Logical, Has the layout been flipped by reassigning the
mapping of x, y etc?}
\item{n}{The number of points to create along the path.}
\item{lineend}{Line end style (round, butt, square).}
\item{linejoin}{Line join style (round, mitre, bevel).}
\item{linemitre}{Line mitre limit (number greater than 1).}
\item{label_colour}{The colour of the edge label. If \code{NA} it will use
the colour of the edge.}
\item{label_alpha}{The opacity of the edge label. If \code{NA} it will use
the opacity of the edge.}
\item{label_parse}{If \code{TRUE}, the labels will be parsed into expressions
and displayed as described in \code{\link[grDevices:plotmath]{grDevices::plotmath()}}.}
\item{check_overlap}{If \code{TRUE}, text that overlaps previous text in the
same layer will not be plotted.}
\item{angle_calc}{Either 'none', 'along', or 'across'. If 'none' the label will
use the angle aesthetic of the geom. If 'along' The label will be written
along the edge direction. If 'across' the label will be written across the
edge direction.}
\item{force_flip}{Logical. If \code{angle_calc} is either 'along' or 'across'
should the label be flipped if it is on it's head. Default to \code{TRUE}.}
\item{label_dodge}{A \code{\link[grid:unit]{grid::unit()}} giving a fixed vertical shift
to add to the label in case of \code{angle_calc} is either 'along' or 'across'}
\item{label_push}{A \code{\link[grid:unit]{grid::unit()}} giving a fixed horizontal shift
to add to the label in case of \code{angle_calc} is either 'along' or 'across'}
\item{show.legend}{logical. Should this layer be included in the legends?
\code{NA}, the default, includes if any aesthetics are mapped.
\code{FALSE} never includes, and \code{TRUE} always includes.
It can also be a named logical vector to finely select the aesthetics to
display.}
\item{...}{Other arguments passed on to \code{\link[ggplot2:layer]{layer()}}. These are
often aesthetics, used to set an aesthetic to a fixed value, like
\code{colour = "red"} or \code{size = 3}. They may also be parameters
to the paired geom/stat.}
}
\description{
This geom draws edges as an angle in the same manner as known from classic
dendrogram plots of hierarchical clustering results. In case a circular
transformation has been applied the first line segment will be drawn as an
arc as expected. This geom is only applicable to layouts that return a
direction for the edges (currently \code{\link[=layout_tbl_graph_dendrogram]{layout_tbl_graph_dendrogram()}},
\code{\link[=layout_tbl_graph_partition]{layout_tbl_graph_partition()}} and
\code{\link[=layout_tbl_graph_igraph]{layout_tbl_graph_igraph()}} with the \code{"tree"} algorithm).
}
\section{Aesthetics}{
\code{geom_edge_elbow} and \code{geom_edge_elbow0} understand the following
aesthetics. Bold aesthetics are automatically set, but can be overridden.
\itemize{
\item \strong{x}
\item \strong{y}
\item \strong{xend}
\item \strong{yend}
\item \strong{circular}
\item \strong{direction}
\item edge_colour
\item edge_width
\item edge_linetype
\item edge_alpha
\item filter
}
\code{geom_edge_elbow2} understand the following aesthetics. Bold aesthetics are
automatically set, but can be overridden.
\itemize{
\item \strong{x}
\item \strong{y}
\item \strong{group}
\item \strong{circular}
\item \strong{direction}
\item edge_colour
\item edge_width
\item edge_linetype
\item edge_alpha
\item filter
}
\code{geom_edge_elbow} and \code{geom_edge_elbow2} furthermore takes the following
aesthetics.
\itemize{
\item start_cap
\item end_cap
\item label
\item label_pos
\item label_size
\item angle
\item hjust
\item vjust
\item family
\item fontface
\item lineheight
}
}
\section{Computed variables}{
\describe{
\item{index}{The position along the path (not computed for the *0 version)}
}
}
\section{Edge variants}{
Many geom_edge_* layers comes in 3 flavors depending on the level of control
needed over the drawing. The default (no numeric postfix) generate a number
of points (\code{n}) along the edge and draws it as a path. Each point along
the line has a numeric value associated with it giving the position along the
path, and it is therefore possible to show the direction of the edge by
mapping to this e.g. \code{colour = stat(index)}. The version postfixed with a
"2" uses the "long" edge format (see \code{\link[=get_edges]{get_edges()}}) and makes it
possible to interpolate node parameter between the start and end node along
the edge. It is considerable less performant so should only be used if this
is needed. The version postfixed with a "0" draws the edge in the most
performant way, often directly using an appropriate grob from the grid
package, but does not allow for gradients along the edge.
Often it is beneficial to stop the drawing of the edge before it reaches the
node, for instance in cases where an arrow should be drawn and the arrowhead
shouldn't lay on top or below the node point. geom_edge_* and geom_edge_*2
supports this through the start_cap and end_cap aesthetics that takes a
\code{\link[=geometry]{geometry()}} specification and dynamically caps the termini of the
edges based on the given specifications. This means that if
\code{end_cap = circle(1, 'cm')} the edges will end at a distance of 1cm even
during resizing of the plot window.
All \verb{geom_edge_*} and \code{geom_edge_*2} have the ability to draw a
label along the edge. The reason this is not a separate geom is that in order
for the label to know the location of the edge it needs to know the edge type
etc. Labels are drawn by providing a label aesthetic. The label_pos can be
used to specify where along the edge it should be drawn by supplying a number
between 0 and 1. The label_size aesthetic can be used to control the size of
the label. Often it is needed to have the label written along the direction
of the edge, but since the actual angle is dependent on the plot dimensions
this cannot be calculated beforehand. Using the angle_calc argument allows
you to specify whether to use the supplied angle aesthetic or whether to draw
the label along or across the edge.
}
\section{Edge aesthetic name expansion}{
In order to avoid excessive typing edge aesthetic names are
automatically expanded. Because of this it is not necessary to write
\code{edge_colour} within the \code{aes()} call as \code{colour} will
automatically be renamed appropriately.
}
\examples{
require(tidygraph)
irisDen <- hclust(dist(iris[1:4], method = 'euclidean'), method = 'ward.D2') \%>\%
as_tbl_graph() \%>\%
mutate(class = sample(letters[1:3], n(), TRUE)) \%>\%
activate(edges) \%>\%
mutate(class = sample(letters[1:3], n(), TRUE))
ggraph(irisDen, 'dendrogram', circular = TRUE) +
geom_edge_elbow(aes(alpha = stat(index)))
ggraph(irisDen, 'dendrogram') +
geom_edge_elbow2(aes(colour = node.class))
ggraph(irisDen, 'dendrogram', height = height) +
geom_edge_elbow0(aes(colour = class))
}
\seealso{
Other geom_edge_*:
\code{\link{geom_edge_arc}()},
\code{\link{geom_edge_bend}()},
\code{\link{geom_edge_density}()},
\code{\link{geom_edge_diagonal}()},
\code{\link{geom_edge_fan}()},
\code{\link{geom_edge_hive}()},
\code{\link{geom_edge_link}()},
\code{\link{geom_edge_loop}()},
\code{\link{geom_edge_parallel}()},
\code{\link{geom_edge_point}()},
\code{\link{geom_edge_span}()},
\code{\link{geom_edge_tile}()}
}
\author{
Thomas Lin Pedersen
}
\concept{geom_edge_*}
ggraph/man/scale_edge_linetype.Rd 0000644 0001762 0000144 00000007030 13617226162 016556 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/scale_edge_linetype.R
\name{scale_edge_linetype}
\alias{scale_edge_linetype}
\alias{scale_edge_linetype_continuous}
\alias{scale_edge_linetype_discrete}
\alias{scale_edge_linetype_manual}
\alias{scale_edge_linetype_identity}
\title{Edge linetype scales}
\usage{
scale_edge_linetype(..., na.value = "blank")
scale_edge_linetype_continuous(...)
scale_edge_linetype_discrete(..., na.value = "blank")
scale_edge_linetype_manual(..., values)
scale_edge_linetype_identity(..., guide = "none")
}
\arguments{
\item{...}{Arguments passed on to \code{discrete_scale}
\describe{
\item{palette}{A palette function that when called with a single integer
argument (the number of levels in the scale) returns the values that
they should take.}
\item{breaks}{One of:
\itemize{
\item \code{NULL} for no breaks
\item \code{waiver()} for the default breaks computed by the
transformation object
\item A character vector of breaks
\item A function that takes the limits as input and returns breaks
as output
}}
\item{limits}{A character vector that defines possible values of the scale
and their order.}
\item{drop}{Should unused factor levels be omitted from the scale?
The default, \code{TRUE}, uses the levels that appear in the data;
\code{FALSE} uses all the levels in the factor.}
\item{na.translate}{Unlike continuous scales, discrete scales can easily show
missing values, and do so by default. If you want to remove missing values
from a discrete scale, specify \code{na.translate = FALSE}.}
\item{aesthetics}{The names of the aesthetics that this scale works with}
\item{scale_name}{The name of the scale}
\item{name}{The name of the scale. Used as the axis or legend title. If
\code{waiver()}, the default, the name of the scale is taken from the first
mapping used for that aesthetic. If \code{NULL}, the legend title will be
omitted.}
\item{labels}{One of:
\itemize{
\item \code{NULL} for no labels
\item \code{waiver()} for the default labels computed by the
transformation object
\item A character vector giving labels (must be same length as \code{breaks})
\item A function that takes the breaks as input and returns labels
as output
}}
\item{guide}{A function used to create a guide or its name. See
\code{\link[ggplot2:guides]{guides()}} for more info.}
\item{super}{The super class to use for the constructed scale}
}}
\item{na.value}{The linetype to use for \code{NA} values.}
\item{values}{a set of aesthetic values to map data values to. If this
is a named vector, then the values will be matched based on the names.
If unnamed, values will be matched in order (usually alphabetical) with
the limits of the scale. Any data values that don't match will be
given \code{na.value}.}
\item{guide}{Guide to use for this scale. Defaults to \code{"none"}.}
}
\value{
A ggproto object inheriting from \code{Scale}
}
\description{
This set of scales defines new linetype scales for edge geoms equivalent to
the ones already defined by ggplot2. See
\code{\link[ggplot2:scale_linetype]{ggplot2::scale_linetype()}} for more information. The different
geoms will know whether to use edge scales or the standard scales so it is
not necessary to write \code{edge_linetype} in the call to the geom - just
use \code{linetype}.
}
\seealso{
Other scale_edge_*:
\code{\link{scale_edge_alpha}()},
\code{\link{scale_edge_colour}},
\code{\link{scale_edge_fill}},
\code{\link{scale_edge_shape}()},
\code{\link{scale_edge_size}()},
\code{\link{scale_edge_width}()},
\code{\link{scale_label_size}()}
}
\concept{scale_edge_*}
ggraph/man/geom_edge_tile.Rd 0000644 0001762 0000144 00000006535 13617226162 015533 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/geom_edge_tile.R
\name{geom_edge_tile}
\alias{geom_edge_tile}
\title{Draw edges as glyphs}
\usage{
geom_edge_tile(
mapping = NULL,
data = get_edges(),
position = "identity",
mirror = FALSE,
show.legend = NA,
...
)
}
\arguments{
\item{mapping}{Set of aesthetic mappings created by \code{\link[ggplot2:aes]{ggplot2::aes()}}
or \code{\link[ggplot2:aes_]{ggplot2::aes_()}}. By default x, y, xend, yend, group and
circular are mapped to x, y, xend, yend, edge.id and circular in the edge
data.}
\item{data}{The return of a call to \code{get_edges()} or a data.frame
giving edges in correct format (see details for for guidance on the format).
See \code{\link[=get_edges]{get_edges()}} for more details on edge extraction.}
\item{position}{Position adjustment, either as a string, or the result of
a call to a position adjustment function.}
\item{mirror}{Logical. Should edge points be duplicated on both sides of the
diagonal. Intended for undirected graphs. Default to \code{FALSE}}
\item{show.legend}{logical. Should this layer be included in the legends?
\code{NA}, the default, includes if any aesthetics are mapped.
\code{FALSE} never includes, and \code{TRUE} always includes.
It can also be a named logical vector to finely select the aesthetics to
display.}
\item{...}{Other arguments passed on to \code{\link[ggplot2:layer]{layer()}}. These are
often aesthetics, used to set an aesthetic to a fixed value, like
\code{colour = "red"} or \code{size = 3}. They may also be parameters
to the paired geom/stat.}
}
\description{
This geom draws edges as tiles with their x-position defined by the
x-position of the start node, and the y-position defined by the y-position of
the end node. As such it will result in a matrix layout when used in
conjunction with \code{\link[=layout_tbl_graph_matrix]{layout_tbl_graph_matrix()}}
}
\section{Aesthetics}{
\code{geom_edge_tile} understands the following
aesthetics. Bold aesthetics are automatically set, but can be overridden.
\itemize{
\item \strong{x}
\item \strong{y}
\item edge_fill
\item edge_colour
\item edge_size
\item edge_alpha
\item filter
}
}
\section{Edge aesthetic name expansion}{
In order to avoid excessive typing edge aesthetic names are
automatically expanded. Because of this it is not necessary to write
\code{edge_colour} within the \code{aes()} call as \code{colour} will
automatically be renamed appropriately.
}
\examples{
require(tidygraph)
gr <- create_notable('zachary') \%>\%
mutate(group = group_infomap()) \%>\%
morph(to_split, group) \%>\%
activate(edges) \%>\%
mutate(edge_group = as.character(.N()$group[1])) \%>\%
unmorph()
ggraph(gr, 'matrix', sort.by = node_rank_hclust()) +
geom_edge_tile(aes(fill = edge_group), mirror = TRUE) +
scale_y_reverse() +
coord_fixed() +
labs(edge_colour = 'Infomap Cluster') +
ggtitle("Zachary' Karate Club")
}
\seealso{
Other geom_edge_*:
\code{\link{geom_edge_arc}()},
\code{\link{geom_edge_bend}()},
\code{\link{geom_edge_density}()},
\code{\link{geom_edge_diagonal}()},
\code{\link{geom_edge_elbow}()},
\code{\link{geom_edge_fan}()},
\code{\link{geom_edge_hive}()},
\code{\link{geom_edge_link}()},
\code{\link{geom_edge_loop}()},
\code{\link{geom_edge_parallel}()},
\code{\link{geom_edge_point}()},
\code{\link{geom_edge_span}()}
}
\author{
Thomas Lin Pedersen
}
\concept{geom_edge_*}
ggraph/man/geom_axis_hive.Rd 0000644 0001762 0000144 00000006063 13617226162 015565 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/geom_axis_hive.R
\name{geom_axis_hive}
\alias{geom_axis_hive}
\title{Draw rectangular bars and labels on hive axes}
\usage{
geom_axis_hive(
mapping = NULL,
data = NULL,
position = "identity",
label = TRUE,
axis = TRUE,
show.legend = NA,
...
)
}
\arguments{
\item{mapping}{Set of aesthetic mappings created by \code{\link[ggplot2:aes]{aes()}} or
\code{\link[ggplot2:aes_]{aes_()}}. If specified and \code{inherit.aes = TRUE} (the
default), it is combined with the default mapping at the top level of the
plot. You must supply \code{mapping} if there is no plot mapping.}
\item{data}{The data to be displayed in this layer. There are three
options:
If \code{NULL}, the default, the data is inherited from the plot
data as specified in the call to \code{\link[ggplot2:ggplot]{ggplot()}}.
A \code{data.frame}, or other object, will override the plot
data. All objects will be fortified to produce a data frame. See
\code{\link[ggplot2:fortify]{fortify()}} for which variables will be created.
A \code{function} will be called with a single argument,
the plot data. The return value must be a \code{data.frame}, and
will be used as the layer data. A \code{function} can be created
from a \code{formula} (e.g. \code{~ head(.x, 10)}).}
\item{position}{Position adjustment, either as a string, or the result of
a call to a position adjustment function.}
\item{label}{Should the axes be labelled. Defaults to \code{TRUE}}
\item{axis}{Should a rectangle be drawn along the axis. Defaults to \code{TRUE}}
\item{show.legend}{logical. Should this layer be included in the legends?
\code{NA}, the default, includes if any aesthetics are mapped.
\code{FALSE} never includes, and \code{TRUE} always includes.
It can also be a named logical vector to finely select the aesthetics to
display.}
\item{...}{Other arguments passed on to \code{\link[ggplot2:layer]{layer()}}. These are
often aesthetics, used to set an aesthetic to a fixed value, like
\code{colour = "red"} or \code{size = 3}. They may also be parameters
to the paired geom/stat.}
}
\description{
This function lets you annotate the axes in a hive plot with labels and
color coded bars.
}
\section{Aesthetics}{
geom_axis_hive understand the following aesthetics.
\itemize{
\item{alpha}
\item{colour}
\item{fill}
\item{size}
\item{linetype}
\item{label_size}
\item{family}
\item{fontface}
\item{lineheight}
}
}
\examples{
# Plot the flare import graph as a hive plot
library(tidygraph)
flareGr <- as_tbl_graph(flare$imports) \%>\%
mutate(
type = dplyr::case_when(
centrality_degree(mode = 'in') == 0 ~ 'Source',
centrality_degree(mode = 'out') == 0 ~ 'Sink',
TRUE ~ 'Both'
)
) \%>\%
activate(edges) \%>\%
mutate(
type = dplyr::case_when(
grepl('flare.analytics', paste(.N()$name[from], .N()$name[to])) ~ 'Analytics',
TRUE ~ 'Other'
)
)
ggraph(flareGr, 'hive', axis = type) +
geom_edge_hive(aes(colour = type), edge_alpha = 0.1) +
geom_axis_hive(aes(colour = type)) +
coord_fixed()
}
\author{
Thomas Lin Pedersen
}
ggraph/man/geom_edge_fan.Rd 0000644 0001762 0000144 00000022106 13617226162 015332 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/geom_edge_fan.R
\name{geom_edge_fan}
\alias{geom_edge_fan}
\alias{geom_edge_fan2}
\alias{geom_edge_fan0}
\title{Draw edges as curves of different curvature}
\usage{
geom_edge_fan(
mapping = NULL,
data = get_edges(),
position = "identity",
arrow = NULL,
strength = 1,
n = 100,
lineend = "butt",
linejoin = "round",
linemitre = 1,
label_colour = "black",
label_alpha = 1,
label_parse = FALSE,
check_overlap = FALSE,
angle_calc = "rot",
force_flip = TRUE,
label_dodge = NULL,
label_push = NULL,
show.legend = NA,
...,
spread
)
geom_edge_fan2(
mapping = NULL,
data = get_edges("long"),
position = "identity",
arrow = NULL,
strength = 1,
n = 100,
lineend = "butt",
linejoin = "round",
linemitre = 1,
label_colour = "black",
label_alpha = 1,
label_parse = FALSE,
check_overlap = FALSE,
angle_calc = "rot",
force_flip = TRUE,
label_dodge = NULL,
label_push = NULL,
show.legend = NA,
...,
spread
)
geom_edge_fan0(
mapping = NULL,
data = get_edges(),
position = "identity",
arrow = NULL,
strength = 1,
lineend = "butt",
show.legend = NA,
...,
spread
)
}
\arguments{
\item{mapping}{Set of aesthetic mappings created by \code{\link[ggplot2:aes]{ggplot2::aes()}}
or \code{\link[ggplot2:aes_]{ggplot2::aes_()}}. By default x, y, xend, yend, group and
circular are mapped to x, y, xend, yend, edge.id and circular in the edge
data.}
\item{data}{The return of a call to \code{get_edges()} or a data.frame
giving edges in correct format (see details for for guidance on the format).
See \code{\link[=get_edges]{get_edges()}} for more details on edge extraction.}
\item{position}{Position adjustment, either as a string, or the result of
a call to a position adjustment function.}
\item{arrow}{Arrow specification, as created by \code{\link[grid:arrow]{grid::arrow()}}.}
\item{strength}{Modify the width of the fans \code{strength > 1} will create
wider fans while the reverse will make them more narrow.}
\item{n}{The number of points to create along the path.}
\item{lineend}{Line end style (round, butt, square).}
\item{linejoin}{Line join style (round, mitre, bevel).}
\item{linemitre}{Line mitre limit (number greater than 1).}
\item{label_colour}{The colour of the edge label. If \code{NA} it will use
the colour of the edge.}
\item{label_alpha}{The opacity of the edge label. If \code{NA} it will use
the opacity of the edge.}
\item{label_parse}{If \code{TRUE}, the labels will be parsed into expressions
and displayed as described in \code{\link[grDevices:plotmath]{grDevices::plotmath()}}.}
\item{check_overlap}{If \code{TRUE}, text that overlaps previous text in the
same layer will not be plotted.}
\item{angle_calc}{Either 'none', 'along', or 'across'. If 'none' the label will
use the angle aesthetic of the geom. If 'along' The label will be written
along the edge direction. If 'across' the label will be written across the
edge direction.}
\item{force_flip}{Logical. If \code{angle_calc} is either 'along' or 'across'
should the label be flipped if it is on it's head. Default to \code{TRUE}.}
\item{label_dodge}{A \code{\link[grid:unit]{grid::unit()}} giving a fixed vertical shift
to add to the label in case of \code{angle_calc} is either 'along' or 'across'}
\item{label_push}{A \code{\link[grid:unit]{grid::unit()}} giving a fixed horizontal shift
to add to the label in case of \code{angle_calc} is either 'along' or 'across'}
\item{show.legend}{logical. Should this layer be included in the legends?
\code{NA}, the default, includes if any aesthetics are mapped.
\code{FALSE} never includes, and \code{TRUE} always includes.
It can also be a named logical vector to finely select the aesthetics to
display.}
\item{...}{Other arguments passed on to \code{\link[ggplot2:layer]{layer()}}. These are
often aesthetics, used to set an aesthetic to a fixed value, like
\code{colour = "red"} or \code{size = 3}. They may also be parameters
to the paired geom/stat.}
\item{spread}{Deprecated. Use \code{strength} instead.}
}
\description{
This geom draws edges as cubic beziers with the control point positioned
half-way between the nodes and at an angle dependent on the presence of
parallel edges. This results in parallel edges being drawn in a
non-overlapping fashion resembling the standard approach used in
\code{\link[igraph:plot.igraph]{igraph::plot.igraph()}}. Before calculating the curvature the edges
are sorted by direction so that edges going the same way will be adjacent.
This geom is currently the only choice for non-simple graphs if edges should
not be overplotted.
}
\section{Aesthetics}{
\code{geom_edge_fan} and \code{geom_edge_fan0} understand the following
aesthetics. Bold aesthetics are automatically set, but can be overridden.
\itemize{
\item \strong{x}
\item \strong{y}
\item \strong{xend}
\item \strong{yend}
\item \strong{from}
\item \strong{to}
\item edge_colour
\item edge_width
\item edge_linetype
\item edge_alpha
\item filter
}
\code{geom_edge_fan2} understand the following aesthetics. Bold aesthetics are
automatically set, but can be overridden.
\itemize{
\item \strong{x}
\item \strong{y}
\item \strong{group}
\item \strong{from}
\item \strong{to}
\item edge_colour
\item edge_width
\item edge_linetype
\item edge_alpha
\item filter
}
\code{geom_edge_fan} and \code{geom_edge_fan2} furthermore takes the following
aesthetics.
\itemize{
\item start_cap
\item end_cap
\item label
\item label_pos
\item label_size
\item angle
\item hjust
\item vjust
\item family
\item fontface
\item lineheight
}
}
\section{Computed variables}{
\describe{
\item{index}{The position along the path (not computed for the *0 version)}
}
}
\section{Edge variants}{
Many geom_edge_* layers comes in 3 flavors depending on the level of control
needed over the drawing. The default (no numeric postfix) generate a number
of points (\code{n}) along the edge and draws it as a path. Each point along
the line has a numeric value associated with it giving the position along the
path, and it is therefore possible to show the direction of the edge by
mapping to this e.g. \code{colour = stat(index)}. The version postfixed with a
"2" uses the "long" edge format (see \code{\link[=get_edges]{get_edges()}}) and makes it
possible to interpolate node parameter between the start and end node along
the edge. It is considerable less performant so should only be used if this
is needed. The version postfixed with a "0" draws the edge in the most
performant way, often directly using an appropriate grob from the grid
package, but does not allow for gradients along the edge.
Often it is beneficial to stop the drawing of the edge before it reaches the
node, for instance in cases where an arrow should be drawn and the arrowhead
shouldn't lay on top or below the node point. geom_edge_* and geom_edge_*2
supports this through the start_cap and end_cap aesthetics that takes a
\code{\link[=geometry]{geometry()}} specification and dynamically caps the termini of the
edges based on the given specifications. This means that if
\code{end_cap = circle(1, 'cm')} the edges will end at a distance of 1cm even
during resizing of the plot window.
All \verb{geom_edge_*} and \code{geom_edge_*2} have the ability to draw a
label along the edge. The reason this is not a separate geom is that in order
for the label to know the location of the edge it needs to know the edge type
etc. Labels are drawn by providing a label aesthetic. The label_pos can be
used to specify where along the edge it should be drawn by supplying a number
between 0 and 1. The label_size aesthetic can be used to control the size of
the label. Often it is needed to have the label written along the direction
of the edge, but since the actual angle is dependent on the plot dimensions
this cannot be calculated beforehand. Using the angle_calc argument allows
you to specify whether to use the supplied angle aesthetic or whether to draw
the label along or across the edge.
}
\section{Edge aesthetic name expansion}{
In order to avoid excessive typing edge aesthetic names are
automatically expanded. Because of this it is not necessary to write
\code{edge_colour} within the \code{aes()} call as \code{colour} will
automatically be renamed appropriately.
}
\examples{
require(tidygraph)
gr <- create_notable('bull') \%>\%
convert(to_directed) \%>\%
bind_edges(data.frame(from = c(1, 2, 2, 3), to = c(2, 1, 3, 2))) \%E>\%
mutate(class = sample(letters[1:3], 9, TRUE)) \%N>\%
mutate(class = sample(c('x', 'y'), 5, TRUE))
ggraph(gr, 'stress') +
geom_edge_fan(aes(alpha = stat(index)))
ggraph(gr, 'stress') +
geom_edge_fan2(aes(colour = node.class))
ggraph(gr, 'stress') +
geom_edge_fan0(aes(colour = class))
}
\seealso{
Other geom_edge_*:
\code{\link{geom_edge_arc}()},
\code{\link{geom_edge_bend}()},
\code{\link{geom_edge_density}()},
\code{\link{geom_edge_diagonal}()},
\code{\link{geom_edge_elbow}()},
\code{\link{geom_edge_hive}()},
\code{\link{geom_edge_link}()},
\code{\link{geom_edge_loop}()},
\code{\link{geom_edge_parallel}()},
\code{\link{geom_edge_point}()},
\code{\link{geom_edge_span}()},
\code{\link{geom_edge_tile}()}
}
\author{
Thomas Lin Pedersen
}
\concept{geom_edge_*}
ggraph/man/scale_edge_colour.Rd 0000644 0001762 0000144 00000021474 13617226162 016240 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/scale_edge_colour.R
\name{scale_edge_colour}
\alias{scale_edge_colour}
\alias{scale_edge_colour_hue}
\alias{scale_edge_colour_brewer}
\alias{scale_edge_colour_distiller}
\alias{scale_edge_colour_gradient}
\alias{scale_edge_colour_gradient2}
\alias{scale_edge_colour_gradientn}
\alias{scale_edge_colour_grey}
\alias{scale_edge_colour_identity}
\alias{scale_edge_colour_manual}
\alias{scale_edge_colour_viridis}
\alias{scale_edge_colour_continuous}
\alias{scale_edge_colour_discrete}
\alias{scale_edge_color_hue}
\alias{scale_edge_color_brewer}
\alias{scale_edge_color_distiller}
\alias{scale_edge_color_gradient}
\alias{scale_edge_color_gradient2}
\alias{scale_edge_color_gradientn}
\alias{scale_edge_color_grey}
\alias{scale_edge_color_identity}
\alias{scale_edge_color_manual}
\alias{scale_edge_color_continuous}
\alias{scale_edge_color_discrete}
\alias{scale_edge_color_viridis}
\title{Edge colour scales}
\usage{
scale_edge_colour_hue(
...,
h = c(0, 360) + 15,
c = 100,
l = 65,
h.start = 0,
direction = 1,
na.value = "grey50"
)
scale_edge_colour_brewer(..., type = "seq", palette = 1, direction = 1)
scale_edge_colour_distiller(
...,
type = "seq",
palette = 1,
direction = -1,
values = NULL,
space = "Lab",
na.value = "grey50",
guide = "edge_colourbar"
)
scale_edge_colour_gradient(
...,
low = "#132B43",
high = "#56B1F7",
space = "Lab",
na.value = "grey50",
guide = "edge_colourbar"
)
scale_edge_colour_gradient2(
...,
low = muted("red"),
mid = "white",
high = muted("blue"),
midpoint = 0,
space = "Lab",
na.value = "grey50",
guide = "edge_colourbar"
)
scale_edge_colour_gradientn(
...,
colours,
values = NULL,
space = "Lab",
na.value = "grey50",
guide = "edge_colourbar",
colors
)
scale_edge_colour_grey(..., start = 0.2, end = 0.8, na.value = "red")
scale_edge_colour_identity(..., guide = "none")
scale_edge_colour_manual(..., values)
scale_edge_colour_viridis(
...,
alpha = 1,
begin = 0,
end = 1,
discrete = FALSE,
option = "D",
direction = 1
)
scale_edge_colour_continuous(
...,
low = "#132B43",
high = "#56B1F7",
space = "Lab",
na.value = "grey50",
guide = "edge_colourbar"
)
scale_edge_colour_discrete(
...,
h = c(0, 360) + 15,
c = 100,
l = 65,
h.start = 0,
direction = 1,
na.value = "grey50"
)
scale_edge_color_hue(
...,
h = c(0, 360) + 15,
c = 100,
l = 65,
h.start = 0,
direction = 1,
na.value = "grey50"
)
scale_edge_color_brewer(..., type = "seq", palette = 1, direction = 1)
scale_edge_color_distiller(
...,
type = "seq",
palette = 1,
direction = -1,
values = NULL,
space = "Lab",
na.value = "grey50",
guide = "edge_colourbar"
)
scale_edge_color_gradient(
...,
low = "#132B43",
high = "#56B1F7",
space = "Lab",
na.value = "grey50",
guide = "edge_colourbar"
)
scale_edge_color_gradient2(
...,
low = muted("red"),
mid = "white",
high = muted("blue"),
midpoint = 0,
space = "Lab",
na.value = "grey50",
guide = "edge_colourbar"
)
scale_edge_color_gradientn(
...,
colours,
values = NULL,
space = "Lab",
na.value = "grey50",
guide = "edge_colourbar",
colors
)
scale_edge_color_grey(..., start = 0.2, end = 0.8, na.value = "red")
scale_edge_color_identity(..., guide = "none")
scale_edge_color_manual(..., values)
scale_edge_color_continuous(
...,
low = "#132B43",
high = "#56B1F7",
space = "Lab",
na.value = "grey50",
guide = "edge_colourbar"
)
scale_edge_color_discrete(
...,
h = c(0, 360) + 15,
c = 100,
l = 65,
h.start = 0,
direction = 1,
na.value = "grey50"
)
scale_edge_color_viridis(
...,
alpha = 1,
begin = 0,
end = 1,
discrete = FALSE,
option = "D",
direction = 1
)
}
\arguments{
\item{...}{Arguments passed on to \code{discrete_scale}
\describe{
\item{palette}{A palette function that when called with a single integer
argument (the number of levels in the scale) returns the values that
they should take.}
\item{breaks}{One of:
\itemize{
\item \code{NULL} for no breaks
\item \code{waiver()} for the default breaks computed by the
transformation object
\item A character vector of breaks
\item A function that takes the limits as input and returns breaks
as output
}}
\item{limits}{A character vector that defines possible values of the scale
and their order.}
\item{drop}{Should unused factor levels be omitted from the scale?
The default, \code{TRUE}, uses the levels that appear in the data;
\code{FALSE} uses all the levels in the factor.}
\item{na.translate}{Unlike continuous scales, discrete scales can easily show
missing values, and do so by default. If you want to remove missing values
from a discrete scale, specify \code{na.translate = FALSE}.}
\item{na.value}{If \code{na.translate = TRUE}, what value aesthetic
value should missing be displayed as? Does not apply to position scales
where \code{NA} is always placed at the far right.}
\item{scale_name}{The name of the scale}
\item{name}{The name of the scale. Used as the axis or legend title. If
\code{waiver()}, the default, the name of the scale is taken from the first
mapping used for that aesthetic. If \code{NULL}, the legend title will be
omitted.}
\item{labels}{One of:
\itemize{
\item \code{NULL} for no labels
\item \code{waiver()} for the default labels computed by the
transformation object
\item A character vector giving labels (must be same length as \code{breaks})
\item A function that takes the breaks as input and returns labels
as output
}}
\item{expand}{Vector of range expansion constants used to add some
padding around the data, to ensure that they are placed some distance
away from the axes. Use the convenience function \code{\link[ggplot2:expand_scale]{expand_scale()}}
to generate the values for the \code{expand} argument. The defaults are to
expand the scale by 5\% on each side for continuous variables, and by
0.6 units on each side for discrete variables.}
\item{guide}{A function used to create a guide or its name. See
\code{\link[ggplot2:guides]{guides()}} for more info.}
\item{position}{The position of the axis. "left" or "right" for vertical
scales, "top" or "bottom" for horizontal scales}
\item{super}{The super class to use for the constructed scale}
}}
\item{h}{range of hues to use, in [0, 360]}
\item{c}{chroma (intensity of colour), maximum value varies depending on
combination of hue and luminance.}
\item{l}{luminance (lightness), in [0, 100]}
\item{h.start}{hue to start at}
\item{direction}{direction to travel around the colour wheel,
1 = clockwise, -1 = counter-clockwise}
\item{na.value}{Colour to use for missing values}
\item{type}{One of seq (sequential), div (diverging) or qual (qualitative)}
\item{palette}{If a string, will use that named palette. If a number, will
index into the list of palettes of appropriate \code{type}}
\item{values}{if colours should not be evenly positioned along the gradient
this vector gives the position (between 0 and 1) for each colour in the
\code{colours} vector. See \code{\link[=rescale]{rescale()}} for a convenience function
to map an arbitrary range to between 0 and 1.}
\item{space}{colour space in which to calculate gradient. Must be "Lab" -
other values are deprecated.}
\item{guide}{Type of legend. Use \code{"colourbar"} for continuous
colour bar, or \code{"legend"} for discrete colour legend.}
\item{low, high}{Colours for low and high ends of the gradient.}
\item{mid}{colour for mid point}
\item{midpoint}{The midpoint (in data value) of the diverging scale.
Defaults to 0.}
\item{colours, colors}{Vector of colours to use for n-colour gradient.}
\item{start}{grey value at low end of palette}
\item{end}{grey value at high end of palette}
\item{alpha}{pass through parameter to \code{viridis}}
\item{begin}{The (corrected) hue in [0,1] at which the viridis colormap begins.}
\item{discrete}{generate a discrete palette? (default: \code{FALSE} - generate continuous palette)}
\item{option}{A character string indicating the colormap option to use. Four
options are available: "magma" (or "A"), "inferno" (or "B"), "plasma" (or "C"),
"viridis" (or "D", the default option) and "cividis" (or "E").}
}
\value{
A ggproto object inheriting from \code{Scale}
}
\description{
This set of scales defines new colour scales for edge geoms equivalent to the
ones already defined by ggplot2. The parameters are equivalent to the ones
from ggplot2 so there is nothing new under the sun. The different geoms will
know whether to use edge scales or the standard scales so it is not necessary
to write \code{edge_colour} in the call to the geom - just use \code{colour}.
}
\seealso{
Other scale_edge_*:
\code{\link{scale_edge_alpha}()},
\code{\link{scale_edge_fill}},
\code{\link{scale_edge_linetype}()},
\code{\link{scale_edge_shape}()},
\code{\link{scale_edge_size}()},
\code{\link{scale_edge_width}()},
\code{\link{scale_label_size}()}
}
\concept{scale_edge_*}
ggraph/man/geom_node_range.Rd 0000644 0001762 0000144 00000005264 13617226162 015711 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/geom_node_range.R
\name{geom_node_range}
\alias{geom_node_range}
\title{Show nodes as a line spanning a horizontal range}
\usage{
geom_node_range(
mapping = NULL,
data = NULL,
position = "identity",
show.legend = NA,
...
)
}
\arguments{
\item{mapping}{Set of aesthetic mappings created by \code{\link[ggplot2:aes]{ggplot2::aes()}}
or \code{\link[ggplot2:aes_]{ggplot2::aes_()}}. By default x is mapped to xmin, xend is mapped to xmax
and y and yend are mapped to y in the node data.}
\item{data}{The data to be displayed in this layer. There are three
options:
If \code{NULL}, the default, the data is inherited from the plot
data as specified in the call to \code{\link[ggplot2:ggplot]{ggplot()}}.
A \code{data.frame}, or other object, will override the plot
data. All objects will be fortified to produce a data frame. See
\code{\link[ggplot2:fortify]{fortify()}} for which variables will be created.
A \code{function} will be called with a single argument,
the plot data. The return value must be a \code{data.frame}, and
will be used as the layer data. A \code{function} can be created
from a \code{formula} (e.g. \code{~ head(.x, 10)}).}
\item{position}{Position adjustment, either as a string, or the result of
a call to a position adjustment function.}
\item{show.legend}{logical. Should this layer be included in the legends?
\code{NA}, the default, includes if any aesthetics are mapped.
\code{FALSE} never includes, and \code{TRUE} always includes.
It can also be a named logical vector to finely select the aesthetics to
display.}
\item{...}{Other arguments passed on to \code{\link[ggplot2:layer]{layer()}}. These are
often aesthetics, used to set an aesthetic to a fixed value, like
\code{colour = "red"} or \code{size = 3}. They may also be parameters
to the paired geom/stat.}
}
\description{
This geom is most useful together with the \link[=layout_tbl_graph_fabric]{fabric}
layout for showing the horizontal span of each node.
}
\section{Aesthetics}{
\code{geom_node_point} understand the following aesthetics. Bold aesthetics are
automatically set, but can be overridden.
\itemize{
\item \strong{x}
\item \strong{xend}
\item \strong{y}
\item \strong{yend}
\item alpha
\item colour
\item linetype
\item size
\item filter
}
}
\examples{
require(tidygraph)
gr <- as_tbl_graph(highschool)
ggraph(gr, layout = 'fabric') +
geom_node_range()
}
\seealso{
Other geom_node_*:
\code{\link{geom_node_arc_bar}()},
\code{\link{geom_node_circle}()},
\code{\link{geom_node_point}()},
\code{\link{geom_node_text}()},
\code{\link{geom_node_tile}()},
\code{\link{geom_node_voronoi}()}
}
\author{
Thomas Lin Pedersen
}
\concept{geom_node_*}
ggraph/man/scale_edge_alpha.Rd 0000644 0001762 0000144 00000003666 13617226162 016025 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/scale_edge_alpha.R
\name{scale_edge_alpha}
\alias{scale_edge_alpha}
\alias{scale_edge_alpha_continuous}
\alias{scale_edge_alpha_discrete}
\alias{scale_edge_alpha_manual}
\alias{scale_edge_alpha_identity}
\title{Edge alpha scales}
\usage{
scale_edge_alpha(..., range = c(0.1, 1))
scale_edge_alpha_continuous(..., range = c(0.1, 1))
scale_edge_alpha_discrete(..., range = c(0.1, 1))
scale_edge_alpha_manual(..., values)
scale_edge_alpha_identity(..., guide = "none")
}
\arguments{
\item{...}{Other arguments passed on to \code{\link[ggplot2:continuous_scale]{continuous_scale()}}
or \code{\link[ggplot2:discrete_scale]{discrete_scale()}} as appropriate, to control name, limits,
breaks, labels and so forth.}
\item{range}{Output range of alpha values. Must lie between 0 and 1.}
\item{values}{a set of aesthetic values to map data values to. If this
is a named vector, then the values will be matched based on the names.
If unnamed, values will be matched in order (usually alphabetical) with
the limits of the scale. Any data values that don't match will be
given \code{na.value}.}
\item{guide}{Guide to use for this scale. Defaults to \code{"none"}.}
}
\value{
A ggproto object inheriting from \code{Scale}
}
\description{
This set of scales defines new alpha scales for edge geoms equivalent to the
ones already defined by ggplot2. See \code{\link[ggplot2:scale_alpha]{ggplot2::scale_alpha()}} for
more information. The different geoms will know whether to use edge scales or
the standard scales so it is not necessary to write \code{edge_alpha} in
the call to the geom - just use \code{alpha}.
}
\seealso{
Other scale_edge_*:
\code{\link{scale_edge_colour}},
\code{\link{scale_edge_fill}},
\code{\link{scale_edge_linetype}()},
\code{\link{scale_edge_shape}()},
\code{\link{scale_edge_size}()},
\code{\link{scale_edge_width}()},
\code{\link{scale_label_size}()}
}
\concept{scale_edge_*}
ggraph/DESCRIPTION 0000644 0001762 0000144 00000003056 13617251652 013244 0 ustar ligges users Package: ggraph
Type: Package
Title: An Implementation of Grammar of Graphics for Graphs and Networks
Version: 2.0.1
Authors@R:
c(person(given = "Thomas Lin",
family = "Pedersen",
role = c("cre", "aut"),
email = "thomasp85@gmail.com",
comment = c(ORCID = "0000-0002-5147-4711")),
person(given = "RStudio",
role = "cph"))
Maintainer: Thomas Lin Pedersen
Description: The grammar of graphics as implemented in ggplot2 is a poor fit for
graph and network visualizations due to its reliance on tabular data input.
ggraph is an extension of the ggplot2 API tailored to graph visualizations
and provides the same flexible approach to building up plots layer by layer.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: TRUE
Imports: Rcpp (>= 0.12.2), dplyr, ggforce (>= 0.3.1), grid, igraph (>=
1.0.0), scales, MASS, digest, gtable, ggrepel, utils, stats,
viridis, rlang, tidygraph, graphlayouts (>= 0.5.0)
Suggests: network, knitr, rmarkdown, purrr, tibble, seriation, deldir,
gganimate
LinkingTo: Rcpp
RoxygenNote: 7.0.2
Depends: R (>= 2.10), ggplot2 (>= 3.0.0)
VignetteBuilder: knitr
URL: https://ggraph.data-imaginist.com,
https://github.com/thomasp85/ggraph
BugReports: https://github.com/thomasp85/ggraph/issues
NeedsCompilation: yes
Packaged: 2020-02-07 10:43:31 UTC; thomas
Author: Thomas Lin Pedersen [cre, aut]
(),
RStudio [cph]
Repository: CRAN
Date/Publication: 2020-02-07 12:10:18 UTC
ggraph/build/ 0000755 0001762 0000144 00000000000 13617237522 012631 5 ustar ligges users ggraph/build/vignette.rds 0000644 0001762 0000144 00000000406 13617237522 015170 0 ustar ligges users RK@ ?'&z N)17b Z:}kfuчh@j! `3xMx,8echËMEgBQl+"QM+!X*OK̮*gWPmM#S 48J"qgv!thA aAU酑Cj` R^d"hõ,ni}7.;, ߎN |״v:j ggraph/src/ 0000755 0001762 0000144 00000000000 13617237522 012321 5 ustar ligges users ggraph/src/pathAttr.cpp 0000644 0001762 0000144 00000002562 13524234420 014610 0 ustar ligges users #include
using namespace Rcpp;
//[[Rcpp::export]]
DataFrame pathAttr(DataFrame paths, int ngroups) {
LogicalVector solid(ngroups, true);
LogicalVector constant(ngroups, true);
int currentGroup, currentIndex, i;
IntegerVector group = paths["group"];
NumericVector alpha = paths["edge_alpha"];
LogicalVector alpha_na = is_na(alpha);
NumericVector width = paths["edge_width"];
LogicalVector width_na = is_na(width);
CharacterVector lty = paths["edge_linetype"];
LogicalVector lty_na = is_na(lty);
CharacterVector colour = paths["edge_colour"];
LogicalVector colour_na = is_na(colour);
currentGroup = group[0];
currentIndex = 0;
for (i = 1; i < group.size(); ++i) {
if (group[i] == currentGroup) {
if (solid[currentIndex]) {
solid[currentIndex] = lty[i] == "solid" && lty[i] == lty[i-1];
}
if (constant[currentIndex]) {
constant[currentIndex] =
((alpha[i] == alpha[i-1]) || (alpha_na[i] && alpha_na[i-1])) &&
((width[i] == width[i-1]) || (width_na[i] && width_na[i-1])) &&
((lty[i] == lty[i-1]) || (lty_na[i] && lty_na[i-1])) &&
((colour[i] == colour[i-1]) || (colour_na[i] && colour_na[i-1]));
}
} else {
currentGroup = group[i];
++currentIndex;
}
}
return DataFrame::create(
Named("solid") = solid,
Named("constant") = constant
);
}
ggraph/src/nodes.h 0000644 0001762 0000144 00000010756 13527301120 013575 0 ustar ligges users #include
using namespace Rcpp;
struct Rectangle {
double x;
double y;
double width;
double height;
};
class Node {
std::vector children;
std::vector< std::vector > allLeafs;
Node* parent;
bool hasParent;
double Weight;
double Height;
int Id;
int Order;
static bool comparePtrToNode(Node* a, Node* b) {
return (a->order() < b->order());
}
public:
Node() {
hasParent = false;
Weight = 0.0;
Height = 0.0;
Id = 0;
Order = 0;
};
Node(int id, int order, double weight) {
hasParent = false;
Id = id;
Order = order;
Weight = weight;
};
Node(int id, int order, double weight, double height) {
hasParent = false;
Id = id;
Order = order;
Weight = weight;
Height = height;
};
void rotate(double angle, double x, double y) {
double s = sin(angle);
double c = cos(angle);
// translate point back to origin:
double new_x = bounds.x - x;
double new_y = bounds.y - y;
// rotate point
bounds.x = new_x * c - new_y * s + x;
bounds.y = new_x * s + new_y * c + y;
for (unsigned int i = 0; i < children.size(); ++i) {
children[i]->rotate(angle, x, y);
}
};
std::vector getChildren() {
std::vector childVec;
for (unsigned int i = 0; i < children.size(); ++i) {
childVec.push_back(children[i]);
}
return childVec;
};
Node* getParent() {
return parent;
};
std::vector getLeafs() {
std::vector leafVec;
collectLeafs(leafVec);
return leafVec;
};
void collectLeafs(std::vector &leafVec) {
if (leaf()) {
leafVec.push_back(this);
} else {
for (unsigned int i = 0; i < children.size(); ++i) {
children[i]->collectLeafs(leafVec);
}
}
};
std::vector getParentLeafs() {
std::vector leafVec;
collectParentLeafs(leafVec);
return leafVec;
};
void collectParentLeafs(std::vector &leafVec) {
if (orphan()) return;
std::vector siblings = parent->children;
for (unsigned int i = 0; i < siblings.size(); ++i) {
if (siblings[i] == this) continue;
siblings[i]->collectLeafs(leafVec);
}
parent->collectParentLeafs(leafVec);
};
void collectAllLeafs() {
if (orphan()) return;
for (unsigned int i = 0; i < children.size(); ++i) {
allLeafs.push_back(children[i]->getLeafs());
}
allLeafs.push_back(getParentLeafs());
};
std::vector< std::vector > getAllLeafs() {
if (allLeafs.empty()) {
collectAllLeafs();
}
std::vector< std::vector > leafs;
for (unsigned int i = 0; i < allLeafs.size(); ++i) {
std::vector leafVec;
for (unsigned int j = 0; j < allLeafs[i].size(); ++j) {
leafVec.push_back(allLeafs[i][j]);
}
leafs.push_back(leafVec);
}
return leafs;
}
unsigned int nChildren() {
return children.size();
};
unsigned int nOffspring() {
unsigned int ret = nChildren();
for (unsigned int i = 0; i < ret; ++i) {
ret += children[i]->nOffspring();
}
return ret;
};
unsigned int nLeafs() {
if (leaf()) return 1;
unsigned int ret = 0;
for (unsigned int i = 0; i < nChildren(); ++i) {
if (children[i]->leaf()) {
ret++;
} else {
ret += children[i]->nLeafs();
}
}
return ret;
}
double weight() {
return Weight;
};
double height() {
return Height;
};
void addNode(Node* n) {
double w = n->weight();
Weight += w;
if (hasParent) {
parent->addWeight(w);
}
n->setParent(this);
children.push_back(n);
};
void addWeight(double w) {
if (hasParent) {
parent->addWeight(w);
}
Weight += w;
};
void setParent(Node* n) {
hasParent = true;
parent = n;
};
bool orphan() {
return !hasParent;
};
bool leaf() {
return nChildren() == 0;
}
int order() {
return Order;
};
void sortChildren() {
std::sort(children.begin(), children.end(), comparePtrToNode);
};
Node* getRoot() {
if (orphan()) {
return this;
} else {
return parent->getRoot();
}
}
Rectangle bounds;
};
std::vector createHierarchy(std::vector parent, std::vector order, std::vector weight);
std::vector createHierarchy(std::vector parent, std::vector order, std::vector weight, std::vector height);
std::vector createUnrooted(std::vector parent, std::vector order, std::vector length);
ggraph/src/circlePack.cpp 0000644 0001762 0000144 00000032123 13527300762 015063 0 ustar ligges users #include
#include
using namespace Rcpp;
inline int randWrapper(const int n) {
return std::floor(float(unif_rand()*n));
}
struct Circle {
double x;
double y;
double r;
int i;
Circle* next;
Circle* prev;
};
class FrontChain {
double center_x;
double center_y;
double total_weight;
Circle enclosure;
Circle* next_circle;
void place(Circle* c, Circle* c1, Circle* c2) {
double r0 = c1->r + c->r;
double r1 = c2->r + c->r;
double dx = c2->x - c1->x;
double dy = c2->y - c1->y;
double d = std::sqrt(float(dx*dx + dy*dy));
double a = (r0*r0 - r1*r1 + d*d) / (2*d);
double h = std::sqrt(float(r0*r0 - a*a));
c->x = c1->x + a*(c2->x - c1->x)/d - h*(c2->y - c1->y)/d;
c->y = c1->y + a*(c2->y - c1->y)/d + h*(c2->x - c1->x)/d;
};
double dist_to_center(Circle* c) {
double dx = c->x - center_x / total_weight;
double dy = c->y - center_y / total_weight;
return c->r + std::sqrt(float(dx*dx + dy*dy));
}
bool circles_intersect(Circle* c1, Circle* c2) {
double dx = c2->x - c1->x;
double dy = c2->y - c1->y;
double dr = c2->r + c1-> r;
return dr*dr > dx*dx + dy*dy;
};
void update_closest_circle() {
Circle* circle_it = next_circle;
Circle* current_close = circle_it;
double dist = dist_to_center(circle_it);
circle_it = circle_it->next;
while(circle_it != next_circle) {
double temp_dist = dist_to_center(circle_it);
if (temp_dist < dist) {
dist = temp_dist;
current_close = circle_it;
}
circle_it = circle_it->next;
}
next_circle = current_close;
};
void update_chain(Circle* from, Circle* to) {
from->next = to;
to->prev = from;
};
bool encloses(Circle enc, Circle* c) {
double dx = c->x - enc.x;
double dy = c->y - enc.y;
double dr = c->r - enc.r;
return dr * dr + 1e-6 > dx * dx + dy * dy;
};
Circle enclose1(Circle* c1) {
Circle enc = {c1->x, c1->y, c1->r};
if (enc.r > 1e10) {
stop("enc1 error");
}
return enc;
};
Circle enclose2(Circle* c1, Circle* c2) {
double dx = c2->x - c1->x;
double dy = c2->y - c1->y;
double dr = c2->r - c1->r;
double l = std::sqrt(float(dx*dx + dy*dy));
Circle enc = {
(c1->x + c2->x + dx / l * dr) / 2,
(c1->y + c2->y + dy / l * dr) / 2,
(l + c1->r + c2->r) / 2
};
if (enc.r > 1e10) {
stop("enc2 error");
}
return enc;
};
Circle enclose3(Circle* c1, Circle* c2, Circle* c3) {
double A2 = 2 * (c1->x - c2->x);
double B2 = 2 * (c1->y - c2->y);
double C2 = 2 * (c2->r - c1->r);
double D2 = c1->x * c1->x + c1->y * c1->y - c1->r * c1->r - c2->x * c2->x - c2->y * c2->y + c2->r * c2->r;
double A3 = 2 * (c1->x - c3->x);
double B3 = 2 * (c1->y - c3->y);
double C3 = 2 * (c3->r - c1->r);
double D3 = c1->x * c1->x + c1->y * c1->y - c1->r * c1->r - c3->x * c3->x - c3->y * c3->y + c3->r * c3->r;
double AB = A3 * B2 - A2 * B3;
double XA = (B2 * D3 - B3 * D2) / AB - c1->x;
double XB = (B3 * C2 - B2 * C3) / AB;
double YA = (A3 * D2 - A2 * D3) / AB - c1->y;
double YB = (A2 * C3 - A3 * C2) / AB;
double A = XB * XB + YB * YB - 1;
double B = 2 * (XA * XB + YA * YB + c1->r);
double C = XA * XA + YA * YA - c1->r * c1->r;
double r = (-B - std::sqrt(float(B * B - 4 * A * C))) / (2 * A);
Circle enc = {
XA + XB * r + c1->x,
YA + YB * r + c1->y,
r
};
if (enc.r > 1e10) {
stop("enc3 error");
}
return enc;
};
Circle encloseN(std::deque::iterator begin_S, std::deque::iterator end_S, std::deque Q) {
Circle enc = {0, 0, 0};
bool has_enc = false;
switch (Q.size()) {
case 1: enc = enclose1(Q[0]);
has_enc = true;
break;
case 2: enc = enclose2(Q[0], Q[1]);
has_enc = true;
break;
case 3: enc = enclose3(Q[0], Q[1], Q[2]);
has_enc = true;
break;
}
std::deque::iterator S_iter = begin_S;
while (S_iter != end_S) {
if (!has_enc || !encloses(enc, *S_iter)) {
Q.push_back(*S_iter);
enc = encloseN(begin_S, S_iter, Q);
has_enc = true;
Q.pop_back();
}
S_iter++;
}
return enc;
};
public:
FrontChain(Circle* c1, Circle* c2, Circle* c3) {
// Set location of first circle to coord center and second at random angle
c1->x = 0;
c1->y = 0;
double d12 = c1->r + c2->r;
double angle2 = (2 * M_PI) * R::runif(0, 1);
c2->x = std::cos(float(angle2)) * d12;
c2->y = std::sin(float(angle2)) * d12;
// Place third circle according to the first two
place(c3, c2, c1);
// Set weighted center
double a1 = c1->r*c1->r;
double a2 = c2->r*c2->r;
double a3 = c3->r*c3->r;
total_weight = a1 + a2 + a3;
center_x = a1*c1->x + a2*c2->x + a3*c3->x;
center_y = a1*c1->y + a2*c2->y + a3*c3->y;
// Inititalize the front chain
c1->next = c2;
c1->prev = c3;
c2->next = c3;
c2->prev = c1;
c3->next = c1;
c3->prev = c2;
next_circle = c1;
};
FrontChain(Circle* c1, Circle* c2) {
// Set location of first circle to coord center and second at random angle
c1->x = 0;
c1->y = 0;
double d12 = c1->r + c2->r;
double angle2 = (2 * M_PI) * R::runif(0, 1);
c2->x = std::cos(float(angle2)) * d12;
c2->y = std::sin(float(angle2)) * d12;
// Inititalize the front chain
c1->next = c2;
c1->prev = c2;
c2->next = c1;
c2->prev = c1;
next_circle = c1;
};
FrontChain(Circle* c1) {
// Set location of first circle to coord center and second at random angle
c1->x = 0;
c1->y = 0;
// Inititalize the front chain
c1->next = c1;
c1->prev = c1;
next_circle = c1;
};
void add(Circle* c) {
Circle* n = next_circle;
Circle* m = next_circle->next;
place(c, n, m);
bool at_m = false;
bool at_n = false;
while(true) {
n = n->prev;
if (n == m) break;
if (circles_intersect(c, n)) {
at_n = true;
break;
}
m = m->next;
if (n == m) break;
if (circles_intersect(c, m)) {
at_m = true;
break;
}
}
if (at_m) {
update_chain(next_circle, m);
add(c);
} else if (at_n) {
update_chain(n, next_circle->next);
next_circle = n;
add(c);
} else {
c->next = next_circle->next;
c->prev = next_circle;
next_circle->next->prev = c;
next_circle->next = c;
double a = c->r*c->r;
total_weight += a;
center_x += a*c->x;
center_y += a*c->y;
update_closest_circle();
}
};
void center(std::deque::iterator first, std::deque::iterator last) {
while (first != last) {
first->x -= enclosure.x;
first->y -= enclosure.y;
first++;
}
enclosure.x = 0;
enclosure.y = 0;
};
double enclose_radius() {
return enclosure.r;
};
std::deque chain_ind() {
std::deque index;
Circle* circle_it = next_circle;
index.push_back(circle_it->i);
circle_it = circle_it->next;
while(circle_it != next_circle) {
index.push_back(circle_it->i);
circle_it = circle_it->next;
}
return index;
};
void enclose() {
std::deque fc;
Circle* circle_it = next_circle;
fc.push_back(circle_it);
circle_it = circle_it->next;
while(circle_it != next_circle) {
fc.push_back(circle_it);
circle_it = circle_it->next;
}
if (fc.size() == 1) {
enclosure = enclose1(fc[0]);
} else if (fc.size() == 2) {
enclosure = enclose2(fc[0], fc[1]);
} else {
std::random_shuffle(fc.begin(), fc.end(), randWrapper);
std::deque Q;
enclosure = encloseN(fc.begin(), fc.end(), Q);
}
}
};
FrontChain pack_circles(std::deque &circles) {
if (circles.size() == 0) {
stop("Cannot pack an empty set of circles");
}
std::deque::iterator itc;
FrontChain fc(&circles[0]);
if (circles.size() == 2) {
fc = FrontChain(&circles[0], &circles[1]);
} else if (circles.size() > 2){
fc = FrontChain(&circles[0], &circles[1], &circles[2]);
for (itc = circles.begin() + 3; itc != circles.end(); itc++) {
fc.add(&(*itc));
}
}
fc.enclose();
fc.center(circles.begin(), circles.end());
return fc;
}
class NodePack {
std::vector children;
NodePack* parent;
bool hasParent;
public:
int Id;
double x;
double y;
double r;
NodePack() {
hasParent = false;
};
NodePack(int id, double weight) {
hasParent = false;
Id = id;
x = 0.0;
y = 0.0;
r = std::sqrt(float( weight / M_PI));
};
int nChildren() {
return children.size();
};
void addNode(NodePack* n) {
n->setParent(this);
children.push_back(n);
};
void setParent(NodePack* n) {
hasParent = true;
parent = n;
};
bool orphan() {
return !hasParent;
};
void packChildren() {
if (nChildren() != 0) {
std::deque circles;
int i;
double max_r = 0;
int max_r_i = 0;
for (i = 0; i != nChildren(); i++) {
children[i]->packChildren();
if (children[i]->r > max_r) {
max_r = children[i]->r;
max_r_i = i;
}
Circle circ = {0, 0, children[i]->r, children[i]->Id};
circles.push_back(circ);
}
std::swap(children[0], children[max_r_i]);
std::swap(circles[0], circles[max_r_i]);
FrontChain fc = pack_circles(circles);
for (i = 0; i != nChildren(); i++) {
children[i]->x = circles[i].x;
children[i]->y = circles[i].y;
}
r = fc.enclose_radius();
}
};
void placeChildren(double center_x, double center_y) {
x += center_x;
y += center_y;
if (nChildren() != 0) {
int i;
for (i = 0; i != nChildren(); i++) {
children[i]->placeChildren(x, y);
}
}
}
};
std::vector createHierarchy(std::vector parent, std::vector weight) {
std::vector nodes;
unsigned int i;
for (i = 0; i < parent.size(); ++i) {
NodePack* node = new NodePack(i + 1, weight[i]);
nodes.push_back(node);
}
for (i = 0; i < parent.size(); ++i) {
if (parent[i] >= 0) {
nodes[parent[i]]->addNode(nodes[i]);
}
}
return nodes;
}
int findTopNode(std::vector& nodes) {
unsigned int i;
bool found = false;
for (i = 0; i < nodes.size(); ++i) {
if (nodes[i]->orphan()) {
found = true;
break;
}
}
if (!found) {
stop("No top node. Is this a tree structure?");
}
return (int) i;
}
//' Pack circles together
//'
//' This function is a direct interface to the circle packing algorithm used by
//' \code{\link{layout_tbl_graph_circlepack}}. It takes a vector of sizes and
//' returns the x and y position of each circle as a two-column matrix.
//'
//' @param areas A vector of circle areas
//'
//' @return A matrix with two columns and the same number of rows as the length
//' of the "areas" vector. The matrix has the following attributes added:
//' "enclosing_radius" giving the radius of the smallest enclosing circle, and
//' "front_chain" giving the terminating members of the front chain (see
//' Wang \emph{et al}. 2006).
//'
//' @references
//' Wang, W., Wang, H. H., Dai, G., & Wang, H. (2006). \emph{Visualization of
//' large hierarchical data by circle packing}. Chi, 517-520.
//'
//' @export
//'
//' @examples
//' library(ggforce)
//' sizes <- sample(10, 100, TRUE)
//'
//' position <- pack_circles(sizes)
//' data <- data.frame(x = position[,1], y = position[,2], r = sqrt(sizes/pi))
//'
//' ggplot() +
//' geom_circle(aes(x0 = x, y0 = y, r = r), data = data, fill = 'steelblue') +
//' geom_circle(aes(x0 = 0, y0 = 0, r = attr(position, 'enclosing_radius'))) +
//' geom_polygon(aes(x = x, y = y),
//' data = data[attr(position, 'front_chain'), ],
//' fill = NA,
//' colour = 'black')
//'
//[[Rcpp::export(name = "pack_circles")]]
NumericMatrix pack(NumericVector areas) {
NumericVector::iterator itr;
std::deque circles;
NumericMatrix res(areas.size(), 2);
for (itr = areas.begin(); itr != areas.end(); itr++) {
Circle c = {0, 0, std::sqrt(float(*itr / M_PI)), static_cast(circles.size()) + 1};
circles.push_back(c);
}
if (circles.size() == 0) {
res.attr("enclosing_radius") = 0;
res.attr("front_chain") = IntegerVector(0);
} else {
FrontChain fc = pack_circles(circles);
for (int i = 0; i < areas.size(); i++) {
res(i, 0) = circles[i].x;
res(i, 1) = circles[i].y;
}
res.attr("enclosing_radius") = fc.enclose_radius();
res.attr("front_chain") = wrap(fc.chain_ind());
}
return res;
}
//[[Rcpp::export]]
NumericMatrix circlePackLayout(IntegerVector parent, NumericVector weight) {
NumericMatrix res(parent.size(), 3);
unsigned int i;
std::vector nodes = createHierarchy(as< std::vector >(parent), as< std::vector >(weight));
int startNode = findTopNode(nodes);
nodes[startNode]->packChildren();
nodes[startNode]->placeChildren(0.0, 0.0);
for (i = 0; i < nodes.size(); ++i) {
res(i, 0) = nodes[i]->x;
res(i, 1) = nodes[i]->y;
res(i, 2) = nodes[i]->r;
delete nodes[i];
}
return res;
}
ggraph/src/unrooted.cpp 0000644 0001762 0000144 00000010455 13527511216 014664 0 ustar ligges users #include
#include "nodes.h"
using namespace Rcpp;
const double PI2 = 6.28318;
void equalAngle(Node* node, double start, double angle) {
if (node->leaf()) return;
double x = node->bounds.x;
double y = node->bounds.y;
std::vector children = node->getChildren();
for (unsigned int i = 0; i < children.size(); ++i) {
double span = children[i]->nLeafs() * angle;
double mid = start + span / 2;
children[i]->bounds.x = x + cos(mid) * children[i]->height();
children[i]->bounds.y = y + sin(mid) * children[i]->height();
equalAngle(children[i], start, angle);
start += span;
}
}
double equalDaylight(Node* node, double rotation_mod) {
if (node->orphan() || node->getParent()->orphan()) return 0;
if (node->nChildren() < 2) return 0;
std::vector< std::vector > leafs = node->getAllLeafs();
std::vector children = node->getChildren();
std::vector bounds_lower, bounds_upper;
double x0 = node->bounds.x;
double y0 = node->bounds.y;
for (unsigned int i = 0; i < leafs.size(); ++i) {
double x1, y1;
if (i < children.size()) {
x1 = children[i]->bounds.x - x0;
y1 = children[i]->bounds.y - y0;
} else {
x1 = node->getParent()->bounds.x - x0;
y1 = node->getParent()->bounds.y - y0;
}
int lower = 0;
int upper = 0;
double lower_angle = PI2;
double upper_angle = -PI2;
for (unsigned int j = 0; j < leafs[i].size(); ++j) {
double x2 = leafs[i][j]->bounds.x - x0;
double y2 = leafs[i][j]->bounds.y - y0;
double dot = x1 * x2 + y1 * y2;
double det = x1 * y2 - y1 * x2;
double angle = atan2(det, dot);
if (angle < lower_angle) {
lower_angle = angle;
lower = j;
}
if (angle > upper_angle) {
upper_angle = angle;
upper = j;
}
}
bounds_lower.push_back(leafs[i][lower]);
bounds_upper.push_back(leafs[i][upper]);
}
std::vector daylight;
double daylight_total = 0;
for (unsigned int i = 0; i < leafs.size(); ++i) {
int prev_i = i - 1;
if (prev_i < 0) prev_i = leafs.size() - 1;
double x1 = bounds_upper[prev_i]->bounds.x - x0;
double y1 = bounds_upper[prev_i]->bounds.y - y0;
double x2 = bounds_lower[i]->bounds.x - x0;
double y2 = bounds_lower[i]->bounds.y - y0;
double dot = x1 * x2 + y1 * y2;
double det = x1 * y2 - y1 * x2;
double d = atan2(det, dot);
daylight.push_back(d);
daylight_total += d;
}
double daylight_ave = daylight_total / leafs.size();
double daylight_acc = 0;
double daylight_change = 0;
for (unsigned int i = 0; i < leafs.size() - 1; ++i) {
daylight_acc = daylight_ave - daylight[i] + daylight_acc;
children[i]->rotate(daylight_acc * rotation_mod, x0, y0);
daylight_change += fabs(daylight_acc);
}
return daylight_change / leafs.size();
}
//[[Rcpp::export]]
NumericMatrix unrooted(IntegerVector parent, IntegerVector order, NumericVector length, bool daylight, double tol, double rotation_mod, int maxiter) {
NumericMatrix rect(parent.size(), 2);
std::vector nodes = createUnrooted(as< std::vector >(parent), as< std::vector >(order), as< std::vector >(length));
Node* startNode = nodes[0]->getRoot();
std::vector children = startNode->getChildren();
for (unsigned int i = 0; i < children.size(); ++i) {
int n_leafs = children[i]->nLeafs();
double split_angle = PI2 / n_leafs;
children[i]->bounds.x = 0;
children[i]->bounds.y = 0;
equalAngle(children[i], 0, split_angle);
}
if (daylight) {
double change = 1e6;
double last_change = 0;
int count = 0;
do {
for (unsigned int i = 0; i < nodes.size(); ++i) {
rect(i, 0) = nodes[i]->bounds.x;
rect(i, 1) = nodes[i]->bounds.y;
}
last_change = change;
change = 0;
for (unsigned int i = 0; i < nodes.size(); ++i) {
double current_change = equalDaylight(nodes[i], rotation_mod);
if (current_change > change) change = current_change;
}
count++;
} while (change < last_change && count < maxiter && change > tol);
} else {
for (unsigned int i = 0; i < nodes.size(); ++i) {
rect(i, 0) = nodes[i]->bounds.x;
rect(i, 1) = nodes[i]->bounds.y;
}
}
for (unsigned int i = 0; i < nodes.size(); ++i) {
delete nodes[i];
}
return rect;
}
ggraph/src/iciclePlot.cpp 0000644 0001762 0000144 00000002262 13526743614 015121 0 ustar ligges users #include
#include "nodes.h"
using namespace Rcpp;
void icicleLayout(Node* node, double x, double y) {
Rectangle r = {x, y, node->weight(), node->height()};
node->bounds = r;
std::vector children = node->getChildren();
if (children.size() != 0) {
y += node->height();
for (unsigned int i = 0; i < children.size(); i++) {
icicleLayout(children[i], x, y);
x += children[i]->weight();
}
}
}
//[[Rcpp::export]]
NumericMatrix partitionTree(IntegerVector parent, IntegerVector order, NumericVector weight, NumericVector height) {
NumericMatrix rect(parent.size(), 4);
unsigned int i;
std::vector nodes = createHierarchy(as< std::vector >(parent), as< std::vector >(order), as< std::vector >(weight), as< std::vector >(height));
for (i = 0; i < nodes.size(); ++i) {
nodes[i]->sortChildren();
}
Node* startNode = nodes[0]->getRoot();
icicleLayout(startNode, 0, 0);
for (i = 0; i < nodes.size(); ++i) {
rect(i, 0) = nodes[i]->bounds.x;
rect(i, 1) = nodes[i]->bounds.y;
rect(i, 2) = nodes[i]->bounds.width;
rect(i, 3) = nodes[i]->bounds.height;
delete nodes[i];
}
return rect;
}
ggraph/src/nodes.cpp 0000644 0001762 0000144 00000002446 13526744005 014141 0 ustar ligges users #include "nodes.h"
std::vector createHierarchy(std::vector parent, std::vector order, std::vector weight) {
std::vector nodes;
unsigned int i;
for (i = 0; i < parent.size(); ++i) {
Node* node = new Node(i, order[i], weight[i]);
nodes.push_back(node);
}
for (i = 0; i < parent.size(); ++i) {
if (parent[i] >= 0) {
nodes[parent[i]]->addNode(nodes[i]);
}
}
return nodes;
}
std::vector createHierarchy(std::vector parent, std::vector order, std::vector weight, std::vector height) {
std::vector nodes;
unsigned int i;
for (i = 0; i < parent.size(); ++i) {
Node* node = new Node(i, order[i], weight[i], height[i]);
nodes.push_back(node);
}
for (i = 0; i < parent.size(); ++i) {
if (parent[i] >= 0) {
nodes[parent[i]]->addNode(nodes[i]);
}
}
return nodes;
}
std::vector createUnrooted(std::vector parent, std::vector order, std::vector length) {
std::vector nodes;
unsigned int i;
for (i = 0; i < parent.size(); ++i) {
Node* node = new Node(i, order[i], 1, length[i]);
nodes.push_back(node);
}
for (i = 0; i < parent.size(); ++i) {
if (parent[i] >= 0) {
nodes[parent[i]]->addNode(nodes[i]);
}
}
return nodes;
}
ggraph/src/lineCutter.cpp 0000644 0001762 0000144 00000016434 13526715112 015146 0 ustar ligges users #include
using namespace Rcpp;
double copy_sign(double from, double to) {
if (from > 0) {
return to > 0 ? to : -1 * to;
} else if (from < 0) {
return to < 0 ? to : -1 * to;
}
return to;
}
struct Point {
double x;
double y;
bool REAL;
};
Point bad_point() {
Point p = {0, 0, false};
return p;
}
Point point(double x, double y) {
Point p = {x, y, true};
return p;
}
Point segment_intersect(Point p, Point p0, Point k, Point k0) {
double pX = p0.x - p.x;
double pY = p0.y - p.y;
double kX = k0.x - k.x;
double kY = k0.y - k.y;
double delta = pX*kY - kX*pY;
if (delta == 0) return bad_point();
double s = (-pY * (p.x - k.x) + pX * (p.y - k.y)) / (-kX * pY + pX * kY);
double t = (kX * (p.y - k.y) - kY * (p.x - k.x)) / (-kX * pY + pX * kY);
if (s >= 0 && s <= 1 && t >= 0 && t <= 1) {
return point(p.x + t * pX, p.y + t * pY);
} else {
return bad_point();
}
}
Point rect_intersection(Point p, Point p0, double width, double height) {
double xmin, xmax, ymin, ymax;
xmin = p0.x - width;
xmax = p0.x + width;
ymin = p0.y - height;
ymax = p0.y + height;
if (p.x < xmin) {
if (p.y > ymin && p.y < ymax) {
return segment_intersect(p, p0, point(xmin, ymin), point(xmin, ymax));
} else if (p.y < ymin) {
Point p_tmp = segment_intersect(p, p0, point(xmin, ymin), point(xmax, ymin));
if (p_tmp.REAL) {
return p_tmp;
} else {
return segment_intersect(p, p0, point(xmin, ymin), point(xmin, ymax));
}
} else {
Point p_tmp = segment_intersect(p, p0, point(xmin, ymax), point(xmax, ymax));
if (p_tmp.REAL) {
return p_tmp;
} else {
return segment_intersect(p, p0, point(xmin, ymin), point(xmin, ymax));
}
}
} else if (p.x > xmax) {
if (p.y > ymin && p.y < ymax) {
return segment_intersect(p, p0, point(xmax, ymin), point(xmax, ymax));
} else if (p.y < ymin) {
Point p_tmp = segment_intersect(p, p0, point(xmin, ymin), point(xmax, ymin));
if (p_tmp.REAL) {
return p_tmp;
} else {
return segment_intersect(p, p0, point(xmax, ymin), point(xmax, ymax));
}
} else {
Point p_tmp = segment_intersect(p, p0, point(xmin, ymax), point(xmax, ymax));
if (p_tmp.REAL) {
return p_tmp;
} else {
return segment_intersect(p, p0, point(xmax, ymin), point(xmax, ymax));
}
}
} else {
if (p.y < ymin) {
return segment_intersect(p, p0, point(xmin, ymin), point(xmax, ymin));
} else {
return segment_intersect(p, p0, point(xmin, ymax), point(xmax, ymax));
}
}
}
Point ellipsis_intersection(Point p, Point p0, double width, double height) {
double pX = p.x - p0.x;
double pY = p.y - p0.y;
double mod = (width * height) / std::sqrt(float(width*width*pY*pY + height*height*pX*pX));
double x = mod * pX;
double y = mod * pY;
x = copy_sign(pX, x);
y = copy_sign(pY, y);
return point(x + p0.x, y + p0.y);
}
bool inside_ellipsis(Point p, Point p0, double width, double height) {
double pX = p.x - p0.x;
double pY = p.y - p0.y;
return (pX * pX) / (width * width) + (pY * pY) / (height * height) < 1;
}
void capRectStart(NumericVector &x, NumericVector &y, int from, int to, double width, double height) {
int i;
Point p;
Point p0 = point(x[from], y[from]);
width /= 2;
height /= 2;
for (i = from; i < to - 1; ++i) {
p.x = x[i];
p.y = y[i];
if (std::abs(p.x - p0.x) <= width && std::abs(p.y - p0.y) <= height) {
x[i] = NA_REAL;
y[i] = NA_REAL;
} else {
Point intersect = rect_intersection(p, p0, width, height);
if (intersect.REAL) {
x[i-1] = intersect.x;
y[i-1] = intersect.y;
}
break;
}
}
}
void capRectEnd(NumericVector &x, NumericVector &y, int from, int to, double width, double height) {
int i = to - 1;
Point p;
Point p0 = point(x[i], y[i]);
width /= 2;
height /= 2;
for (; i >= from; --i) {
p.x = x[i];
p.y = y[i];
if (std::abs(p.x - p0.x) <= width && std::abs(p.y - p0.y) <= height) {
x[i] = NA_REAL;
y[i] = NA_REAL;
} else {
Point intersect = rect_intersection(p, p0, width, height);
if (intersect.REAL) {
x[i+1] = intersect.x;
y[i+1] = intersect.y;
}
break;
}
}
}
void capEllipStart(NumericVector &x, NumericVector &y, int from, int to, double width, double height) {
int i;
Point p;
Point p0 = point(x[from], y[from]);
width /= 2;
height /= 2;
for (i = from; i < to - 1; ++i) {
p.x = x[i];
p.y = y[i];
if (inside_ellipsis(p, p0, width, height)) {
x[i] = NA_REAL;
y[i] = NA_REAL;
} else {
Point intersect = ellipsis_intersection(p, p0, width, height);
if (intersect.REAL) {
x[i-1] = intersect.x;
y[i-1] = intersect.y;
}
break;
}
}
}
void capEllipEnd(NumericVector &x, NumericVector &y, int from, int to, double width, double height) {
int i = to - 1;
Point p;
Point p0 = point(x[i], y[i]);
width /= 2;
height /= 2;
for (; i >= from; --i) {
p.x = x[i];
p.y = y[i];
if (inside_ellipsis(p, p0, width, height)) {
x[i] = NA_REAL;
y[i] = NA_REAL;
} else {
Point intersect = ellipsis_intersection(p, p0, width, height);
if (intersect.REAL) {
x[i+1] = intersect.x;
y[i+1] = intersect.y;
}
break;
}
}
}
//[[Rcpp::export]]
List cut_lines(NumericVector x, NumericVector y, IntegerVector id, NumericVector start_width, NumericVector start_height, NumericVector end_width, NumericVector end_height, CharacterVector start_type, CharacterVector end_type) {
NumericVector new_x = clone(x);
NumericVector new_y = clone(y);
int i, j, group, group_ind;
group_ind = j = 0;
group = id[group_ind];
for (i = 0; i < id.size(); ++i) {
if (group != id[i]) {
if (start_width[group_ind] != 0 && start_height[group_ind] != 0) {
if (start_type[group_ind] == "circle") {
capEllipStart(new_x, new_y, j, i, start_width[group_ind], start_height[group_ind]);
} else if (start_type[group_ind] == "rect") {
capRectStart(new_x, new_y, j, i, start_width[group_ind], start_height[group_ind]);
}
}
if (end_width[group_ind] != 0 && end_height[group_ind] != 0) {
if (end_type[group_ind] == "circle") {
capEllipEnd(new_x, new_y, j, i, end_width[group_ind], end_height[group_ind]);
} else if (end_type[group_ind] == "rect") {
capRectEnd(new_x, new_y, j, i, end_width[group_ind], end_height[group_ind]);
}
}
group = id[i];
++group_ind;
j = i;
}
}
if (start_width[group_ind] != 0 && start_height[group_ind] != 0) {
if (start_type[group_ind] == "circle") {
capEllipStart(new_x, new_y, j, i, start_width[group_ind], start_height[group_ind]);
} else if (start_type[group_ind] == "rect") {
capRectStart(new_x, new_y, j, i, start_width[group_ind], start_height[group_ind]);
}
}
if (end_width[group_ind] != 0 && end_height[group_ind] != 0) {
if (end_type[group_ind] == "circle") {
capEllipEnd(new_x, new_y, j, i, end_width[group_ind], end_height[group_ind]);
} else if (end_type[group_ind] == "rect") {
capRectEnd(new_x, new_y, j, i, end_width[group_ind], end_height[group_ind]);
}
}
return List::create(Named("x") = new_x, Named("y") = new_y);
}
ggraph/src/RcppExports.cpp 0000644 0001762 0000144 00000014060 13527207727 015323 0 ustar ligges users // Generated by using Rcpp::compileAttributes() -> do not edit by hand
// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
#include
using namespace Rcpp;
// pack
NumericMatrix pack(NumericVector areas);
RcppExport SEXP _ggraph_pack(SEXP areasSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< NumericVector >::type areas(areasSEXP);
rcpp_result_gen = Rcpp::wrap(pack(areas));
return rcpp_result_gen;
END_RCPP
}
// circlePackLayout
NumericMatrix circlePackLayout(IntegerVector parent, NumericVector weight);
RcppExport SEXP _ggraph_circlePackLayout(SEXP parentSEXP, SEXP weightSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< IntegerVector >::type parent(parentSEXP);
Rcpp::traits::input_parameter< NumericVector >::type weight(weightSEXP);
rcpp_result_gen = Rcpp::wrap(circlePackLayout(parent, weight));
return rcpp_result_gen;
END_RCPP
}
// partitionTree
NumericMatrix partitionTree(IntegerVector parent, IntegerVector order, NumericVector weight, NumericVector height);
RcppExport SEXP _ggraph_partitionTree(SEXP parentSEXP, SEXP orderSEXP, SEXP weightSEXP, SEXP heightSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< IntegerVector >::type parent(parentSEXP);
Rcpp::traits::input_parameter< IntegerVector >::type order(orderSEXP);
Rcpp::traits::input_parameter< NumericVector >::type weight(weightSEXP);
Rcpp::traits::input_parameter< NumericVector >::type height(heightSEXP);
rcpp_result_gen = Rcpp::wrap(partitionTree(parent, order, weight, height));
return rcpp_result_gen;
END_RCPP
}
// cut_lines
List cut_lines(NumericVector x, NumericVector y, IntegerVector id, NumericVector start_width, NumericVector start_height, NumericVector end_width, NumericVector end_height, CharacterVector start_type, CharacterVector end_type);
RcppExport SEXP _ggraph_cut_lines(SEXP xSEXP, SEXP ySEXP, SEXP idSEXP, SEXP start_widthSEXP, SEXP start_heightSEXP, SEXP end_widthSEXP, SEXP end_heightSEXP, SEXP start_typeSEXP, SEXP end_typeSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< NumericVector >::type x(xSEXP);
Rcpp::traits::input_parameter< NumericVector >::type y(ySEXP);
Rcpp::traits::input_parameter< IntegerVector >::type id(idSEXP);
Rcpp::traits::input_parameter< NumericVector >::type start_width(start_widthSEXP);
Rcpp::traits::input_parameter< NumericVector >::type start_height(start_heightSEXP);
Rcpp::traits::input_parameter< NumericVector >::type end_width(end_widthSEXP);
Rcpp::traits::input_parameter< NumericVector >::type end_height(end_heightSEXP);
Rcpp::traits::input_parameter< CharacterVector >::type start_type(start_typeSEXP);
Rcpp::traits::input_parameter< CharacterVector >::type end_type(end_typeSEXP);
rcpp_result_gen = Rcpp::wrap(cut_lines(x, y, id, start_width, start_height, end_width, end_height, start_type, end_type));
return rcpp_result_gen;
END_RCPP
}
// pathAttr
DataFrame pathAttr(DataFrame paths, int ngroups);
RcppExport SEXP _ggraph_pathAttr(SEXP pathsSEXP, SEXP ngroupsSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< DataFrame >::type paths(pathsSEXP);
Rcpp::traits::input_parameter< int >::type ngroups(ngroupsSEXP);
rcpp_result_gen = Rcpp::wrap(pathAttr(paths, ngroups));
return rcpp_result_gen;
END_RCPP
}
// splitTreemap
NumericMatrix splitTreemap(IntegerVector parent, IntegerVector order, NumericVector weight, double width, double height);
RcppExport SEXP _ggraph_splitTreemap(SEXP parentSEXP, SEXP orderSEXP, SEXP weightSEXP, SEXP widthSEXP, SEXP heightSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< IntegerVector >::type parent(parentSEXP);
Rcpp::traits::input_parameter< IntegerVector >::type order(orderSEXP);
Rcpp::traits::input_parameter< NumericVector >::type weight(weightSEXP);
Rcpp::traits::input_parameter< double >::type width(widthSEXP);
Rcpp::traits::input_parameter< double >::type height(heightSEXP);
rcpp_result_gen = Rcpp::wrap(splitTreemap(parent, order, weight, width, height));
return rcpp_result_gen;
END_RCPP
}
// unrooted
NumericMatrix unrooted(IntegerVector parent, IntegerVector order, NumericVector length, bool daylight, double tol, double rotation_mod, int maxiter);
RcppExport SEXP _ggraph_unrooted(SEXP parentSEXP, SEXP orderSEXP, SEXP lengthSEXP, SEXP daylightSEXP, SEXP tolSEXP, SEXP rotation_modSEXP, SEXP maxiterSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< IntegerVector >::type parent(parentSEXP);
Rcpp::traits::input_parameter< IntegerVector >::type order(orderSEXP);
Rcpp::traits::input_parameter< NumericVector >::type length(lengthSEXP);
Rcpp::traits::input_parameter< bool >::type daylight(daylightSEXP);
Rcpp::traits::input_parameter< double >::type tol(tolSEXP);
Rcpp::traits::input_parameter< double >::type rotation_mod(rotation_modSEXP);
Rcpp::traits::input_parameter< int >::type maxiter(maxiterSEXP);
rcpp_result_gen = Rcpp::wrap(unrooted(parent, order, length, daylight, tol, rotation_mod, maxiter));
return rcpp_result_gen;
END_RCPP
}
static const R_CallMethodDef CallEntries[] = {
{"_ggraph_pack", (DL_FUNC) &_ggraph_pack, 1},
{"_ggraph_circlePackLayout", (DL_FUNC) &_ggraph_circlePackLayout, 2},
{"_ggraph_partitionTree", (DL_FUNC) &_ggraph_partitionTree, 4},
{"_ggraph_cut_lines", (DL_FUNC) &_ggraph_cut_lines, 9},
{"_ggraph_pathAttr", (DL_FUNC) &_ggraph_pathAttr, 2},
{"_ggraph_splitTreemap", (DL_FUNC) &_ggraph_splitTreemap, 5},
{"_ggraph_unrooted", (DL_FUNC) &_ggraph_unrooted, 7},
{NULL, NULL, 0}
};
RcppExport void R_init_ggraph(DllInfo *dll) {
R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
R_useDynamicSymbols(dll, FALSE);
}
ggraph/src/treemap.cpp 0000644 0001762 0000144 00000005156 13526715234 014471 0 ustar ligges users #include
#include "nodes.h"
using namespace Rcpp;
double w(std::vector& nodes) {
double w = 0;
for (unsigned int i = 0; i < nodes.size(); ++i) {
w += nodes[i]->weight();
}
return w;
}
void splitLayout(std::vector items, Rectangle r) {
if (items.size() == 0) {
return;
}
if (items.size() == 1) {
items[0]->bounds = r;
splitLayout(items[0]->getChildren(), r); // Layout the children within
} else {
Rectangle r1, r2;
std::vector s1, s2;
if (items.size() == 2) {
s1.push_back(items[0]);
s2.push_back(items[1]);
} else {
double halfSize = w(items) / 2;
double wH = 0;
double tmp = 0;
bool completed = false;
// Pick out half the weight into l1, half into l2
for (unsigned int i = 0; i < items.size(); ++i) {
if (completed) {
s2.push_back(items[i]);
} else {
tmp = wH + items[i]->weight();
// Test if it got worse by picking another item
if (std::abs(halfSize - tmp) > std::abs(halfSize - wH)) {
s2.push_back(items[i]);
completed = true;
} else {
s1.push_back(items[i]);
wH = tmp;
}
}
}
}
double w1 = w(s1);
double w2 = w(s2);
if (r.width > r.height) {
r1.x = r.x;
r1.y = r.y;
r1.width = r.width * w1/(w1 + w2);
r1.height = r.height;
r2.x = r.x + r1.width;
r2.y = r.y;
r2.width = r.width - r1.width;
r2.height = r.height;
} else {
r1.x = r.x;
r1.y = r.y;
r1.width = r.width;
r1.height = r.height * w1/(w1 + w2);
r2.x = r.x;
r2.y = r.y + r1.height;
r2.width = r.width;
r2.height = r.height - r1.height;
}
splitLayout(s1, r1);
splitLayout(s2, r2);
}
}
//[[Rcpp::export]]
NumericMatrix splitTreemap(IntegerVector parent, IntegerVector order, NumericVector weight, double width, double height) {
NumericMatrix rect(parent.size(), 4);
unsigned int i;
std::vector nodes = createHierarchy(as< std::vector >(parent), as< std::vector >(order), as< std::vector >(weight));
for (i = 0; i < nodes.size(); ++i) {
nodes[i]->sortChildren();
}
Node* startNode = nodes[0]->getRoot();
Rectangle r = {
0,
0,
width,
height
};
startNode->bounds = r;
splitLayout(startNode->getChildren(), r);
for (i = 0; i < nodes.size(); ++i) {
rect(i, 0) = nodes[i]->bounds.x;
rect(i, 1) = nodes[i]->bounds.y;
rect(i, 2) = nodes[i]->bounds.width;
rect(i, 3) = nodes[i]->bounds.height;
delete nodes[i];
}
return rect;
}
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[](https://travis-ci.org/thomasp85/ggraph)
[](https://ci.appveyor.com/project/thomasp85/ggraph)
[](https://CRAN.R-project.org/package=ggraph)
[](https://CRAN.R-project.org/package=ggraph)
*/dʒiː.dʒɪˈrɑːf/* (or g-giraffe)
## A grammar of graphics for relational data
ggraph is an extension of [`ggplot2`](http://ggplot2.tidyverse.org)
aimed at supporting relational data structures such as networks, graphs,
and trees. While it builds upon the foundation of `ggplot2` and its API
it comes with its own self-contained set of geoms, facets, etc., as well
as adding the concept of *layouts* to the grammar.
### An example
``` r
library(ggraph)
#> Loading required package: ggplot2
library(tidygraph)
#>
#> Attaching package: 'tidygraph'
#> The following object is masked from 'package:stats':
#>
#> filter
# Create graph of highschool friendships
graph <- as_tbl_graph(highschool) %>%
mutate(Popularity = centrality_degree(mode = 'in'))
# plot using ggraph
ggraph(graph, layout = 'kk') +
geom_edge_fan(aes(alpha = stat(index)), show.legend = FALSE) +
geom_node_point(aes(size = Popularity)) +
facet_edges(~year) +
theme_graph(foreground = 'steelblue', fg_text_colour = 'white')
```
### The core concepts
`ggraph` builds upon three core concepts that are quite easy to
understand:
1. [**The
Layout**](http://www.data-imaginist.com/2017/ggraph-introduction-layouts/)
defines how nodes are placed on the plot, that is, it is a
conversion of the relational structure into an x and y value for
each node in the graph. `ggraph` has access to all layout functions
available in `igraph` and furthermore provides a large selection of
its own, such as hive plots, treemaps, and circle packing.
2. [**The
Nodes**](http://www.data-imaginist.com/2017/ggraph-introduction-nodes/)
are the connected entities in the relational structure. These can be
plotted using the `geom_node_*()` family of geoms. Some node geoms
make more sense for certain layouts, e.g. `geom_node_tile()` for
treemaps and icicle plots, while others are more general purpose,
e.g. `geom_node_point()`.
3. [**The
Edges**](http://www.data-imaginist.com/2017/ggraph-introduction-edges/)
are the connections between the entities in the relational
structure. These can be visualized using the `geom_edge_*()` family
of geoms that contain a lot of different edge types for different
scenarios. Sometimes the edges are implied by the layout (e.g. with
treemaps) and need not be plotted, but often some sort of line is
warranted.
All of the tree concepts have been discussed in detail in dedicated blog
posts that are also available as vignettes in the package. Please refer
to these for more information.
> **Note:** The linked blog posts are based on ggraph v1. After ggraph
> v1.1 the underlying implementation was moved to tidygraph and cleaned
> up, but this resulted in some breaking changes in the process.
> Therefore the vignette versions are generally recommended as they have
> been updated.
### Supported data types
There are many different ways to store and work with relational data in
R. `ggraph` is built upon `tidygraph` and the large swath of data
structures it supports are thus natively supported in `ggraph`. In order
to get a data type supported by `ggraph`, simply provide an
`as_tbl_graph` method for it.
## Installation
`ggraph` is available through CRAN and can be installed with
`install.packages('ggraph')`. The package is under active development
though and the latest set of features can be obtained by installing from
this repository using `devtools`
``` r
devtools::install_github('thomasp85/ggraph')
```
## Related work
`ggraph` is not the only package to provide some sort of support for
relational data in `ggplot2`, though I’m fairly certain that it is the
most ambitious.
[`ggdendro`](https://CRAN.R-project.org/package=ggdendro) provides
support for `dendrogram` and `hclust` objects through conversion of the
structures into line segments that can then be plotted with
`geom_segment()`. [`ggtree`](http://bioconductor.org/packages/ggtree/)
provides more extensive support for all things tree-related, though it
lacks some of the layouts and edge types that `ggraph` offers (it has
other features that `ggraph` lacks though). For more standard *hairball*
network plots
[`ggnetwork`](https://CRAN.R-project.org/package=ggnetwork),
[`geomnet`](https://CRAN.R-project.org/package=geomnet), and
[`GGally`](https://CRAN.R-project.org/package=GGally) all provide some
functionality though none of them are as extensive in scope as `ggraph`.
## Code of Conduct
Please note that the ‘ggraph’ project is released with a [Contributor
Code of
Conduct](https://ggraph.data-imaginist.com/CODE_OF_CONDUCT.html). By
contributing to this project, you agree to abide by its terms.
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