ggsci/ 0000755 0001762 0000144 00000000000 13276211255 011352 5 ustar ligges users ggsci/TODO 0000644 0001762 0000144 00000001361 13221611720 012032 0 ustar ligges users # TODO
- Okabe, Masataka and Kei Ito's Color Universal Design (CUD) for color blindness: http://jfly.iam.u-tokyo.ac.jp/color/ https://www.chronicle.com/blogs/profhacker/color-blind-accessible-figures/59189 https://www.nature.com/articles/nmeth.1618
- Marvel's The Defenders (colors from opening titles). Red - Daredevil; Blue - Jessica Jones; Orange - Luke Cage; Green - Iron Fist.
- Gephi: https://github.com/gephi/gephi/blob/master/modules/Utils/src/main/java/org/gephi/utils/PaletteUtils.java#L83-L110
- Apple Human Interface Guidelines: https://developer.apple.com/ios/human-interface-guidelines/visual-design/color/ one discrete, one continuous.
- Add a function for displaying all color palettes
- Color palette extraction: http://colormind.io/
ggsci/inst/ 0000755 0001762 0000144 00000000000 13276174761 012341 5 ustar ligges users ggsci/inst/doc/ 0000755 0001762 0000144 00000000000 13276174761 013106 5 ustar ligges users ggsci/inst/doc/ggsci.html 0000644 0001762 0000144 00017257715 13276174761 015121 0 ustar ligges users
Scientific Journal and Sci-Fi Themed Color Palettes for ggplot2
Scientific Journal and Sci-Fi Themed
Color Palettes for ggplot2
2018-05-13
Introduction
My eyes were finally opened and I understood nature.
I learned at the same time to love it.
— Claude Monet
ggsci offers a collection of high-quality color palettes inspired by colors used in scientific journals, data visualization libraries, science fiction movies, and TV shows. The color palettes in ggsci are available as ggplot2 scales. For all the color palettes, the corresponding scales are named as:
scale_color_palname()scale_fill_palname()
We also provided aliases, such as scale_colour_palname() for scale_color_palname(). All available color palettes are summarized in the table below.
| NPG |
scale_color_npg() scale_fill_npg() |
"nrc" |
pal_npg() |
| AAAS |
scale_color_aaas() scale_fill_aaas() |
"default" |
pal_aaas() |
| NEJM |
scale_color_nejm() scale_fill_nejm() |
"default" |
pal_nejm() |
| Lancet |
scale_color_lancet() scale_fill_lancet() |
"lanonc" |
pal_lancet() |
| JAMA |
scale_color_jama() scale_fill_jama() |
"default" |
pal_jama() |
| JCO |
scale_color_jco() scale_fill_jco() |
"default" |
pal_jco() |
| UCSCGB |
scale_color_ucscgb() scale_fill_ucscgb() |
"default" |
pal_ucscgb() |
| D3 |
scale_color_d3()
scale_fill_d3() |
"category10" "category20" "category20b" "category20c" |
pal_d3() |
| LocusZoom |
scale_color_locuszoom() scale_fill_locuszoom() |
"default" |
pal_locuszoom() |
| IGV |
scale_color_igv() scale_fill_igv() |
"default"
"alternating" |
pal_igv() |
| UChicago |
scale_color_uchicago() scale_fill_uchicago() |
"default"
"light"
"dark" |
pal_uchicago() |
| Star Trek |
scale_color_startrek() scale_fill_startrek() |
"uniform" |
pal_startrek() |
| Tron Legacy |
scale_color_tron() scale_fill_tron() |
"legacy" |
pal_tron() |
| Futurama |
scale_color_futurama() scale_fill_futurama() |
"planetexpress" |
pal_futurama() |
| Rick and Morty |
scale_color_rickandmorty() scale_fill_rickandmorty() |
"schwifty" |
pal_rickandmorty() |
| The Simpsons |
scale_color_simpsons() scale_fill_simpsons() |
"springfield" |
pal_simpsons() |
| GSEA |
scale_color_gsea() scale_fill_gsea() |
"default" |
pal_gsea() |
| Material Design |
scale_color_material() scale_fill_material() |
"red" "pink"
"purple" "deep-purple"
"indigo" "blue"
"light-blue" "cyan"
"teal" "green"
"light-green" "lime"
"yellow" "amber"
"orange" "deep-orange"
"brown" "grey"
"blue-grey" |
pal_material() |
Discrete Color Palettes
We will use scatterplots with smooth curves, and bar plots to demonstrate the discrete color palettes in ggsci.
library("ggsci")
library("ggplot2")
library("gridExtra")
data("diamonds")
p1 = ggplot(subset(diamonds, carat >= 2.2),
aes(x = table, y = price, colour = cut)) +
geom_point(alpha = 0.7) +
geom_smooth(method = "loess", alpha = 0.05, size = 1, span = 1) +
theme_bw()
p2 = ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
aes(x = depth, fill = cut)) +
geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
theme_bw()
NPG
The NPG palette is inspired by the plots in the journals published by Nature Publishing Group:
AAAS
The AAAS palette is inspired by the plots in the journals published by American Association for the Advancement of Science:
NEJM
The NEJM palette is inspired by the plots in The New England Journal of Medicine:
Lancet
The Lancet palette is inspired by the plots in Lancet journals, such as Lancet Oncology:
JAMA
The JAMA palette is inspired by the plots in The Journal of the American Medical Association:
JCO
The JCO palette is inspired by the the plots in Journal of Clinical Oncology:
UCSCGB
The UCSCGB palette is from the colors used by UCSC Genome Browser for representing chromosomes. This palette has been intensively used in visualizations produced by Circos.
D3
The D3 palette is from the categorical colors used by D3.js (version 3.x and before). There are four palette types (category10, category20, category20b, category20c) available.
LocusZoom
The LocusZoom palette is based on the colors used by LocusZoom.
IGV
The IGV palette is from the colors used by Integrative Genomics Viewer for representing chromosomes. There are two palette types (default, alternating) available.
UChicago
The UChicago palette is based on the colors used by the University of Chicago. There are three palette types (default, light, dark) available.
Star Trek
This palette is inspired by the (uniform) colors in Star Trek:
Tron Legacy
This palette is inspired by the colors used in Tron Legacy. It is suitable for displaying data when using a dark theme:
Futurama
This palette is inspired by the colors used in the TV show Futurama:
Rick and Morty
This palette is inspired by the colors used in the TV show Rick and Morty:
The Simpsons
This palette is inspired by the colors used in the TV show The Simpsons:
Continuous Color Palettes
We will use a correlation matrix visualization (a special type of heatmap) to demonstrate the continuous color palettes in ggsci.
GSEA
The GSEA palette (continuous) is inspired by the heatmaps generated by GSEA GenePattern.
Material Design
The Material Design color palettes are from the material design color guidelines.
We generate a random matrix first:
library("reshape2")
set.seed(42)
k = 9
x = diag(k)
x[upper.tri(x)] = runif(sum(1:(k - 1)), 0, 1)
x_melt = melt(x)
p4 = ggplot(x_melt, aes(x = Var1, y = Var2, fill = value)) +
geom_tile(colour = "black", size = 0.3) +
scale_x_continuous(expand = c(0, 0)) +
scale_y_continuous(expand = c(0, 0)) +
theme_bw() + theme(
legend.position = "none", plot.background = element_blank(),
axis.line = element_blank(), axis.ticks = element_blank(),
axis.text.x = element_blank(), axis.text.y = element_blank(),
axis.title.x = element_blank(), axis.title.y = element_blank(),
panel.background = element_blank(), panel.border = element_blank(),
panel.grid.major = element_blank(), panel.grid.minor = element_blank())
Plot the matrix with the 19 material design color palettes:
grid.arrange(
p4 + scale_fill_material("red"), p4 + scale_fill_material("pink"),
p4 + scale_fill_material("purple"), p4 + scale_fill_material("deep-purple"),
p4 + scale_fill_material("indigo"), p4 + scale_fill_material("blue"),
p4 + scale_fill_material("light-blue"), p4 + scale_fill_material("cyan"),
p4 + scale_fill_material("teal"), p4 + scale_fill_material("green"),
p4 + scale_fill_material("light-green"), p4 + scale_fill_material("lime"),
p4 + scale_fill_material("yellow"), p4 + scale_fill_material("amber"),
p4 + scale_fill_material("orange"), p4 + scale_fill_material("deep-orange"),
p4 + scale_fill_material("brown"), p4 + scale_fill_material("grey"),
p4 + scale_fill_material("blue-grey"),
ncol = 6)
From the figure above, we can see that even though an identical matrix was visualized by all plots, some palettes are more preferrable than the others because our eyes are more sensitive to the changes of their saturation levels.
Non-ggplot2 Graphics
To apply the color palettes in ggsci to other graphics systems (such as base graphics and lattice graphics), simply use the palette generator functions in the table above. For example:
## [1] "#E64B35B2" "#4DBBD5B2" "#00A087B2" "#3C5488B2" "#F39B7FB2" "#8491B4B2"
## [7] "#91D1C2B2" "#DC0000B2" "#7E6148B2"
You will be able to use the generated hex color codes for such graphics systems accordingly. The transparent level of the entire palette is easily adjustable via the argument "alpha" in every generator or scale function.
Discussion
Please note some of the palettes might not be the best choice for certain purposes, such as color-blind safe, photocopy safe, or print friendly. If you do have such considerations, you might want to check out color palettes like ColorBrewer and viridis.
The color palettes in this package are solely created for research purposes. The authors are not responsible for the usage of such palettes.
ggsci/inst/doc/ggsci.R 0000644 0001762 0000144 00000015011 13276174760 014322 0 ustar ligges users ## ------------------------------------------------------------------------
library("ggsci")
library("ggplot2")
library("gridExtra")
data("diamonds")
p1 = ggplot(subset(diamonds, carat >= 2.2),
aes(x = table, y = price, colour = cut)) +
geom_point(alpha = 0.7) +
geom_smooth(method = "loess", alpha = 0.05, size = 1, span = 1) +
theme_bw()
p2 = ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
aes(x = depth, fill = cut)) +
geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
theme_bw()
## ---- fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150----
p1_npg = p1 + scale_color_npg()
p2_npg = p2 + scale_fill_npg()
grid.arrange(p1_npg, p2_npg, ncol = 2)
## ---- fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150----
p1_aaas = p1 + scale_color_aaas()
p2_aaas = p2 + scale_fill_aaas()
grid.arrange(p1_aaas, p2_aaas, ncol = 2)
## ---- fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150----
p1_nejm = p1 + scale_color_nejm()
p2_nejm = p2 + scale_fill_nejm()
grid.arrange(p1_nejm, p2_nejm, ncol = 2)
## ---- fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150----
p1_lancet = p1 + scale_color_lancet()
p2_lancet = p2 + scale_fill_lancet()
grid.arrange(p1_lancet, p2_lancet, ncol = 2)
## ---- fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150----
p1_jama = p1 + scale_color_jama()
p2_jama = p2 + scale_fill_jama()
grid.arrange(p1_jama, p2_jama, ncol = 2)
## ---- fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150----
p1_jco = p1 + scale_color_jco()
p2_jco = p2 + scale_fill_jco()
grid.arrange(p1_jco, p2_jco, ncol = 2)
## ---- fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150----
p1_ucscgb = p1 + scale_color_ucscgb()
p2_ucscgb = p2 + scale_fill_ucscgb()
grid.arrange(p1_ucscgb, p2_ucscgb, ncol = 2)
## ---- fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150----
p1_d3 = p1 + scale_color_d3()
p2_d3 = p2 + scale_fill_d3()
grid.arrange(p1_d3, p2_d3, ncol = 2)
## ---- fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150----
p1_locuszoom = p1 + scale_color_locuszoom()
p2_locuszoom = p2 + scale_fill_locuszoom()
grid.arrange(p1_locuszoom, p2_locuszoom, ncol = 2)
## ---- fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150----
p1_igv_default = p1 + scale_color_igv()
p2_igv_default = p2 + scale_fill_igv()
grid.arrange(p1_igv_default, p2_igv_default, ncol = 2)
## ---- fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150----
p1_uchicago = p1 + scale_color_uchicago()
p2_uchicago = p2 + scale_fill_uchicago()
grid.arrange(p1_uchicago, p2_uchicago, ncol = 2)
## ---- fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150----
p1_startrek = p1 + scale_color_startrek()
p2_startrek = p2 + scale_fill_startrek()
grid.arrange(p1_startrek, p2_startrek, ncol = 2)
## ---- fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150----
p1_tron = p1 + theme_dark() + theme(
panel.background = element_rect(fill = "#2D2D2D"),
legend.key = element_rect(fill = "#2D2D2D")) +
scale_color_tron()
p2_tron = p2 + theme_dark() + theme(
panel.background = element_rect(fill = "#2D2D2D")) +
scale_fill_tron()
grid.arrange(p1_tron, p2_tron, ncol = 2)
## ---- fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150----
p1_futurama = p1 + scale_color_futurama()
p2_futurama = p2 + scale_fill_futurama()
grid.arrange(p1_futurama, p2_futurama, ncol = 2)
## ---- fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150----
p1_rickandmorty = p1 + scale_color_rickandmorty()
p2_rickandmorty = p2 + scale_fill_rickandmorty()
grid.arrange(p1_rickandmorty, p2_rickandmorty, ncol = 2)
## ---- fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150----
p1_simpsons = p1 + scale_color_simpsons()
p2_simpsons = p2 + scale_fill_simpsons()
grid.arrange(p1_simpsons, p2_simpsons, ncol = 2)
## ------------------------------------------------------------------------
library("reshape2")
data("mtcars")
cor = cor(unname(cbind(mtcars, mtcars, mtcars, mtcars)))
cor_melt = melt(cor)
p3 = ggplot(cor_melt,
aes(x = Var1, y = Var2, fill = value)) +
geom_tile(colour = "black", size = 0.3) +
theme_bw() +
theme(axis.title.x = element_blank(),
axis.title.y = element_blank())
## ---- fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150----
p3_gsea = p3 + scale_fill_gsea()
p3_gsea_inv = p3 + scale_fill_gsea(reverse = TRUE)
grid.arrange(p3_gsea, p3_gsea_inv, ncol = 2)
## ------------------------------------------------------------------------
library("reshape2")
set.seed(42)
k = 9
x = diag(k)
x[upper.tri(x)] = runif(sum(1:(k - 1)), 0, 1)
x_melt = melt(x)
p4 = ggplot(x_melt, aes(x = Var1, y = Var2, fill = value)) +
geom_tile(colour = "black", size = 0.3) +
scale_x_continuous(expand = c(0, 0)) +
scale_y_continuous(expand = c(0, 0)) +
theme_bw() + theme(
legend.position = "none", plot.background = element_blank(),
axis.line = element_blank(), axis.ticks = element_blank(),
axis.text.x = element_blank(), axis.text.y = element_blank(),
axis.title.x = element_blank(), axis.title.y = element_blank(),
panel.background = element_blank(), panel.border = element_blank(),
panel.grid.major = element_blank(), panel.grid.minor = element_blank())
## ---- fig.width = 10.67, fig.height = 7.12, out.width = 800, out.height = 533, dpi = 150----
grid.arrange(
p4 + scale_fill_material("red"), p4 + scale_fill_material("pink"),
p4 + scale_fill_material("purple"), p4 + scale_fill_material("deep-purple"),
p4 + scale_fill_material("indigo"), p4 + scale_fill_material("blue"),
p4 + scale_fill_material("light-blue"), p4 + scale_fill_material("cyan"),
p4 + scale_fill_material("teal"), p4 + scale_fill_material("green"),
p4 + scale_fill_material("light-green"), p4 + scale_fill_material("lime"),
p4 + scale_fill_material("yellow"), p4 + scale_fill_material("amber"),
p4 + scale_fill_material("orange"), p4 + scale_fill_material("deep-orange"),
p4 + scale_fill_material("brown"), p4 + scale_fill_material("grey"),
p4 + scale_fill_material("blue-grey"),
ncol = 6)
## ---- fig.width = 6.67, fig.height = 6.67, out.width = 500, out.height = 500, dpi = 150----
mypal = pal_npg("nrc", alpha = 0.7)(9)
mypal
library("scales")
show_col(mypal)
ggsci/inst/doc/ggsci.Rmd 0000644 0001762 0000144 00000045114 13276174703 014647 0 ustar ligges users ---
title: "Scientific Journal and Sci-Fi Themed
Color Palettes for ggplot2"
author: "Nan Xiao <>
Miaozhu Li <>"
date: "`r Sys.Date()`"
output:
rmarkdown::html_vignette:
toc: true
number_sections: true
css: ggsci.css
vignette: >
%\VignetteEngine{knitr::rmarkdown}
%\VignetteIndexEntry{Scientific Journal and Sci-Fi Themed Color Palettes for ggplot2}
---
# Introduction
> My eyes were finally opened and I understood nature.
>
> I learned at the same time to love it.
>
> --- Claude Monet
`ggsci` offers a collection of high-quality color palettes inspired by
colors used in scientific journals, data visualization libraries,
science fiction movies, and TV shows. The color palettes in `ggsci`
are available as `ggplot2` scales. For all the color palettes,
the corresponding scales are named as:
* `scale_color_palname()`
* `scale_fill_palname()`
We also provided aliases, such as `scale_colour_palname()` for
`scale_color_palname()`. All available color palettes are
summarized in the table below.
+-----------------+------------------------------+--------------------------------+----------------------+
| Name | Scales | Palette Types | Palette Generator |
+=================+==============================+================================+======================+
| NPG | `scale_color_npg()` | `"nrc"` | `pal_npg()` |
| | `scale_fill_npg()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| AAAS | `scale_color_aaas()` | `"default"` | `pal_aaas()` |
| | `scale_fill_aaas()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| NEJM | `scale_color_nejm()` | `"default"` | `pal_nejm()` |
| | `scale_fill_nejm()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| Lancet | `scale_color_lancet()` | `"lanonc"` | `pal_lancet()` |
| | `scale_fill_lancet()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| JAMA | `scale_color_jama()` | `"default"` | `pal_jama()` |
| | `scale_fill_jama()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| JCO | `scale_color_jco()` | `"default"` | `pal_jco()` |
| | `scale_fill_jco()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| UCSCGB | `scale_color_ucscgb()` | `"default"` | `pal_ucscgb()` |
| | `scale_fill_ucscgb()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| D3 | `scale_color_d3()`
| `"category10"` | `pal_d3()` |
| | `scale_fill_d3()` | `"category20"` | |
| | | `"category20b"` | |
| | | `"category20c"` | |
+-----------------+------------------------------+--------------------------------+----------------------+
| LocusZoom | `scale_color_locuszoom()` | `"default"` | `pal_locuszoom()` |
| | `scale_fill_locuszoom()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| IGV | `scale_color_igv()` | `"default"`
| `pal_igv()` |
| | `scale_fill_igv()` | `"alternating"` | |
+-----------------+------------------------------+--------------------------------+----------------------+
| UChicago | `scale_color_uchicago()` | `"default"`
| `pal_uchicago()` |
| | `scale_fill_uchicago()` | `"light"`
| |
| | | `"dark"` | |
+-----------------+------------------------------+--------------------------------+----------------------+
| Star Trek | `scale_color_startrek()` | `"uniform"` | `pal_startrek()` |
| | `scale_fill_startrek()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| Tron Legacy | `scale_color_tron()` | `"legacy"` | `pal_tron()` |
| | `scale_fill_tron()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| Futurama | `scale_color_futurama()` | `"planetexpress"` | `pal_futurama()` |
| | `scale_fill_futurama()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| Rick and Morty | `scale_color_rickandmorty()` | `"schwifty"` | `pal_rickandmorty()` |
| | `scale_fill_rickandmorty()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| The Simpsons | `scale_color_simpsons()` | `"springfield"` | `pal_simpsons()` |
| | `scale_fill_simpsons()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| GSEA | `scale_color_gsea()` | `"default"` | `pal_gsea()` |
| | `scale_fill_gsea()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| Material Design | `scale_color_material()` | `"red"` `"pink"`
| `pal_material()` |
| | `scale_fill_material()` | `"purple"` `"deep-purple"`
| |
| | | `"indigo"` `"blue"`
| |
| | | `"light-blue"` `"cyan"`
| |
| | | `"teal"` `"green"`
| |
| | | `"light-green"` `"lime"`
| |
| | | `"yellow"` `"amber"`
| |
| | | `"orange"` `"deep-orange"`
| |
| | | `"brown"` `"grey"`
| |
| | | `"blue-grey"` | |
+-----------------+------------------------------+--------------------------------+----------------------+
# Discrete Color Palettes
We will use scatterplots with smooth curves, and bar plots to demonstrate
the discrete color palettes in `ggsci`.
```{r}
library("ggsci")
library("ggplot2")
library("gridExtra")
data("diamonds")
p1 = ggplot(subset(diamonds, carat >= 2.2),
aes(x = table, y = price, colour = cut)) +
geom_point(alpha = 0.7) +
geom_smooth(method = "loess", alpha = 0.05, size = 1, span = 1) +
theme_bw()
p2 = ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
aes(x = depth, fill = cut)) +
geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
theme_bw()
```
## NPG
The NPG palette is inspired by the plots in the journals published by
Nature Publishing Group:
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_npg = p1 + scale_color_npg()
p2_npg = p2 + scale_fill_npg()
grid.arrange(p1_npg, p2_npg, ncol = 2)
```
## AAAS
The AAAS palette is inspired by the plots in the journals published by
American Association for the Advancement of Science:
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_aaas = p1 + scale_color_aaas()
p2_aaas = p2 + scale_fill_aaas()
grid.arrange(p1_aaas, p2_aaas, ncol = 2)
```
## NEJM
The NEJM palette is inspired by the plots in
The New England Journal of Medicine:
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_nejm = p1 + scale_color_nejm()
p2_nejm = p2 + scale_fill_nejm()
grid.arrange(p1_nejm, p2_nejm, ncol = 2)
```
## Lancet
The Lancet palette is inspired by the plots in Lancet journals,
such as Lancet Oncology:
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_lancet = p1 + scale_color_lancet()
p2_lancet = p2 + scale_fill_lancet()
grid.arrange(p1_lancet, p2_lancet, ncol = 2)
```
## JAMA
The JAMA palette is inspired by the plots in
The Journal of the American Medical Association:
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_jama = p1 + scale_color_jama()
p2_jama = p2 + scale_fill_jama()
grid.arrange(p1_jama, p2_jama, ncol = 2)
```
## JCO
The JCO palette is inspired by the the plots in
Journal of Clinical Oncology:
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_jco = p1 + scale_color_jco()
p2_jco = p2 + scale_fill_jco()
grid.arrange(p1_jco, p2_jco, ncol = 2)
```
## UCSCGB
The UCSCGB palette is from the colors used by
[UCSC Genome Browser](https://genome.ucsc.edu) for
representing chromosomes. This palette has been intensively
used in visualizations produced by [Circos](http://circos.ca).
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_ucscgb = p1 + scale_color_ucscgb()
p2_ucscgb = p2 + scale_fill_ucscgb()
grid.arrange(p1_ucscgb, p2_ucscgb, ncol = 2)
```
## D3
The D3 palette is from the categorical colors used by
[D3.js](https://d3js.org) (version 3.x and before).
There are four palette types (`category10`, `category20`,
`category20b`, `category20c`) available.
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_d3 = p1 + scale_color_d3()
p2_d3 = p2 + scale_fill_d3()
grid.arrange(p1_d3, p2_d3, ncol = 2)
```
## LocusZoom
The LocusZoom palette is based on the colors used by
[LocusZoom](http://locuszoom.org/).
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_locuszoom = p1 + scale_color_locuszoom()
p2_locuszoom = p2 + scale_fill_locuszoom()
grid.arrange(p1_locuszoom, p2_locuszoom, ncol = 2)
```
## IGV
The IGV palette is from the colors used by
[Integrative Genomics Viewer](http://software.broadinstitute.org/software/igv/)
for representing chromosomes. There are two palette types
(`default`, `alternating`) available.
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_igv_default = p1 + scale_color_igv()
p2_igv_default = p2 + scale_fill_igv()
grid.arrange(p1_igv_default, p2_igv_default, ncol = 2)
```
## UChicago
The UChicago palette is based on
[the colors](https://news.uchicago.edu/sites/default/files/attachments/_uchicago.identity.guidelines.pdf)
used by the University of Chicago.
There are three palette types (`default`, `light`, `dark`) available.
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_uchicago = p1 + scale_color_uchicago()
p2_uchicago = p2 + scale_fill_uchicago()
grid.arrange(p1_uchicago, p2_uchicago, ncol = 2)
```
## Star Trek
This palette is inspired by the (uniform) colors in Star Trek:
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_startrek = p1 + scale_color_startrek()
p2_startrek = p2 + scale_fill_startrek()
grid.arrange(p1_startrek, p2_startrek, ncol = 2)
```
## Tron Legacy
This palette is inspired by the colors used in Tron Legacy.
It is suitable for displaying data when using a dark theme:
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_tron = p1 + theme_dark() + theme(
panel.background = element_rect(fill = "#2D2D2D"),
legend.key = element_rect(fill = "#2D2D2D")) +
scale_color_tron()
p2_tron = p2 + theme_dark() + theme(
panel.background = element_rect(fill = "#2D2D2D")) +
scale_fill_tron()
grid.arrange(p1_tron, p2_tron, ncol = 2)
```
## Futurama
This palette is inspired by the colors used in the TV show Futurama:
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_futurama = p1 + scale_color_futurama()
p2_futurama = p2 + scale_fill_futurama()
grid.arrange(p1_futurama, p2_futurama, ncol = 2)
```
## Rick and Morty
This palette is inspired by the colors used in the TV show Rick and Morty:
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_rickandmorty = p1 + scale_color_rickandmorty()
p2_rickandmorty = p2 + scale_fill_rickandmorty()
grid.arrange(p1_rickandmorty, p2_rickandmorty, ncol = 2)
```
## The Simpsons
This palette is inspired by the colors used in the TV show
The Simpsons:
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_simpsons = p1 + scale_color_simpsons()
p2_simpsons = p2 + scale_fill_simpsons()
grid.arrange(p1_simpsons, p2_simpsons, ncol = 2)
```
# Continuous Color Palettes
We will use a correlation matrix visualization (a special type of heatmap)
to demonstrate the continuous color palettes in `ggsci`.
```{r}
library("reshape2")
data("mtcars")
cor = cor(unname(cbind(mtcars, mtcars, mtcars, mtcars)))
cor_melt = melt(cor)
p3 = ggplot(cor_melt,
aes(x = Var1, y = Var2, fill = value)) +
geom_tile(colour = "black", size = 0.3) +
theme_bw() +
theme(axis.title.x = element_blank(),
axis.title.y = element_blank())
```
## GSEA
The GSEA palette (continuous) is inspired by the heatmaps generated by
[GSEA GenePattern](https://software.broadinstitute.org/cancer/software/genepattern/).
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p3_gsea = p3 + scale_fill_gsea()
p3_gsea_inv = p3 + scale_fill_gsea(reverse = TRUE)
grid.arrange(p3_gsea, p3_gsea_inv, ncol = 2)
```
## Material Design
The Material Design color palettes are from the [material design
color guidelines](https://material.io/guidelines/style/color.html).
We generate a random matrix first:
```{r}
library("reshape2")
set.seed(42)
k = 9
x = diag(k)
x[upper.tri(x)] = runif(sum(1:(k - 1)), 0, 1)
x_melt = melt(x)
p4 = ggplot(x_melt, aes(x = Var1, y = Var2, fill = value)) +
geom_tile(colour = "black", size = 0.3) +
scale_x_continuous(expand = c(0, 0)) +
scale_y_continuous(expand = c(0, 0)) +
theme_bw() + theme(
legend.position = "none", plot.background = element_blank(),
axis.line = element_blank(), axis.ticks = element_blank(),
axis.text.x = element_blank(), axis.text.y = element_blank(),
axis.title.x = element_blank(), axis.title.y = element_blank(),
panel.background = element_blank(), panel.border = element_blank(),
panel.grid.major = element_blank(), panel.grid.minor = element_blank())
```
Plot the matrix with the 19 material design color palettes:
```{r, fig.width = 10.67, fig.height = 7.12, out.width = 800, out.height = 533, dpi = 150}
grid.arrange(
p4 + scale_fill_material("red"), p4 + scale_fill_material("pink"),
p4 + scale_fill_material("purple"), p4 + scale_fill_material("deep-purple"),
p4 + scale_fill_material("indigo"), p4 + scale_fill_material("blue"),
p4 + scale_fill_material("light-blue"), p4 + scale_fill_material("cyan"),
p4 + scale_fill_material("teal"), p4 + scale_fill_material("green"),
p4 + scale_fill_material("light-green"), p4 + scale_fill_material("lime"),
p4 + scale_fill_material("yellow"), p4 + scale_fill_material("amber"),
p4 + scale_fill_material("orange"), p4 + scale_fill_material("deep-orange"),
p4 + scale_fill_material("brown"), p4 + scale_fill_material("grey"),
p4 + scale_fill_material("blue-grey"),
ncol = 6)
```
From the figure above, we can see that even though an identical matrix
was visualized by all plots, some palettes are more preferrable
than the others because our eyes are more sensitive to the changes
of their saturation levels.
# Non-ggplot2 Graphics
To apply the color palettes in `ggsci` to other graphics systems
(such as base graphics and lattice graphics), simply use the
palette generator functions in the table above. For example:
```{r, fig.width = 6.67, fig.height = 6.67, out.width = 500, out.height = 500, dpi = 150}
mypal = pal_npg("nrc", alpha = 0.7)(9)
mypal
library("scales")
show_col(mypal)
```
You will be able to use the generated hex color codes for such
graphics systems accordingly. The transparent level of the
entire palette is easily adjustable via the argument `"alpha"`
in every generator or scale function.
# Discussion
Please note some of the palettes might not be the best choice for certain
purposes, such as color-blind safe, photocopy safe, or print friendly.
If you do have such considerations, you might want to check out
color palettes like [ColorBrewer](http://colorbrewer2.org)
and [viridis](https://cran.r-project.org/package=viridis).
The color palettes in this package are solely created for research purposes.
The authors are not responsible for the usage of such palettes.
ggsci/NAMESPACE 0000644 0001762 0000144 00000004070 13276174722 012601 0 ustar ligges users # Generated by roxygen2: do not edit by hand
export(pal_aaas)
export(pal_d3)
export(pal_futurama)
export(pal_gsea)
export(pal_igv)
export(pal_jama)
export(pal_jco)
export(pal_lancet)
export(pal_locuszoom)
export(pal_material)
export(pal_nejm)
export(pal_npg)
export(pal_rickandmorty)
export(pal_simpsons)
export(pal_startrek)
export(pal_tron)
export(pal_uchicago)
export(pal_ucscgb)
export(rgb_gsea)
export(rgb_material)
export(scale_color_aaas)
export(scale_color_d3)
export(scale_color_futurama)
export(scale_color_gsea)
export(scale_color_igv)
export(scale_color_jama)
export(scale_color_jco)
export(scale_color_lancet)
export(scale_color_locuszoom)
export(scale_color_material)
export(scale_color_nejm)
export(scale_color_npg)
export(scale_color_rickandmorty)
export(scale_color_simpsons)
export(scale_color_startrek)
export(scale_color_tron)
export(scale_color_uchicago)
export(scale_color_ucscgb)
export(scale_colour_aaas)
export(scale_colour_d3)
export(scale_colour_futurama)
export(scale_colour_gsea)
export(scale_colour_igv)
export(scale_colour_jama)
export(scale_colour_jco)
export(scale_colour_lancet)
export(scale_colour_locuszoom)
export(scale_colour_material)
export(scale_colour_nejm)
export(scale_colour_npg)
export(scale_colour_rickandmorty)
export(scale_colour_simpsons)
export(scale_colour_startrek)
export(scale_colour_tron)
export(scale_colour_uchicago)
export(scale_colour_ucscgb)
export(scale_fill_aaas)
export(scale_fill_d3)
export(scale_fill_futurama)
export(scale_fill_gsea)
export(scale_fill_igv)
export(scale_fill_jama)
export(scale_fill_jco)
export(scale_fill_lancet)
export(scale_fill_locuszoom)
export(scale_fill_material)
export(scale_fill_nejm)
export(scale_fill_npg)
export(scale_fill_rickandmorty)
export(scale_fill_simpsons)
export(scale_fill_startrek)
export(scale_fill_tron)
export(scale_fill_uchicago)
export(scale_fill_ucscgb)
importFrom(ggplot2,discrete_scale)
importFrom(ggplot2,scale_color_gradientn)
importFrom(ggplot2,scale_fill_gradientn)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRamp)
importFrom(grDevices,rgb)
importFrom(scales,manual_pal)
ggsci/NEWS.md 0000644 0001762 0000144 00000001621 13276173326 012456 0 ustar ligges users # ggsci 2.9 (2018-05-13)
## Improvements
- New URL for the documentation website: https://nanx.me/ggsci/.
# ggsci 2.8 (2017-09-30)
## Improvements
- Use system font stack instead of Google Fonts in vignettes to avoid pandoc SSL issue.
# ggsci 2.7 (2017-06-12)
## New Features
Two new discrete color palettes:
- JAMA
- Tron Legacy
One new collection of continuous palettes with 19 color options:
- Material Design
# ggsci 2.4 (2017-03-07)
## New Features
Four new discrete color palettes:
- NEJM
- LocusZoom
- IGV
- Star Trek
# ggsci 2.0 (2016-11-20)
## New Features
Two new discrete color palettes:
- D3.js (v3)
- Futurama (Planet Express)
The first continuous color palette:
- GSEA GenePattern
# ggsci 1.0 (2016-04-01)
## New Features
Eight discrete color palettes:
- NPG
- AAAS
- Lancet
- JCO
- UCSCGB
- UChicago
- The Simpsons (Springfield)
- Rick and Morty (Schwifty)
ggsci/R/ 0000755 0001762 0000144 00000000000 13221611720 011542 5 ustar ligges users ggsci/R/discrete-ucscgb.R 0000644 0001762 0000144 00000004761 13221611720 014743 0 ustar ligges users #' UCSC Genome Browser Color Palette
#'
#' Color palette from UCSC Genome Browser chromosome colors.
#'
#' @param palette Palette type.
#' Currently there is one available option: \code{"default"}
#' (26-color palette).
#' @param alpha Transparency level, a real number in (0, 1].
#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details.
#'
#' @export pal_ucscgb
#'
#' @importFrom grDevices col2rgb rgb
#' @importFrom scales manual_pal
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @examples
#' library("scales")
#' show_col(pal_ucscgb("default")(26))
#' show_col(pal_ucscgb("default", alpha = 0.6)(26))
pal_ucscgb = function (palette = c('default'), alpha = 1) {
palette = match.arg(palette)
if (alpha > 1L | alpha <= 0L) stop('alpha must be in (0, 1]')
raw_cols = ggsci_db$'ucscgb'[[palette]]
raw_cols_rgb = col2rgb(raw_cols)
alpha_cols = rgb(
raw_cols_rgb[1L, ], raw_cols_rgb[2L, ], raw_cols_rgb[3L, ],
alpha = alpha * 255L, names = names(raw_cols),
maxColorValue = 255L)
manual_pal(unname(alpha_cols))
}
#' UCSC Genome Browser Color Scales
#'
#' See \code{\link{pal_ucscgb}} for details.
#'
#' @inheritParams pal_ucscgb
#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}}
#'
#' @export scale_color_ucscgb
#'
#' @importFrom ggplot2 discrete_scale
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @rdname scale_ucscgb
#'
#' @examples
#' library("ggplot2")
#' data("diamonds")
#'
#' ggplot(subset(diamonds, carat >= 2.2),
#' aes(x = table, y = price, colour = cut)) +
#' geom_point(alpha = 0.7) +
#' geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
#' theme_bw() + scale_color_ucscgb()
#'
#' ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
#' aes(x = depth, fill = cut)) +
#' geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
#' theme_bw() + scale_fill_ucscgb()
scale_color_ucscgb = function (palette = c('default'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('colour', 'ucscgb', pal_ucscgb(palette, alpha), ...)
}
#' @export scale_colour_ucscgb
#' @rdname scale_ucscgb
scale_colour_ucscgb = scale_color_ucscgb
#' @export scale_fill_ucscgb
#' @importFrom ggplot2 discrete_scale
#' @rdname scale_ucscgb
scale_fill_ucscgb = function (palette = c('default'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('fill', 'ucscgb', pal_ucscgb(palette, alpha), ...)
}
ggsci/R/discrete-locuszoom.R 0000644 0001762 0000144 00000005316 13221611720 015524 0 ustar ligges users #' LocusZoom Color Palette
#'
#' Color palettes based on the colors used by LocusZoom.
#'
#' @param palette Palette type.
#' Currently there is one available option: \code{"default"}
#' (7-color palette).
#' @param alpha Transparency level, a real number in (0, 1].
#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details.
#'
#' @export pal_locuszoom
#'
#' @importFrom grDevices col2rgb rgb
#' @importFrom scales manual_pal
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @references
#' Pruim, Randall J., et al. (2010). LocusZoom: regional visualization of
#' genome-wide association scan results. \emph{Bioinformatics},
#' 26(18), 2336--2337.
#'
#' @examples
#' library("scales")
#' show_col(pal_locuszoom("default")(7))
#' show_col(pal_locuszoom("default", alpha = 0.6)(7))
pal_locuszoom = function (palette = c('default'), alpha = 1) {
palette = match.arg(palette)
if (alpha > 1L | alpha <= 0L) stop('alpha must be in (0, 1]')
raw_cols = ggsci_db$'locuszoom'[[palette]]
raw_cols_rgb = col2rgb(raw_cols)
alpha_cols = rgb(
raw_cols_rgb[1L, ], raw_cols_rgb[2L, ], raw_cols_rgb[3L, ],
alpha = alpha * 255L, names = names(raw_cols),
maxColorValue = 255L)
manual_pal(unname(alpha_cols))
}
#' LocusZoom Color Scales
#'
#' See \code{\link{pal_locuszoom}} for details.
#'
#' @inheritParams pal_locuszoom
#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}}
#'
#' @export scale_color_locuszoom
#'
#' @importFrom ggplot2 discrete_scale
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @rdname scale_locuszoom
#'
#' @examples
#' library("ggplot2")
#' data("diamonds")
#'
#' ggplot(subset(diamonds, carat >= 2.2),
#' aes(x = table, y = price, colour = cut)) +
#' geom_point(alpha = 0.7) +
#' geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
#' theme_bw() + scale_color_locuszoom()
#'
#' ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
#' aes(x = depth, fill = cut)) +
#' geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
#' theme_bw() + scale_fill_locuszoom()
scale_color_locuszoom = function (palette = c('default'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('colour', 'locuszoom', pal_locuszoom(palette, alpha), ...)
}
#' @export scale_colour_locuszoom
#' @rdname scale_locuszoom
scale_colour_locuszoom = scale_color_locuszoom
#' @export scale_fill_locuszoom
#' @importFrom ggplot2 discrete_scale
#' @rdname scale_locuszoom
scale_fill_locuszoom = function (palette = c('default'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('fill', 'locuszoom', pal_locuszoom(palette, alpha), ...)
}
ggsci/R/discrete-uchicago.R 0000644 0001762 0000144 00000006236 13276174433 015275 0 ustar ligges users #' The University of Chicago Color Palettes
#'
#' Color palettes based on the colors used by the University of Chicago.
#'
#' @param palette Palette type.
#' There are 3 available options:
#' \code{"default"} (9-color palette);
#' \code{"light"} (9-color light palette);
#' \code{"dark"} (9-color dark palette).
#' @param alpha Transparency level, a real number in (0, 1].
#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details.
#'
#' @export pal_uchicago
#'
#' @importFrom grDevices col2rgb rgb
#' @importFrom scales manual_pal
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @references \url{https://news.uchicago.edu/sites/default/files/attachments/_uchicago.identity.guidelines.pdf}
#'
#' @examples
#' library("scales")
#' show_col(pal_uchicago("default")(9))
#' show_col(pal_uchicago("light")(9))
#' show_col(pal_uchicago("dark")(9))
pal_uchicago = function (
palette = c('default', 'light', 'dark'), alpha = 1) {
palette = match.arg(palette)
if (alpha > 1L | alpha <= 0L) stop('alpha must be in (0, 1]')
raw_cols = ggsci_db$'uchicago'[[palette]]
raw_cols_rgb = col2rgb(raw_cols)
alpha_cols = rgb(
raw_cols_rgb[1L, ], raw_cols_rgb[2L, ], raw_cols_rgb[3L, ],
alpha = alpha * 255L, names = names(raw_cols),
maxColorValue = 255L)
manual_pal(unname(alpha_cols))
}
#' The University of Chicago Color Scales
#'
#' See \code{\link{pal_uchicago}} for details.
#'
#' @inheritParams pal_uchicago
#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}}
#'
#' @export scale_color_uchicago
#'
#' @importFrom ggplot2 discrete_scale
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @references \url{https://news.uchicago.edu/sites/default/files/attachments/_uchicago.identity.guidelines.pdf}
#'
#' @rdname scale_uchicago
#'
#' @examples
#' library("ggplot2")
#' data("diamonds")
#'
#' p1 = ggplot(subset(diamonds, carat >= 2.2),
#' aes(x = table, y = price, colour = cut)) +
#' geom_point(alpha = 0.7) +
#' geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
#' theme_bw()
#'
#' p2 = ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
#' aes(x = depth, fill = cut)) +
#' geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
#' theme_bw()
#'
#' p1 + scale_color_uchicago()
#' p2 + scale_fill_uchicago()
#'
#' p1 + scale_color_uchicago(palette = "light")
#' p2 + scale_fill_uchicago(palette = "light")
#'
#' p1 + scale_color_uchicago(palette = "dark")
#' p2 + scale_fill_uchicago(palette = "dark")
scale_color_uchicago = function (
palette = c('default', 'light', 'dark'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('colour', 'uchicago', pal_uchicago(palette, alpha), ...)
}
#' @export scale_colour_uchicago
#' @rdname scale_uchicago
scale_colour_uchicago = scale_color_uchicago
#' @export scale_fill_uchicago
#' @importFrom ggplot2 discrete_scale
#' @rdname scale_uchicago
scale_fill_uchicago = function (
palette = c('default', 'light', 'dark'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('fill', 'uchicago', pal_uchicago(palette, alpha), ...)
}
ggsci/R/discrete-igv.R 0000644 0001762 0000144 00000005741 13221611720 014261 0 ustar ligges users #' Integrative Genomics Viewer (IGV) Color Palettes
#'
#' Color palettes based on the colors used by
#' Integrative Genomics Viewer (IGV).
#'
#' @param palette Palette type.
#' There are two available options:
#' \code{"default"} (51-color palette);
#' \code{"alternating"} (2-color palette).
#' @param alpha Transparency level, a real number in (0, 1].
#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details.
#'
#' @export pal_igv
#'
#' @importFrom grDevices col2rgb rgb
#' @importFrom scales manual_pal
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @references
#' James T. Robinson, Helga Thorvaldsd\'{o}ttir, Wendy Winckler,
#' Mitchell Guttman, Eric S. Lander, Gad Getz, Jill P. Mesirov.
#' Integrative Genomics Viewer. \emph{Nature Biotechnology} 29, 24--26 (2011).
#'
#' @examples
#' library("scales")
#' show_col(pal_igv("default")(51))
#' show_col(pal_igv("alternating")(2))
pal_igv = function (
palette = c('default', 'alternating'), alpha = 1) {
palette = match.arg(palette)
if (alpha > 1L | alpha <= 0L) stop('alpha must be in (0, 1]')
raw_cols = ggsci_db$'igv'[[palette]]
raw_cols_rgb = col2rgb(raw_cols)
alpha_cols = rgb(
raw_cols_rgb[1L, ], raw_cols_rgb[2L, ], raw_cols_rgb[3L, ],
alpha = alpha * 255L, names = names(raw_cols),
maxColorValue = 255L)
manual_pal(unname(alpha_cols))
}
#' Integrative Genomics Viewer (IGV) Color Scales
#'
#' See \code{\link{pal_igv}} for details.
#'
#' @inheritParams pal_igv
#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}}
#'
#' @export scale_color_igv
#'
#' @importFrom ggplot2 discrete_scale
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @rdname scale_igv
#'
#' @examples
#' library("ggplot2")
#' data("diamonds")
#'
#' p1 = ggplot(subset(diamonds, carat >= 2.2),
#' aes(x = table, y = price, colour = cut)) +
#' geom_point(alpha = 0.7) +
#' geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
#' theme_bw()
#'
#' p2 = ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
#' aes(x = depth, fill = cut)) +
#' geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
#' theme_bw()
#'
#' p1 + scale_color_igv()
#' p2 + scale_fill_igv()
#'
#' p1 + scale_colour_manual(
#' values = rep(pal_igv("alternating")(2), times = 3))
#' p2 + scale_fill_manual(
#' values = rep(pal_igv("alternating")(2), times = 3))
scale_color_igv = function (
palette = c('default', 'alternating'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('colour', 'igv', pal_igv(palette, alpha), ...)
}
#' @export scale_colour_igv
#' @rdname scale_igv
scale_colour_igv = scale_color_igv
#' @export scale_fill_igv
#' @importFrom ggplot2 discrete_scale
#' @rdname scale_igv
scale_fill_igv = function (
palette = c('default', 'alternating'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('fill', 'igv', pal_igv(palette, alpha), ...)
}
ggsci/R/discrete-d3.R 0000644 0001762 0000144 00000006376 13221611720 014007 0 ustar ligges users #' D3.js Color Palettes
#'
#' Color palettes based on the colors used by D3.js.
#'
#' @param palette Palette type.
#' There are 4 available options:
#' \code{"category10"} (10-color palette);
#' \code{"category20"} (20-color palette);
#' \code{"category20b"} (20-color palette);
#' \code{"category20c"} (20-color palette).
#' @param alpha Transparency level, a real number in (0, 1].
#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details.
#'
#' @export pal_d3
#'
#' @importFrom grDevices col2rgb rgb
#' @importFrom scales manual_pal
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @references \url{https://github.com/d3/d3-3.x-api-reference/blob/master/Ordinal-Scales.md}
#'
#' @examples
#' library("scales")
#' show_col(pal_d3("category10")(10))
#' show_col(pal_d3("category20")(20))
#' show_col(pal_d3("category20b")(20))
#' show_col(pal_d3("category20c")(20))
pal_d3 = function (
palette = c('category10', 'category20',
'category20b', 'category20c'), alpha = 1) {
palette = match.arg(palette)
if (alpha > 1L | alpha <= 0L) stop('alpha must be in (0, 1]')
raw_cols = ggsci_db$'d3'[[palette]]
raw_cols_rgb = col2rgb(raw_cols)
alpha_cols = rgb(
raw_cols_rgb[1L, ], raw_cols_rgb[2L, ], raw_cols_rgb[3L, ],
alpha = alpha * 255L, names = names(raw_cols),
maxColorValue = 255L)
manual_pal(unname(alpha_cols))
}
#' D3.js Color Scales
#'
#' See \code{\link{pal_d3}} for details.
#'
#' @inheritParams pal_d3
#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}}
#'
#' @export scale_color_d3
#'
#' @importFrom ggplot2 discrete_scale
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @references \url{https://github.com/d3/d3-3.x-api-reference/blob/master/Ordinal-Scales.md}
#'
#' @rdname scale_d3
#'
#' @examples
#' library("ggplot2")
#' data("diamonds")
#'
#' p1 = ggplot(subset(diamonds, carat >= 2.2),
#' aes(x = table, y = price, colour = cut)) +
#' geom_point(alpha = 0.7) +
#' geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
#' theme_bw()
#'
#' p2 = ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
#' aes(x = depth, fill = cut)) +
#' geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
#' theme_bw()
#'
#' p1 + scale_color_d3()
#' p2 + scale_fill_d3()
#'
#' p1 + scale_color_d3(palette = "category20")
#' p2 + scale_fill_d3(palette = "category20")
#'
#' p1 + scale_color_d3(palette = "category20b")
#' p2 + scale_fill_d3(palette = "category20b")
#'
#' p1 + scale_color_d3(palette = "category20c")
#' p2 + scale_fill_d3(palette = "category20c")
scale_color_d3 = function (
palette = c('category10', 'category20',
'category20b', 'category20c'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('colour', 'd3', pal_d3(palette, alpha), ...)
}
#' @export scale_colour_d3
#' @rdname scale_d3
scale_colour_d3 = scale_color_d3
#' @export scale_fill_d3
#' @importFrom ggplot2 discrete_scale
#' @rdname scale_d3
scale_fill_d3 = function (
palette = c('category10', 'category20',
'category20b', 'category20c'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('fill', 'd3', pal_d3(palette, alpha), ...)
}
ggsci/R/discrete-nejm.R 0000644 0001762 0000144 00000004673 13221611720 014430 0 ustar ligges users #' NEJM Color Palettes
#'
#' Color palette inspired by plots in
#' \emph{The New England Journal of Medicine}.
#'
#' @param palette Palette type.
#' Currently there is one available option: \code{"default"}
#' (8-color palette).
#' @param alpha Transparency level, a real number in (0, 1].
#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details.
#'
#' @export pal_nejm
#'
#' @importFrom grDevices col2rgb rgb
#' @importFrom scales manual_pal
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @examples
#' library("scales")
#' show_col(pal_nejm("default")(8))
#' show_col(pal_nejm("default", alpha = 0.6)(8))
pal_nejm = function (palette = c('default'), alpha = 1) {
palette = match.arg(palette)
if (alpha > 1L | alpha <= 0L) stop('alpha must be in (0, 1]')
raw_cols = ggsci_db$'nejm'[[palette]]
raw_cols_rgb = col2rgb(raw_cols)
alpha_cols = rgb(
raw_cols_rgb[1L, ], raw_cols_rgb[2L, ], raw_cols_rgb[3L, ],
alpha = alpha * 255L, names = names(raw_cols),
maxColorValue = 255L)
manual_pal(unname(alpha_cols))
}
#' NEJM Color Scales
#'
#' See \code{\link{pal_nejm}} for details.
#'
#' @inheritParams pal_nejm
#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}}
#'
#' @export scale_color_nejm
#'
#' @importFrom ggplot2 discrete_scale
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @rdname scale_nejm
#'
#' @examples
#' library("ggplot2")
#' data("diamonds")
#'
#' ggplot(subset(diamonds, carat >= 2.2),
#' aes(x = table, y = price, colour = cut)) +
#' geom_point(alpha = 0.7) +
#' geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
#' theme_bw() + scale_color_nejm()
#'
#' ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
#' aes(x = depth, fill = cut)) +
#' geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
#' theme_bw() + scale_fill_nejm()
scale_color_nejm = function (palette = c('default'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('colour', 'nejm', pal_nejm(palette, alpha), ...)
}
#' @export scale_colour_nejm
#' @rdname scale_nejm
scale_colour_nejm = scale_color_nejm
#' @export scale_fill_nejm
#' @importFrom ggplot2 discrete_scale
#' @rdname scale_nejm
scale_fill_nejm = function (palette = c('default'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('fill', 'nejm', pal_nejm(palette, alpha), ...)
}
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"T$Sz*N^ˎq. <8/I%.v/@r1x> Q8gζK즙U#ϧnݮN^o7.6w5j~:Tݦ?Hz}M|ٿ z+E ggsci/R/discrete-futurama.R 0000644 0001762 0000144 00000005073 13221611720 015316 0 ustar ligges users #' The Futurama Color Palettes
#'
#' Color palettes inspired by the colors used in \emph{Futurama}.
#'
#' @param palette Palette type.
#' Currently there is one available option: \code{"planetexpress"}
#' (12-color palette).
#' @param alpha Transparency level, a real number in (0, 1].
#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details.
#'
#' @export pal_futurama
#'
#' @importFrom grDevices col2rgb rgb
#' @importFrom scales manual_pal
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @examples
#' library("scales")
#' show_col(pal_futurama("planetexpress")(12))
#' show_col(pal_futurama("planetexpress", alpha = 0.6)(12))
pal_futurama = function (palette = c('planetexpress'), alpha = 1) {
palette = match.arg(palette)
if (alpha > 1L | alpha <= 0L) stop('alpha must be in (0, 1]')
raw_cols = ggsci_db$'futurama'[[palette]]
raw_cols_rgb = col2rgb(raw_cols)
alpha_cols = rgb(
raw_cols_rgb[1L, ], raw_cols_rgb[2L, ], raw_cols_rgb[3L, ],
alpha = alpha * 255L, names = names(raw_cols),
maxColorValue = 255L)
manual_pal(unname(alpha_cols))
}
#' The Futurama Color Scales
#'
#' See \code{\link{pal_futurama}} for details.
#'
#' @inheritParams pal_futurama
#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}}
#'
#' @export scale_color_futurama
#'
#' @importFrom ggplot2 discrete_scale
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @rdname scale_futurama
#'
#' @examples
#' library("ggplot2")
#' data("diamonds")
#'
#' ggplot(subset(diamonds, carat >= 2.2),
#' aes(x = table, y = price, colour = cut)) +
#' geom_point(alpha = 0.7) +
#' geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
#' theme_bw() + scale_color_futurama()
#'
#' ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
#' aes(x = depth, fill = cut)) +
#' geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
#' theme_bw() + scale_fill_futurama()
scale_color_futurama = function (palette = c('planetexpress'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('colour', 'futurama', pal_futurama(palette, alpha), ...)
}
#' @export scale_colour_futurama
#' @rdname scale_futurama
scale_colour_futurama = scale_color_futurama
#' @export scale_fill_futurama
#' @importFrom ggplot2 discrete_scale
#' @rdname scale_futurama
scale_fill_futurama = function (palette = c('planetexpress'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('fill', 'futurama', pal_futurama(palette, alpha), ...)
}
ggsci/R/continuous-gsea.R 0000644 0001762 0000144 00000007063 13221611720 015016 0 ustar ligges users #' The GSEA GenePattern Color Palettes
#'
#' Color palette inspired by the colors used in the
#' heatmaps plotted by GSEA GenePattern.
#'
#' @param palette Palette type.
#' Currently there is one available option: \code{"default"}
#' (continuous palette with 12 base colors).
#' @param n Number of individual colors to be generated.
#' @param alpha Transparency level, a real number in (0, 1].
#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details.
#' @param reverse Logical. Should the order of the colors be reversed?
#'
#' @export rgb_gsea
#'
#' @importFrom grDevices colorRamp rgb
#' @importFrom scales manual_pal
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @note The 12 base colors used in this palette are derived from
#' \href{ftp://ftp.broad.mit.edu/pub/genepattern/modules/HeatMapImage/broad.mit.edu:cancer.software.genepattern.module.analysis/00032/6/HeatMapImage.pdf}{this document}.
#'
#' @examples
#' library("scales")
#' show_col(pal_gsea("default")(12))
#' show_col(pal_gsea("default", n = 30, alpha = 0.6, reverse = TRUE)(30))
rgb_gsea = function (
palette = c('default'), n = 12, alpha = 1, reverse = FALSE) {
palette = match.arg(palette)
if (alpha > 1L | alpha <= 0L) stop('alpha must be in (0, 1]')
raw_cols = ggsci_db$'gsea'[[palette]]
func_cols = colorRamp(raw_cols, space = 'Lab', interpolate = 'spline')
mat_cols = func_cols(seq(0L, 1L, length.out = n))
alpha_cols = rgb(
mat_cols[, 1L], mat_cols[, 2L], mat_cols[, 3L],
alpha = alpha * 255L, maxColorValue = 255L)
if (reverse) alpha_cols = rev(alpha_cols)
alpha_cols
}
#' The GSEA GenePattern Color Palettes
#'
#' Color palette inspired by the colors used in the
#' heatmaps plotted by GSEA GenePattern.
#'
#' @inheritParams rgb_gsea
#'
#' @export pal_gsea
#'
#' @importFrom scales manual_pal
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @examples
#' library("scales")
#' show_col(pal_gsea("default")(12))
#' show_col(pal_gsea("default", n = 30, alpha = 0.6, reverse = TRUE)(30))
pal_gsea = function (
palette = c('default'), n = 12, alpha = 1, reverse = FALSE) {
palette = match.arg(palette)
alpha_cols = rgb_gsea(palette, n, alpha, reverse)
manual_pal(unname(alpha_cols))
}
#' The GSEA GenePattern Color Scales
#'
#' See \code{\link{pal_gsea}} for details.
#'
#' @inheritParams pal_gsea
#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}}
#'
#' @export scale_color_gsea
#'
#' @importFrom ggplot2 scale_color_gradientn
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @rdname scale_gsea
#'
#' @examples
#' library("ggplot2")
#' library("reshape2")
#' data("mtcars")
#'
#' cor = cor(mtcars)
#' cor_melt = melt(cor)
#'
#' ggplot(cor_melt,
#' aes(x = Var1, y = Var2, fill = value)) +
#' geom_tile(colour = "black", size = 0.3) +
#' theme_bw() + scale_fill_gsea()
scale_color_gsea = function (
palette = c('default'), alpha = 1, reverse = FALSE, ...) {
palette = match.arg(palette)
scale_color_gradientn(colours = rgb_gsea(
palette, n = 512, alpha = alpha, reverse = reverse),
...)
}
#' @export scale_colour_gsea
#' @rdname scale_gsea
scale_colour_gsea = scale_color_gsea
#' @export scale_fill_gsea
#' @importFrom ggplot2 scale_fill_gradientn
#' @rdname scale_gsea
scale_fill_gsea = function (
palette = c('default'), alpha = 1, reverse = FALSE, ...) {
palette = match.arg(palette)
scale_fill_gradientn(colours = rgb_gsea(
palette, n = 512, alpha = alpha, reverse = reverse),
...)
}
ggsci/R/discrete-startrek.R 0000644 0001762 0000144 00000005017 13221611720 015327 0 ustar ligges users #' Star Trek Color Palettes
#'
#' Color palettes inspired by the colors used in \emph{Star Trek}.
#'
#' @param palette Palette type.
#' Currently there is one available option: \code{"uniform"}
#' (7-color palette).
#' @param alpha Transparency level, a real number in (0, 1].
#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details.
#'
#' @export pal_startrek
#'
#' @importFrom grDevices col2rgb rgb
#' @importFrom scales manual_pal
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @examples
#' library("scales")
#' show_col(pal_startrek("uniform")(7))
#' show_col(pal_startrek("uniform", alpha = 0.6)(7))
pal_startrek = function (palette = c('uniform'), alpha = 1) {
palette = match.arg(palette)
if (alpha > 1L | alpha <= 0L) stop('alpha must be in (0, 1]')
raw_cols = ggsci_db$'startrek'[[palette]]
raw_cols_rgb = col2rgb(raw_cols)
alpha_cols = rgb(
raw_cols_rgb[1L, ], raw_cols_rgb[2L, ], raw_cols_rgb[3L, ],
alpha = alpha * 255L, names = names(raw_cols),
maxColorValue = 255L)
manual_pal(unname(alpha_cols))
}
#' Star Trek Color Scales
#'
#' See \code{\link{pal_startrek}} for details.
#'
#' @inheritParams pal_startrek
#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}}
#'
#' @export scale_color_startrek
#'
#' @importFrom ggplot2 discrete_scale
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @rdname scale_startrek
#'
#' @examples
#' library("ggplot2")
#' data("diamonds")
#'
#' ggplot(subset(diamonds, carat >= 2.2),
#' aes(x = table, y = price, colour = cut)) +
#' geom_point(alpha = 0.7) +
#' geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
#' theme_bw() + scale_color_startrek()
#'
#' ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
#' aes(x = depth, fill = cut)) +
#' geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
#' theme_bw() + scale_fill_startrek()
scale_color_startrek = function (palette = c('uniform'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('colour', 'startrek', pal_startrek(palette, alpha), ...)
}
#' @export scale_colour_startrek
#' @rdname scale_startrek
scale_colour_startrek = scale_color_startrek
#' @export scale_fill_startrek
#' @importFrom ggplot2 discrete_scale
#' @rdname scale_startrek
scale_fill_startrek = function (palette = c('uniform'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('fill', 'startrek', pal_startrek(palette, alpha), ...)
}
ggsci/R/discrete-rickandmorty.R 0000644 0001762 0000144 00000005203 13221611720 016173 0 ustar ligges users #' Rick and Morty Color Palettes
#'
#' Color palettes inspired by the colors used in \emph{Rick and Morty}.
#'
#' @param palette Palette type.
#' Currently there is one available option: \code{"schwifty"}
#' (12-color palette).
#' @param alpha Transparency level, a real number in (0, 1].
#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details.
#'
#' @export pal_rickandmorty
#'
#' @importFrom grDevices col2rgb rgb
#' @importFrom scales manual_pal
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @examples
#' library("scales")
#' show_col(pal_rickandmorty("schwifty")(12))
#' show_col(pal_rickandmorty("schwifty", alpha = 0.6)(12))
pal_rickandmorty = function (palette = c('schwifty'), alpha = 1) {
palette = match.arg(palette)
if (alpha > 1L | alpha <= 0L) stop('alpha must be in (0, 1]')
raw_cols = ggsci_db$'rickandmorty'[[palette]]
raw_cols_rgb = col2rgb(raw_cols)
alpha_cols = rgb(
raw_cols_rgb[1L, ], raw_cols_rgb[2L, ], raw_cols_rgb[3L, ],
alpha = alpha * 255L, names = names(raw_cols),
maxColorValue = 255L)
manual_pal(unname(alpha_cols))
}
#' Rick and Morty Color Scales
#'
#' See \code{\link{pal_rickandmorty}} for details.
#'
#' @inheritParams pal_rickandmorty
#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}}
#'
#' @export scale_color_rickandmorty
#'
#' @importFrom ggplot2 discrete_scale
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @rdname scale_rickandmorty
#'
#' @examples
#' library("ggplot2")
#' data("diamonds")
#'
#' ggplot(subset(diamonds, carat >= 2.2),
#' aes(x = table, y = price, colour = cut)) +
#' geom_point(alpha = 0.7) +
#' geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
#' theme_bw() + scale_color_rickandmorty()
#'
#' ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
#' aes(x = depth, fill = cut)) +
#' geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
#' theme_bw() + scale_fill_rickandmorty()
scale_color_rickandmorty = function (palette = c('schwifty'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('colour', 'rickandmorty', pal_rickandmorty(palette, alpha), ...)
}
#' @export scale_colour_rickandmorty
#' @rdname scale_rickandmorty
scale_colour_rickandmorty = scale_color_rickandmorty
#' @export scale_fill_rickandmorty
#' @importFrom ggplot2 discrete_scale
#' @rdname scale_rickandmorty
scale_fill_rickandmorty = function (palette = c('schwifty'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('fill', 'rickandmorty', pal_rickandmorty(palette, alpha), ...)
}
ggsci/R/discrete-jama.R 0000644 0001762 0000144 00000005025 13221611720 014377 0 ustar ligges users #' Journal of the American Medical Association Color Palettes
#'
#' Color palette inspired by plots in
#' \emph{The Journal of the American Medical Association}.
#'
#' @param palette Palette type.
#' Currently there is one available option: \code{"default"}
#' (7-color palette).
#' @param alpha Transparency level, a real number in (0, 1].
#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details.
#'
#' @export pal_jama
#'
#' @importFrom grDevices col2rgb rgb
#' @importFrom scales manual_pal
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @examples
#' library("scales")
#' show_col(pal_jama("default")(7))
#' show_col(pal_jama("default", alpha = 0.6)(7))
pal_jama = function (palette = c('default'), alpha = 1) {
palette = match.arg(palette)
if (alpha > 1L | alpha <= 0L) stop('alpha must be in (0, 1]')
raw_cols = ggsci_db$'jama'[[palette]]
raw_cols_rgb = col2rgb(raw_cols)
alpha_cols = rgb(
raw_cols_rgb[1L, ], raw_cols_rgb[2L, ], raw_cols_rgb[3L, ],
alpha = alpha * 255L, names = names(raw_cols),
maxColorValue = 255L)
manual_pal(unname(alpha_cols))
}
#' Journal of the American Medical Association Color Scales
#'
#' See \code{\link{pal_jama}} for details.
#'
#' @inheritParams pal_jama
#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}}
#'
#' @export scale_color_jama
#'
#' @importFrom ggplot2 discrete_scale
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @rdname scale_jama
#'
#' @examples
#' library("ggplot2")
#' data("diamonds")
#'
#' ggplot(subset(diamonds, carat >= 2.2),
#' aes(x = table, y = price, colour = cut)) +
#' geom_point(alpha = 0.7) +
#' geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
#' theme_bw() + scale_color_jama()
#'
#' ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
#' aes(x = depth, fill = cut)) +
#' geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
#' theme_bw() + scale_fill_jama()
scale_color_jama = function (palette = c('default'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('colour', 'jama', pal_jama(palette, alpha), ...)
}
#' @export scale_colour_jama
#' @rdname scale_jama
scale_colour_jama = scale_color_jama
#' @export scale_fill_jama
#' @importFrom ggplot2 discrete_scale
#' @rdname scale_jama
scale_fill_jama = function (palette = c('default'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('fill', 'jama', pal_jama(palette, alpha), ...)
}
ggsci/R/discrete-tron.R 0000644 0001762 0000144 00000005173 13221611720 014455 0 ustar ligges users #' Tron Legacy Color Palettes
#'
#' Color palettes inspired by the colors used in \emph{Tron Legacy}.
#'
#' @param palette Palette type.
#' Currently there is one available option: \code{"legacy"}
#' (7-color palette).
#' @param alpha Transparency level, a real number in (0, 1].
#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details.
#'
#' @export pal_tron
#'
#' @importFrom grDevices col2rgb rgb
#' @importFrom scales manual_pal
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @examples
#' library("scales")
#' show_col(pal_tron("legacy")(7))
#' show_col(pal_tron("legacy", alpha = 0.6)(7))
pal_tron = function (palette = c('legacy'), alpha = 1) {
palette = match.arg(palette)
if (alpha > 1L | alpha <= 0L) stop('alpha must be in (0, 1]')
raw_cols = ggsci_db$'tron'[[palette]]
raw_cols_rgb = col2rgb(raw_cols)
alpha_cols = rgb(
raw_cols_rgb[1L, ], raw_cols_rgb[2L, ], raw_cols_rgb[3L, ],
alpha = alpha * 255L, names = names(raw_cols),
maxColorValue = 255L)
manual_pal(unname(alpha_cols))
}
#' Tron Legacy Color Scales
#'
#' See \code{\link{pal_tron}} for details.
#'
#' @inheritParams pal_tron
#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}}
#'
#' @export scale_color_tron
#'
#' @importFrom ggplot2 discrete_scale
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @rdname scale_tron
#'
#' @examples
#' library("ggplot2")
#' data("diamonds")
#'
#' ggplot(subset(diamonds, carat >= 2.2),
#' aes(x = table, y = price, colour = cut)) +
#' geom_point(alpha = 0.7) +
#' geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
#' theme_dark() + theme(
#' panel.background = element_rect(fill = "#2D2D2D"),
#' legend.key = element_rect(fill = "#2D2D2D")) +
#' scale_color_tron()
#'
#' ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
#' aes(x = depth, fill = cut)) +
#' geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
#' theme_dark() + theme(
#' panel.background = element_rect(fill = "#2D2D2D")) +
#' scale_fill_tron()
scale_color_tron = function (palette = c('legacy'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('colour', 'tron', pal_tron(palette, alpha), ...)
}
#' @export scale_colour_tron
#' @rdname scale_tron
scale_colour_tron = scale_color_tron
#' @export scale_fill_tron
#' @importFrom ggplot2 discrete_scale
#' @rdname scale_tron
scale_fill_tron = function (palette = c('legacy'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('fill', 'tron', pal_tron(palette, alpha), ...)
}
ggsci/R/discrete-simpsons.R 0000644 0001762 0000144 00000005063 13221611720 015344 0 ustar ligges users #' The Simpsons Color Palettes
#'
#' Color palettes inspired by the colors used in \emph{The Simpsons}.
#'
#' @param palette Palette type.
#' Currently there is one available option: \code{"springfield"}
#' (16-color palette).
#' @param alpha Transparency level, a real number in (0, 1].
#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details.
#'
#' @export pal_simpsons
#'
#' @importFrom grDevices col2rgb rgb
#' @importFrom scales manual_pal
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @examples
#' library("scales")
#' show_col(pal_simpsons("springfield")(16))
#' show_col(pal_simpsons("springfield", alpha = 0.6)(16))
pal_simpsons = function (palette = c('springfield'), alpha = 1) {
palette = match.arg(palette)
if (alpha > 1L | alpha <= 0L) stop('alpha must be in (0, 1]')
raw_cols = ggsci_db$'simpsons'[[palette]]
raw_cols_rgb = col2rgb(raw_cols)
alpha_cols = rgb(
raw_cols_rgb[1L, ], raw_cols_rgb[2L, ], raw_cols_rgb[3L, ],
alpha = alpha * 255L, names = names(raw_cols),
maxColorValue = 255L)
manual_pal(unname(alpha_cols))
}
#' The Simpsons Color Scales
#'
#' See \code{\link{pal_simpsons}} for details.
#'
#' @inheritParams pal_simpsons
#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}}
#'
#' @export scale_color_simpsons
#'
#' @importFrom ggplot2 discrete_scale
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @rdname scale_simpsons
#'
#' @examples
#' library("ggplot2")
#' data("diamonds")
#'
#' ggplot(subset(diamonds, carat >= 2.2),
#' aes(x = table, y = price, colour = cut)) +
#' geom_point(alpha = 0.7) +
#' geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
#' theme_bw() + scale_color_simpsons()
#'
#' ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
#' aes(x = depth, fill = cut)) +
#' geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
#' theme_bw() + scale_fill_simpsons()
scale_color_simpsons = function (palette = c('springfield'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('colour', 'simpsons', pal_simpsons(palette, alpha), ...)
}
#' @export scale_colour_simpsons
#' @rdname scale_simpsons
scale_colour_simpsons = scale_color_simpsons
#' @export scale_fill_simpsons
#' @importFrom ggplot2 discrete_scale
#' @rdname scale_simpsons
scale_fill_simpsons = function (palette = c('springfield'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('fill', 'simpsons', pal_simpsons(palette, alpha), ...)
}
ggsci/R/discrete-lancet.R 0000644 0001762 0000144 00000005040 13221611720 014732 0 ustar ligges users #' Lancet Journal Color Palettes
#'
#' Color palettes inspired by plots in Lancet journals,
#' such as \emph{Lancet Oncology}.
#'
#' @param palette Palette type.
#' Currently there is one available option: \code{"lanonc"}
#' (9-color palette inspired by \emph{Lancet Oncology}).
#' @param alpha Transparency level, a real number in (0, 1].
#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details.
#'
#' @export pal_lancet
#'
#' @importFrom grDevices col2rgb rgb
#' @importFrom scales manual_pal
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @examples
#' library("scales")
#' show_col(pal_lancet("lanonc")(9))
#' show_col(pal_lancet("lanonc", alpha = 0.6)(9))
pal_lancet = function (palette = c('lanonc'), alpha = 1) {
palette = match.arg(palette)
if (alpha > 1L | alpha <= 0L) stop('alpha must be in (0, 1]')
raw_cols = ggsci_db$'lancet'[[palette]]
raw_cols_rgb = col2rgb(raw_cols)
alpha_cols = rgb(
raw_cols_rgb[1L, ], raw_cols_rgb[2L, ], raw_cols_rgb[3L, ],
alpha = alpha * 255L, names = names(raw_cols),
maxColorValue = 255L)
manual_pal(unname(alpha_cols))
}
#' Lancet Journal Color Scales
#'
#' See \code{\link{pal_lancet}} for details.
#'
#' @inheritParams pal_lancet
#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}}
#'
#' @export scale_color_lancet
#'
#' @importFrom ggplot2 discrete_scale
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @rdname scale_lancet
#'
#' @examples
#' library("ggplot2")
#' data("diamonds")
#'
#' ggplot(subset(diamonds, carat >= 2.2),
#' aes(x = table, y = price, colour = cut)) +
#' geom_point(alpha = 0.7) +
#' geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
#' theme_bw() + scale_color_lancet()
#'
#' ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
#' aes(x = depth, fill = cut)) +
#' geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
#' theme_bw() + scale_fill_lancet()
scale_color_lancet = function (palette = c('lanonc'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('colour', 'lancet', pal_lancet(palette, alpha), ...)
}
#' @export scale_colour_lancet
#' @rdname scale_lancet
scale_colour_lancet = scale_color_lancet
#' @export scale_fill_lancet
#' @importFrom ggplot2 discrete_scale
#' @rdname scale_lancet
scale_fill_lancet = function (palette = c('lanonc'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('fill', 'lancet', pal_lancet(palette, alpha), ...)
}
ggsci/R/discrete-jco.R 0000644 0001762 0000144 00000004715 13221611720 014247 0 ustar ligges users #' Journal of Clinical Oncology Color Palettes
#'
#' Color palette inspired by plots in \emph{Journal of Clinical Oncology}.
#'
#' @param palette Palette type.
#' Currently there is one available option: \code{"default"}
#' (10-color palette).
#' @param alpha Transparency level, a real number in (0, 1].
#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details.
#'
#' @export pal_jco
#'
#' @importFrom grDevices col2rgb rgb
#' @importFrom scales manual_pal
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @examples
#' library("scales")
#' show_col(pal_jco("default")(10))
#' show_col(pal_jco("default", alpha = 0.6)(10))
pal_jco = function (palette = c('default'), alpha = 1) {
palette = match.arg(palette)
if (alpha > 1L | alpha <= 0L) stop('alpha must be in (0, 1]')
raw_cols = ggsci_db$'jco'[[palette]]
raw_cols_rgb = col2rgb(raw_cols)
alpha_cols = rgb(
raw_cols_rgb[1L, ], raw_cols_rgb[2L, ], raw_cols_rgb[3L, ],
alpha = alpha * 255L, names = names(raw_cols),
maxColorValue = 255L)
manual_pal(unname(alpha_cols))
}
#' Journal of Clinical Oncology Color Scales
#'
#' See \code{\link{pal_jco}} for details.
#'
#' @inheritParams pal_jco
#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}}
#'
#' @export scale_color_jco
#'
#' @importFrom ggplot2 discrete_scale
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @rdname scale_jco
#'
#' @examples
#' library("ggplot2")
#' data("diamonds")
#'
#' ggplot(subset(diamonds, carat >= 2.2),
#' aes(x = table, y = price, colour = cut)) +
#' geom_point(alpha = 0.7) +
#' geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
#' theme_bw() + scale_color_jco()
#'
#' ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
#' aes(x = depth, fill = cut)) +
#' geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
#' theme_bw() + scale_fill_jco()
scale_color_jco = function (palette = c('default'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('colour', 'jco', pal_jco(palette, alpha), ...)
}
#' @export scale_colour_jco
#' @rdname scale_jco
scale_colour_jco = scale_color_jco
#' @export scale_fill_jco
#' @importFrom ggplot2 discrete_scale
#' @rdname scale_jco
scale_fill_jco = function (palette = c('default'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('fill', 'jco', pal_jco(palette, alpha), ...)
}
ggsci/R/ggsci-package.R 0000644 0001762 0000144 00000000667 13221611720 014363 0 ustar ligges users #' Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2'
#'
#' Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2'
#'
#' Opened the vignette via \code{vignette("ggsci")}.
#'
#' \tabular{ll}{ Package: \tab ggsci\cr
#' Type: \tab Package\cr
#' License: \tab GPL-3\cr }
#'
#' @name ggsci-package
#' @docType package
#' @author Nan Xiao <\email{me@@nanx.me}>
#' Miaozhu Li <\email{miaozhu.li@@duke.edu}>
NULL
ggsci/R/continuous-material.R 0000644 0001762 0000144 00000011231 13221611720 015665 0 ustar ligges users #' Material Design Color Palettes
#'
#' The Material Design color palettes.
#'
#' @param palette Palette type.
#' There are 19 available options:
#' \itemize{
#' \item \code{"red"}
#' \item \code{"pink"}
#' \item \code{"purple"}
#' \item \code{"deep-purple"}
#' \item \code{"indigo"}
#' \item \code{"blue"}
#' \item \code{"light-blue"}
#' \item \code{"cyan"}
#' \item \code{"teal"}
#' \item \code{"green"}
#' \item \code{"light-green"}
#' \item \code{"lime"}
#' \item \code{"yellow"}
#' \item \code{"amber"}
#' \item \code{"orange"},
#' \item \code{"deep-orange"}
#' \item \code{"brown"}
#' \item \code{"grey"}
#' \item \code{"blue-grey"}}
#' See the \href{https://material.io/guidelines/style/color.html}{material
#' design color guidelines} for details.
#' @param n Number of individual colors to be generated.
#' @param alpha Transparency level, a real number in (0, 1].
#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details.
#' @param reverse Logical. Should the order of the colors be reversed?
#'
#' @export rgb_material
#'
#' @importFrom grDevices colorRamp rgb
#' @importFrom scales manual_pal
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @references
#' \url{https://material.io/guidelines/style/color.html}
#'
#' @examples
#' library("scales")
#' show_col(pal_material("indigo")(10))
#' show_col(pal_material("indigo", n = 30, alpha = 0.6, reverse = TRUE)(30))
rgb_material = function (palette = c(
'red', 'pink', 'purple', 'deep-purple', 'indigo', 'blue',
'light-blue', 'cyan', 'teal', 'green', 'light-green', 'lime',
'yellow', 'amber', 'orange', 'deep-orange', 'brown', 'grey', 'blue-grey'),
n = 10, alpha = 1, reverse = FALSE) {
palette = match.arg(palette)
if (alpha > 1L | alpha <= 0L) stop('alpha must be in (0, 1]')
raw_cols = ggsci_db$'material'[[palette]]
func_cols = colorRamp(raw_cols, space = 'Lab', interpolate = 'spline')
mat_cols = func_cols(seq(0L, 1L, length.out = n))
alpha_cols = rgb(
mat_cols[, 1L], mat_cols[, 2L], mat_cols[, 3L],
alpha = alpha * 255L, maxColorValue = 255L)
if (reverse) alpha_cols = rev(alpha_cols)
alpha_cols
}
#' Material Design Color Palettes
#'
#' The Material Design color palettes.
#'
#' @inheritParams rgb_material
#'
#' @export pal_material
#'
#' @importFrom scales manual_pal
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @examples
#' library("scales")
#' show_col(pal_material("indigo")(10))
#' show_col(pal_material("indigo", n = 30, alpha = 0.6, reverse = TRUE)(30))
pal_material = function (palette = c(
'red', 'pink', 'purple', 'deep-purple', 'indigo', 'blue',
'light-blue', 'cyan', 'teal', 'green', 'light-green', 'lime',
'yellow', 'amber', 'orange', 'deep-orange', 'brown', 'grey', 'blue-grey'),
n = 10, alpha = 1, reverse = FALSE) {
palette = match.arg(palette)
alpha_cols = rgb_material(palette, n, alpha, reverse)
manual_pal(unname(alpha_cols))
}
#' Material Design Color Palettes
#'
#' See \code{\link{pal_material}} for details.
#'
#' @inheritParams pal_material
#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}}
#'
#' @export scale_color_material
#'
#' @importFrom ggplot2 scale_color_gradientn
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @rdname scale_material
#'
#' @examples
#' library("ggplot2")
#' library("reshape2")
#' data("mtcars")
#'
#' cor = abs(cor(mtcars))
#' cor_melt = melt(cor)
#'
#' ggplot(cor_melt,
#' aes(x = Var1, y = Var2, fill = value)) +
#' geom_tile(colour = "black", size = 0.3) +
#' theme_bw() + scale_fill_material("blue-grey")
scale_color_material = function (palette = c(
'red', 'pink', 'purple', 'deep-purple', 'indigo', 'blue',
'light-blue', 'cyan', 'teal', 'green', 'light-green', 'lime',
'yellow', 'amber', 'orange', 'deep-orange', 'brown', 'grey', 'blue-grey'),
alpha = 1, reverse = FALSE, ...) {
palette = match.arg(palette)
scale_color_gradientn(colours = rgb_material(
palette, n = 512, alpha = alpha, reverse = reverse),
...)
}
#' @export scale_colour_material
#' @rdname scale_material
scale_colour_material = scale_color_material
#' @export scale_fill_material
#' @importFrom ggplot2 scale_fill_gradientn
#' @rdname scale_material
scale_fill_material = function (palette = c(
'red', 'pink', 'purple', 'deep-purple', 'indigo', 'blue',
'light-blue', 'cyan', 'teal', 'green', 'light-green', 'lime',
'yellow', 'amber', 'orange', 'deep-orange', 'brown', 'grey', 'blue-grey'),
alpha = 1, reverse = FALSE, ...) {
palette = match.arg(palette)
scale_fill_gradientn(colours = rgb_material(
palette, n = 512, alpha = alpha, reverse = reverse),
...)
}
ggsci/R/discrete-npg.R 0000644 0001762 0000144 00000004760 13221611720 014260 0 ustar ligges users #' NPG Journal Color Palettes
#'
#' Color palettes inspired by plots in journals published by
#' Nature Publishing Group, such as \emph{Nature Reviews Cancer}.
#'
#' @param palette Palette type.
#' Currently there is one available option: \code{"nrc"}
#' (10-color palette inspired by \emph{Nature Reviews Cancer}).
#' @param alpha Transparency level, a real number in (0, 1].
#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details.
#'
#' @export pal_npg
#'
#' @importFrom grDevices col2rgb rgb
#' @importFrom scales manual_pal
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @examples
#' library("scales")
#' show_col(pal_npg("nrc")(10))
#' show_col(pal_npg("nrc", alpha = 0.6)(10))
pal_npg = function (palette = c('nrc'), alpha = 1) {
palette = match.arg(palette)
if (alpha > 1L | alpha <= 0L) stop('alpha must be in (0, 1]')
raw_cols = ggsci_db$'npg'[[palette]]
raw_cols_rgb = col2rgb(raw_cols)
alpha_cols = rgb(
raw_cols_rgb[1L, ], raw_cols_rgb[2L, ], raw_cols_rgb[3L, ],
alpha = alpha * 255L, names = names(raw_cols),
maxColorValue = 255L)
manual_pal(unname(alpha_cols))
}
#' NPG Journal Color Scales
#'
#' See \code{\link{pal_npg}} for details.
#'
#' @inheritParams pal_npg
#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}}
#'
#' @export scale_color_npg
#'
#' @importFrom ggplot2 discrete_scale
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @rdname scale_npg
#'
#' @examples
#' library("ggplot2")
#' data("diamonds")
#'
#' ggplot(subset(diamonds, carat >= 2.2),
#' aes(x = table, y = price, colour = cut)) +
#' geom_point(alpha = 0.7) +
#' geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
#' theme_bw() + scale_color_npg()
#'
#' ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
#' aes(x = depth, fill = cut)) +
#' geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
#' theme_bw() + scale_fill_npg()
scale_color_npg = function (palette = c('nrc'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('colour', 'npg', pal_npg(palette, alpha), ...)
}
#' @export scale_colour_npg
#' @rdname scale_npg
scale_colour_npg = scale_color_npg
#' @export scale_fill_npg
#' @importFrom ggplot2 discrete_scale
#' @rdname scale_npg
scale_fill_npg = function (palette = c('nrc'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('fill', 'npg', pal_npg(palette, alpha), ...)
}
ggsci/R/discrete-aaas.R 0000644 0001762 0000144 00000005125 13221611720 014375 0 ustar ligges users #' AAAS Journal Color Palettes
#'
#' Color palettes inspired by plots in journals published by
#' American Association for the Advancement of Science (AAAS),
#' such as \emph{Science} and \emph{Science Translational Medicine}.
#'
#' @param palette Palette type.
#' Currently there is one available option: \code{"default"}
#' (10-color palette inspired by \emph{Science}).
#' @param alpha Transparency level, a real number in (0, 1].
#' See \code{alpha} in \code{\link[grDevices]{rgb}} for details.
#'
#' @export pal_aaas
#'
#' @importFrom grDevices col2rgb rgb
#' @importFrom scales manual_pal
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @examples
#' library("scales")
#' show_col(pal_aaas("default")(10))
#' show_col(pal_aaas("default", alpha = 0.6)(10))
pal_aaas = function (palette = c('default'), alpha = 1) {
palette = match.arg(palette)
if (alpha > 1L | alpha <= 0L) stop('alpha must be in (0, 1]')
raw_cols = ggsci_db$'aaas'[[palette]]
raw_cols_rgb = col2rgb(raw_cols)
alpha_cols = rgb(
raw_cols_rgb[1L, ], raw_cols_rgb[2L, ], raw_cols_rgb[3L, ],
alpha = alpha * 255L, names = names(raw_cols),
maxColorValue = 255L)
manual_pal(unname(alpha_cols))
}
#' AAAS Journal Color Scales
#'
#' See \code{\link{pal_aaas}} for details.
#'
#' @inheritParams pal_aaas
#' @param ... additional parameters for \code{\link[ggplot2]{discrete_scale}}
#'
#' @export scale_color_aaas
#'
#' @importFrom ggplot2 discrete_scale
#'
#' @author Nan Xiao <\email{me@@nanx.me}> |
#' <\href{https://nanx.me}{https://nanx.me}>
#'
#' @rdname scale_aaas
#'
#' @examples
#' library("ggplot2")
#' data("diamonds")
#'
#' ggplot(subset(diamonds, carat >= 2.2),
#' aes(x = table, y = price, colour = cut)) +
#' geom_point(alpha = 0.7) +
#' geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
#' theme_bw() + scale_color_aaas()
#'
#' ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
#' aes(x = depth, fill = cut)) +
#' geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
#' theme_bw() + scale_fill_aaas()
scale_color_aaas = function (palette = c('default'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('colour', 'aaas', pal_aaas(palette, alpha), ...)
}
#' @export scale_colour_aaas
#' @rdname scale_aaas
scale_colour_aaas = scale_color_aaas
#' @export scale_fill_aaas
#' @importFrom ggplot2 discrete_scale
#' @rdname scale_aaas
scale_fill_aaas = function (palette = c('default'), alpha = 1, ...) {
palette = match.arg(palette)
discrete_scale('fill', 'aaas', pal_aaas(palette, alpha), ...)
}
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} ggsci/vignettes/ggsci.Rmd 0000644 0001762 0000144 00000045114 13276174703 015135 0 ustar ligges users ---
title: "Scientific Journal and Sci-Fi Themed
Color Palettes for ggplot2"
author: "Nan Xiao <>
Miaozhu Li <>"
date: "`r Sys.Date()`"
output:
rmarkdown::html_vignette:
toc: true
number_sections: true
css: ggsci.css
vignette: >
%\VignetteEngine{knitr::rmarkdown}
%\VignetteIndexEntry{Scientific Journal and Sci-Fi Themed Color Palettes for ggplot2}
---
# Introduction
> My eyes were finally opened and I understood nature.
>
> I learned at the same time to love it.
>
> --- Claude Monet
`ggsci` offers a collection of high-quality color palettes inspired by
colors used in scientific journals, data visualization libraries,
science fiction movies, and TV shows. The color palettes in `ggsci`
are available as `ggplot2` scales. For all the color palettes,
the corresponding scales are named as:
* `scale_color_palname()`
* `scale_fill_palname()`
We also provided aliases, such as `scale_colour_palname()` for
`scale_color_palname()`. All available color palettes are
summarized in the table below.
+-----------------+------------------------------+--------------------------------+----------------------+
| Name | Scales | Palette Types | Palette Generator |
+=================+==============================+================================+======================+
| NPG | `scale_color_npg()` | `"nrc"` | `pal_npg()` |
| | `scale_fill_npg()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| AAAS | `scale_color_aaas()` | `"default"` | `pal_aaas()` |
| | `scale_fill_aaas()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| NEJM | `scale_color_nejm()` | `"default"` | `pal_nejm()` |
| | `scale_fill_nejm()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| Lancet | `scale_color_lancet()` | `"lanonc"` | `pal_lancet()` |
| | `scale_fill_lancet()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| JAMA | `scale_color_jama()` | `"default"` | `pal_jama()` |
| | `scale_fill_jama()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| JCO | `scale_color_jco()` | `"default"` | `pal_jco()` |
| | `scale_fill_jco()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| UCSCGB | `scale_color_ucscgb()` | `"default"` | `pal_ucscgb()` |
| | `scale_fill_ucscgb()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| D3 | `scale_color_d3()`
| `"category10"` | `pal_d3()` |
| | `scale_fill_d3()` | `"category20"` | |
| | | `"category20b"` | |
| | | `"category20c"` | |
+-----------------+------------------------------+--------------------------------+----------------------+
| LocusZoom | `scale_color_locuszoom()` | `"default"` | `pal_locuszoom()` |
| | `scale_fill_locuszoom()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| IGV | `scale_color_igv()` | `"default"`
| `pal_igv()` |
| | `scale_fill_igv()` | `"alternating"` | |
+-----------------+------------------------------+--------------------------------+----------------------+
| UChicago | `scale_color_uchicago()` | `"default"`
| `pal_uchicago()` |
| | `scale_fill_uchicago()` | `"light"`
| |
| | | `"dark"` | |
+-----------------+------------------------------+--------------------------------+----------------------+
| Star Trek | `scale_color_startrek()` | `"uniform"` | `pal_startrek()` |
| | `scale_fill_startrek()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| Tron Legacy | `scale_color_tron()` | `"legacy"` | `pal_tron()` |
| | `scale_fill_tron()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| Futurama | `scale_color_futurama()` | `"planetexpress"` | `pal_futurama()` |
| | `scale_fill_futurama()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| Rick and Morty | `scale_color_rickandmorty()` | `"schwifty"` | `pal_rickandmorty()` |
| | `scale_fill_rickandmorty()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| The Simpsons | `scale_color_simpsons()` | `"springfield"` | `pal_simpsons()` |
| | `scale_fill_simpsons()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| GSEA | `scale_color_gsea()` | `"default"` | `pal_gsea()` |
| | `scale_fill_gsea()` | | |
+-----------------+------------------------------+--------------------------------+----------------------+
| Material Design | `scale_color_material()` | `"red"` `"pink"`
| `pal_material()` |
| | `scale_fill_material()` | `"purple"` `"deep-purple"`
| |
| | | `"indigo"` `"blue"`
| |
| | | `"light-blue"` `"cyan"`
| |
| | | `"teal"` `"green"`
| |
| | | `"light-green"` `"lime"`
| |
| | | `"yellow"` `"amber"`
| |
| | | `"orange"` `"deep-orange"`
| |
| | | `"brown"` `"grey"`
| |
| | | `"blue-grey"` | |
+-----------------+------------------------------+--------------------------------+----------------------+
# Discrete Color Palettes
We will use scatterplots with smooth curves, and bar plots to demonstrate
the discrete color palettes in `ggsci`.
```{r}
library("ggsci")
library("ggplot2")
library("gridExtra")
data("diamonds")
p1 = ggplot(subset(diamonds, carat >= 2.2),
aes(x = table, y = price, colour = cut)) +
geom_point(alpha = 0.7) +
geom_smooth(method = "loess", alpha = 0.05, size = 1, span = 1) +
theme_bw()
p2 = ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
aes(x = depth, fill = cut)) +
geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
theme_bw()
```
## NPG
The NPG palette is inspired by the plots in the journals published by
Nature Publishing Group:
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_npg = p1 + scale_color_npg()
p2_npg = p2 + scale_fill_npg()
grid.arrange(p1_npg, p2_npg, ncol = 2)
```
## AAAS
The AAAS palette is inspired by the plots in the journals published by
American Association for the Advancement of Science:
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_aaas = p1 + scale_color_aaas()
p2_aaas = p2 + scale_fill_aaas()
grid.arrange(p1_aaas, p2_aaas, ncol = 2)
```
## NEJM
The NEJM palette is inspired by the plots in
The New England Journal of Medicine:
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_nejm = p1 + scale_color_nejm()
p2_nejm = p2 + scale_fill_nejm()
grid.arrange(p1_nejm, p2_nejm, ncol = 2)
```
## Lancet
The Lancet palette is inspired by the plots in Lancet journals,
such as Lancet Oncology:
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_lancet = p1 + scale_color_lancet()
p2_lancet = p2 + scale_fill_lancet()
grid.arrange(p1_lancet, p2_lancet, ncol = 2)
```
## JAMA
The JAMA palette is inspired by the plots in
The Journal of the American Medical Association:
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_jama = p1 + scale_color_jama()
p2_jama = p2 + scale_fill_jama()
grid.arrange(p1_jama, p2_jama, ncol = 2)
```
## JCO
The JCO palette is inspired by the the plots in
Journal of Clinical Oncology:
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_jco = p1 + scale_color_jco()
p2_jco = p2 + scale_fill_jco()
grid.arrange(p1_jco, p2_jco, ncol = 2)
```
## UCSCGB
The UCSCGB palette is from the colors used by
[UCSC Genome Browser](https://genome.ucsc.edu) for
representing chromosomes. This palette has been intensively
used in visualizations produced by [Circos](http://circos.ca).
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_ucscgb = p1 + scale_color_ucscgb()
p2_ucscgb = p2 + scale_fill_ucscgb()
grid.arrange(p1_ucscgb, p2_ucscgb, ncol = 2)
```
## D3
The D3 palette is from the categorical colors used by
[D3.js](https://d3js.org) (version 3.x and before).
There are four palette types (`category10`, `category20`,
`category20b`, `category20c`) available.
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_d3 = p1 + scale_color_d3()
p2_d3 = p2 + scale_fill_d3()
grid.arrange(p1_d3, p2_d3, ncol = 2)
```
## LocusZoom
The LocusZoom palette is based on the colors used by
[LocusZoom](http://locuszoom.org/).
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_locuszoom = p1 + scale_color_locuszoom()
p2_locuszoom = p2 + scale_fill_locuszoom()
grid.arrange(p1_locuszoom, p2_locuszoom, ncol = 2)
```
## IGV
The IGV palette is from the colors used by
[Integrative Genomics Viewer](http://software.broadinstitute.org/software/igv/)
for representing chromosomes. There are two palette types
(`default`, `alternating`) available.
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_igv_default = p1 + scale_color_igv()
p2_igv_default = p2 + scale_fill_igv()
grid.arrange(p1_igv_default, p2_igv_default, ncol = 2)
```
## UChicago
The UChicago palette is based on
[the colors](https://news.uchicago.edu/sites/default/files/attachments/_uchicago.identity.guidelines.pdf)
used by the University of Chicago.
There are three palette types (`default`, `light`, `dark`) available.
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_uchicago = p1 + scale_color_uchicago()
p2_uchicago = p2 + scale_fill_uchicago()
grid.arrange(p1_uchicago, p2_uchicago, ncol = 2)
```
## Star Trek
This palette is inspired by the (uniform) colors in Star Trek:
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_startrek = p1 + scale_color_startrek()
p2_startrek = p2 + scale_fill_startrek()
grid.arrange(p1_startrek, p2_startrek, ncol = 2)
```
## Tron Legacy
This palette is inspired by the colors used in Tron Legacy.
It is suitable for displaying data when using a dark theme:
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_tron = p1 + theme_dark() + theme(
panel.background = element_rect(fill = "#2D2D2D"),
legend.key = element_rect(fill = "#2D2D2D")) +
scale_color_tron()
p2_tron = p2 + theme_dark() + theme(
panel.background = element_rect(fill = "#2D2D2D")) +
scale_fill_tron()
grid.arrange(p1_tron, p2_tron, ncol = 2)
```
## Futurama
This palette is inspired by the colors used in the TV show Futurama:
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_futurama = p1 + scale_color_futurama()
p2_futurama = p2 + scale_fill_futurama()
grid.arrange(p1_futurama, p2_futurama, ncol = 2)
```
## Rick and Morty
This palette is inspired by the colors used in the TV show Rick and Morty:
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_rickandmorty = p1 + scale_color_rickandmorty()
p2_rickandmorty = p2 + scale_fill_rickandmorty()
grid.arrange(p1_rickandmorty, p2_rickandmorty, ncol = 2)
```
## The Simpsons
This palette is inspired by the colors used in the TV show
The Simpsons:
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p1_simpsons = p1 + scale_color_simpsons()
p2_simpsons = p2 + scale_fill_simpsons()
grid.arrange(p1_simpsons, p2_simpsons, ncol = 2)
```
# Continuous Color Palettes
We will use a correlation matrix visualization (a special type of heatmap)
to demonstrate the continuous color palettes in `ggsci`.
```{r}
library("reshape2")
data("mtcars")
cor = cor(unname(cbind(mtcars, mtcars, mtcars, mtcars)))
cor_melt = melt(cor)
p3 = ggplot(cor_melt,
aes(x = Var1, y = Var2, fill = value)) +
geom_tile(colour = "black", size = 0.3) +
theme_bw() +
theme(axis.title.x = element_blank(),
axis.title.y = element_blank())
```
## GSEA
The GSEA palette (continuous) is inspired by the heatmaps generated by
[GSEA GenePattern](https://software.broadinstitute.org/cancer/software/genepattern/).
```{r, fig.width = 10.67, fig.height = 4, out.width = 800, out.height = 300, dpi = 150}
p3_gsea = p3 + scale_fill_gsea()
p3_gsea_inv = p3 + scale_fill_gsea(reverse = TRUE)
grid.arrange(p3_gsea, p3_gsea_inv, ncol = 2)
```
## Material Design
The Material Design color palettes are from the [material design
color guidelines](https://material.io/guidelines/style/color.html).
We generate a random matrix first:
```{r}
library("reshape2")
set.seed(42)
k = 9
x = diag(k)
x[upper.tri(x)] = runif(sum(1:(k - 1)), 0, 1)
x_melt = melt(x)
p4 = ggplot(x_melt, aes(x = Var1, y = Var2, fill = value)) +
geom_tile(colour = "black", size = 0.3) +
scale_x_continuous(expand = c(0, 0)) +
scale_y_continuous(expand = c(0, 0)) +
theme_bw() + theme(
legend.position = "none", plot.background = element_blank(),
axis.line = element_blank(), axis.ticks = element_blank(),
axis.text.x = element_blank(), axis.text.y = element_blank(),
axis.title.x = element_blank(), axis.title.y = element_blank(),
panel.background = element_blank(), panel.border = element_blank(),
panel.grid.major = element_blank(), panel.grid.minor = element_blank())
```
Plot the matrix with the 19 material design color palettes:
```{r, fig.width = 10.67, fig.height = 7.12, out.width = 800, out.height = 533, dpi = 150}
grid.arrange(
p4 + scale_fill_material("red"), p4 + scale_fill_material("pink"),
p4 + scale_fill_material("purple"), p4 + scale_fill_material("deep-purple"),
p4 + scale_fill_material("indigo"), p4 + scale_fill_material("blue"),
p4 + scale_fill_material("light-blue"), p4 + scale_fill_material("cyan"),
p4 + scale_fill_material("teal"), p4 + scale_fill_material("green"),
p4 + scale_fill_material("light-green"), p4 + scale_fill_material("lime"),
p4 + scale_fill_material("yellow"), p4 + scale_fill_material("amber"),
p4 + scale_fill_material("orange"), p4 + scale_fill_material("deep-orange"),
p4 + scale_fill_material("brown"), p4 + scale_fill_material("grey"),
p4 + scale_fill_material("blue-grey"),
ncol = 6)
```
From the figure above, we can see that even though an identical matrix
was visualized by all plots, some palettes are more preferrable
than the others because our eyes are more sensitive to the changes
of their saturation levels.
# Non-ggplot2 Graphics
To apply the color palettes in `ggsci` to other graphics systems
(such as base graphics and lattice graphics), simply use the
palette generator functions in the table above. For example:
```{r, fig.width = 6.67, fig.height = 6.67, out.width = 500, out.height = 500, dpi = 150}
mypal = pal_npg("nrc", alpha = 0.7)(9)
mypal
library("scales")
show_col(mypal)
```
You will be able to use the generated hex color codes for such
graphics systems accordingly. The transparent level of the
entire palette is easily adjustable via the argument `"alpha"`
in every generator or scale function.
# Discussion
Please note some of the palettes might not be the best choice for certain
purposes, such as color-blind safe, photocopy safe, or print friendly.
If you do have such considerations, you might want to check out
color palettes like [ColorBrewer](http://colorbrewer2.org)
and [viridis](https://cran.r-project.org/package=viridis).
The color palettes in this package are solely created for research purposes.
The authors are not responsible for the usage of such palettes.
ggsci/README.md 0000644 0001762 0000144 00000005610 13274177012 012633 0 ustar ligges users # ggsci 
[](https://travis-ci.org/road2stat/ggsci)
[](https://ci.appveyor.com/project/road2stat/ggsci)
[](https://cran.r-project.org/package=ggsci)
[](https://cran.r-project.org/package=ggsci)
`ggsci` offers a collection of `ggplot2` color palettes inspired by scientific journals, data visualization libraries, science fiction movies, and TV shows.
## Installation
Install `ggsci` from CRAN:
```r
install.packages("ggsci")
```
Or try the development version on GitHub:
```r
# install.packages("devtools")
devtools::install_github("road2stat/ggsci")
```
[Browse the vignette](https://nanx.me/ggsci/articles/ggsci.html) (or open with `vignette("ggsci")` in R) for a quick-start guide.
## Gallery
### NPG
### AAAS
### NEJM
### Lancet
### JAMA
### JCO
### UCSCGB
### D3
### LocusZoom
### IGV
### UChicago
### Star Trek
### Tron Legacy
### Futurama
### Rick and Morty
### The Simpsons
### GSEA
### Material Design
## Contribute
To contribute to this project, please take a look at the [Contributing Guidelines](CONTRIBUTING.md) first. Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms.
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0 @|; ;Eԃײfе7\tKCDGןNP=߰(Lے;.EFWd)N1=K NZjC7LP sg\st*Ö>ӯ2Jh+VBb@&}dY3h{TH}&I[ۺ ~>
gh(d{hęeqn~ 6 ggsci/DESCRIPTION 0000644 0001762 0000144 00000002112 13276211255 013054 0 ustar ligges users Package: ggsci
Type: Package
Title: Scientific Journal and Sci-Fi Themed Color Palettes for
'ggplot2'
Version: 2.9
Authors@R: c(
person("Nan", "Xiao", email = "me@nanx.me", role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-0250-5673")),
person("Miaozhu", "Li", email = "miaozhu.li@duke.edu", role = "ctb"))
Maintainer: Nan Xiao
Description: A collection of 'ggplot2' color palettes inspired by
plots in scientific journals, data visualization libraries,
science fiction movies, and TV shows.
License: GPL-3 | file LICENSE
LazyData: TRUE
VignetteBuilder: knitr
URL: https://nanx.me/ggsci/, https://github.com/road2stat/ggsci
BugReports: https://github.com/road2stat/ggsci/issues
Depends: R (>= 3.0.2)
Imports: grDevices, scales, ggplot2 (>= 2.0.0)
Suggests: knitr, rmarkdown, gridExtra, reshape2
Encoding: UTF-8
RoxygenNote: 6.0.1.9000
NeedsCompilation: no
Packaged: 2018-05-14 02:52:33 UTC; nanx
Author: Nan Xiao [aut, cre] (),
Miaozhu Li [ctb]
Repository: CRAN
Date/Publication: 2018-05-14 04:38:05 UTC
ggsci/man/ 0000755 0001762 0000144 00000000000 13221611720 012114 5 ustar ligges users ggsci/man/scale_igv.Rd 0000644 0001762 0000144 00000003123 13221611720 014336 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-igv.R
\name{scale_color_igv}
\alias{scale_color_igv}
\alias{scale_colour_igv}
\alias{scale_fill_igv}
\title{Integrative Genomics Viewer (IGV) Color Scales}
\usage{
scale_color_igv(palette = c("default", "alternating"), alpha = 1, ...)
scale_colour_igv(palette = c("default", "alternating"), alpha = 1, ...)
scale_fill_igv(palette = c("default", "alternating"), alpha = 1, ...)
}
\arguments{
\item{palette}{Palette type.
There are two available options:
\code{"default"} (51-color palette);
\code{"alternating"} (2-color palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}}
}
\description{
See \code{\link{pal_igv}} for details.
}
\examples{
library("ggplot2")
data("diamonds")
p1 = ggplot(subset(diamonds, carat >= 2.2),
aes(x = table, y = price, colour = cut)) +
geom_point(alpha = 0.7) +
geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
theme_bw()
p2 = ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
aes(x = depth, fill = cut)) +
geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
theme_bw()
p1 + scale_color_igv()
p2 + scale_fill_igv()
p1 + scale_colour_manual(
values = rep(pal_igv("alternating")(2), times = 3))
p2 + scale_fill_manual(
values = rep(pal_igv("alternating")(2), times = 3))
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/ggsci-package.Rd 0000644 0001762 0000144 00000001044 13221611720 015067 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/ggsci-package.R
\docType{package}
\name{ggsci-package}
\alias{ggsci-package}
\title{Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2'}
\description{
Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2'
}
\details{
Opened the vignette via \code{vignette("ggsci")}.
\tabular{ll}{ Package: \tab ggsci\cr
Type: \tab Package\cr
License: \tab GPL-3\cr }
}
\author{
Nan Xiao <\email{me@nanx.me}>
Miaozhu Li <\email{miaozhu.li@duke.edu}>
}
ggsci/man/pal_d3.Rd 0000644 0001762 0000144 00000002004 13221611720 013541 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-d3.R
\name{pal_d3}
\alias{pal_d3}
\title{D3.js Color Palettes}
\usage{
pal_d3(palette = c("category10", "category20", "category20b", "category20c"),
alpha = 1)
}
\arguments{
\item{palette}{Palette type.
There are 4 available options:
\code{"category10"} (10-color palette);
\code{"category20"} (20-color palette);
\code{"category20b"} (20-color palette);
\code{"category20c"} (20-color palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
}
\description{
Color palettes based on the colors used by D3.js.
}
\examples{
library("scales")
show_col(pal_d3("category10")(10))
show_col(pal_d3("category20")(20))
show_col(pal_d3("category20b")(20))
show_col(pal_d3("category20c")(20))
}
\references{
\url{https://github.com/d3/d3-3.x-api-reference/blob/master/Ordinal-Scales.md}
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/pal_ucscgb.Rd 0000644 0001762 0000144 00000001356 13221611720 014512 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-ucscgb.R
\name{pal_ucscgb}
\alias{pal_ucscgb}
\title{UCSC Genome Browser Color Palette}
\usage{
pal_ucscgb(palette = c("default"), alpha = 1)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"default"}
(26-color palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
}
\description{
Color palette from UCSC Genome Browser chromosome colors.
}
\examples{
library("scales")
show_col(pal_ucscgb("default")(26))
show_col(pal_ucscgb("default", alpha = 0.6)(26))
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/pal_igv.Rd 0000644 0001762 0000144 00000001772 13221611720 014033 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-igv.R
\name{pal_igv}
\alias{pal_igv}
\title{Integrative Genomics Viewer (IGV) Color Palettes}
\usage{
pal_igv(palette = c("default", "alternating"), alpha = 1)
}
\arguments{
\item{palette}{Palette type.
There are two available options:
\code{"default"} (51-color palette);
\code{"alternating"} (2-color palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
}
\description{
Color palettes based on the colors used by
Integrative Genomics Viewer (IGV).
}
\examples{
library("scales")
show_col(pal_igv("default")(51))
show_col(pal_igv("alternating")(2))
}
\references{
James T. Robinson, Helga Thorvaldsd\'{o}ttir, Wendy Winckler,
Mitchell Guttman, Eric S. Lander, Gad Getz, Jill P. Mesirov.
Integrative Genomics Viewer. \emph{Nature Biotechnology} 29, 24--26 (2011).
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/pal_simpsons.Rd 0000644 0001762 0000144 00000001415 13221611720 015113 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-simpsons.R
\name{pal_simpsons}
\alias{pal_simpsons}
\title{The Simpsons Color Palettes}
\usage{
pal_simpsons(palette = c("springfield"), alpha = 1)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"springfield"}
(16-color palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
}
\description{
Color palettes inspired by the colors used in \emph{The Simpsons}.
}
\examples{
library("scales")
show_col(pal_simpsons("springfield")(16))
show_col(pal_simpsons("springfield", alpha = 0.6)(16))
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/scale_nejm.Rd 0000644 0001762 0000144 00000002471 13221611720 014507 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-nejm.R
\name{scale_color_nejm}
\alias{scale_color_nejm}
\alias{scale_colour_nejm}
\alias{scale_fill_nejm}
\title{NEJM Color Scales}
\usage{
scale_color_nejm(palette = c("default"), alpha = 1, ...)
scale_colour_nejm(palette = c("default"), alpha = 1, ...)
scale_fill_nejm(palette = c("default"), alpha = 1, ...)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"default"}
(8-color palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}}
}
\description{
See \code{\link{pal_nejm}} for details.
}
\examples{
library("ggplot2")
data("diamonds")
ggplot(subset(diamonds, carat >= 2.2),
aes(x = table, y = price, colour = cut)) +
geom_point(alpha = 0.7) +
geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
theme_bw() + scale_color_nejm()
ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
aes(x = depth, fill = cut)) +
geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
theme_bw() + scale_fill_nejm()
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/rgb_material.Rd 0000644 0001762 0000144 00000003204 13221611720 015032 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/continuous-material.R
\name{rgb_material}
\alias{rgb_material}
\title{Material Design Color Palettes}
\usage{
rgb_material(palette = c("red", "pink", "purple", "deep-purple", "indigo",
"blue", "light-blue", "cyan", "teal", "green", "light-green", "lime",
"yellow", "amber", "orange", "deep-orange", "brown", "grey", "blue-grey"),
n = 10, alpha = 1, reverse = FALSE)
}
\arguments{
\item{palette}{Palette type.
There are 19 available options:
\itemize{
\item \code{"red"}
\item \code{"pink"}
\item \code{"purple"}
\item \code{"deep-purple"}
\item \code{"indigo"}
\item \code{"blue"}
\item \code{"light-blue"}
\item \code{"cyan"}
\item \code{"teal"}
\item \code{"green"}
\item \code{"light-green"}
\item \code{"lime"}
\item \code{"yellow"}
\item \code{"amber"}
\item \code{"orange"},
\item \code{"deep-orange"}
\item \code{"brown"}
\item \code{"grey"}
\item \code{"blue-grey"}}
See the \href{https://material.io/guidelines/style/color.html}{material
design color guidelines} for details.}
\item{n}{Number of individual colors to be generated.}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
\item{reverse}{Logical. Should the order of the colors be reversed?}
}
\description{
The Material Design color palettes.
}
\examples{
library("scales")
show_col(pal_material("indigo")(10))
show_col(pal_material("indigo", n = 30, alpha = 0.6, reverse = TRUE)(30))
}
\references{
\url{https://material.io/guidelines/style/color.html}
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/pal_tron.Rd 0000644 0001762 0000144 00000001334 13221611720 014222 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-tron.R
\name{pal_tron}
\alias{pal_tron}
\title{Tron Legacy Color Palettes}
\usage{
pal_tron(palette = c("legacy"), alpha = 1)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"legacy"}
(7-color palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
}
\description{
Color palettes inspired by the colors used in \emph{Tron Legacy}.
}
\examples{
library("scales")
show_col(pal_tron("legacy")(7))
show_col(pal_tron("legacy", alpha = 0.6)(7))
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/scale_jco.Rd 0000644 0001762 0000144 00000002507 13221611720 014331 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-jco.R
\name{scale_color_jco}
\alias{scale_color_jco}
\alias{scale_colour_jco}
\alias{scale_fill_jco}
\title{Journal of Clinical Oncology Color Scales}
\usage{
scale_color_jco(palette = c("default"), alpha = 1, ...)
scale_colour_jco(palette = c("default"), alpha = 1, ...)
scale_fill_jco(palette = c("default"), alpha = 1, ...)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"default"}
(10-color palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}}
}
\description{
See \code{\link{pal_jco}} for details.
}
\examples{
library("ggplot2")
data("diamonds")
ggplot(subset(diamonds, carat >= 2.2),
aes(x = table, y = price, colour = cut)) +
geom_point(alpha = 0.7) +
geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
theme_bw() + scale_color_jco()
ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
aes(x = depth, fill = cut)) +
geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
theme_bw() + scale_fill_jco()
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/pal_lancet.Rd 0000644 0001762 0000144 00000001441 13221611720 014505 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-lancet.R
\name{pal_lancet}
\alias{pal_lancet}
\title{Lancet Journal Color Palettes}
\usage{
pal_lancet(palette = c("lanonc"), alpha = 1)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"lanonc"}
(9-color palette inspired by \emph{Lancet Oncology}).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
}
\description{
Color palettes inspired by plots in Lancet journals,
such as \emph{Lancet Oncology}.
}
\examples{
library("scales")
show_col(pal_lancet("lanonc")(9))
show_col(pal_lancet("lanonc", alpha = 0.6)(9))
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/pal_jco.Rd 0000644 0001762 0000144 00000001364 13221611720 014016 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-jco.R
\name{pal_jco}
\alias{pal_jco}
\title{Journal of Clinical Oncology Color Palettes}
\usage{
pal_jco(palette = c("default"), alpha = 1)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"default"}
(10-color palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
}
\description{
Color palette inspired by plots in \emph{Journal of Clinical Oncology}.
}
\examples{
library("scales")
show_col(pal_jco("default")(10))
show_col(pal_jco("default", alpha = 0.6)(10))
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/pal_nejm.Rd 0000644 0001762 0000144 00000001346 13221611720 014174 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-nejm.R
\name{pal_nejm}
\alias{pal_nejm}
\title{NEJM Color Palettes}
\usage{
pal_nejm(palette = c("default"), alpha = 1)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"default"}
(8-color palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
}
\description{
Color palette inspired by plots in
\emph{The New England Journal of Medicine}.
}
\examples{
library("scales")
show_col(pal_nejm("default")(8))
show_col(pal_nejm("default", alpha = 0.6)(8))
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/scale_tron.Rd 0000644 0001762 0000144 00000002765 13221611720 014546 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-tron.R
\name{scale_color_tron}
\alias{scale_color_tron}
\alias{scale_colour_tron}
\alias{scale_fill_tron}
\title{Tron Legacy Color Scales}
\usage{
scale_color_tron(palette = c("legacy"), alpha = 1, ...)
scale_colour_tron(palette = c("legacy"), alpha = 1, ...)
scale_fill_tron(palette = c("legacy"), alpha = 1, ...)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"legacy"}
(7-color palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}}
}
\description{
See \code{\link{pal_tron}} for details.
}
\examples{
library("ggplot2")
data("diamonds")
ggplot(subset(diamonds, carat >= 2.2),
aes(x = table, y = price, colour = cut)) +
geom_point(alpha = 0.7) +
geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
theme_dark() + theme(
panel.background = element_rect(fill = "#2D2D2D"),
legend.key = element_rect(fill = "#2D2D2D")) +
scale_color_tron()
ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
aes(x = depth, fill = cut)) +
geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
theme_dark() + theme(
panel.background = element_rect(fill = "#2D2D2D")) +
scale_fill_tron()
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/scale_npg.Rd 0000644 0001762 0000144 00000002517 13221611720 014343 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-npg.R
\name{scale_color_npg}
\alias{scale_color_npg}
\alias{scale_colour_npg}
\alias{scale_fill_npg}
\title{NPG Journal Color Scales}
\usage{
scale_color_npg(palette = c("nrc"), alpha = 1, ...)
scale_colour_npg(palette = c("nrc"), alpha = 1, ...)
scale_fill_npg(palette = c("nrc"), alpha = 1, ...)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"nrc"}
(10-color palette inspired by \emph{Nature Reviews Cancer}).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}}
}
\description{
See \code{\link{pal_npg}} for details.
}
\examples{
library("ggplot2")
data("diamonds")
ggplot(subset(diamonds, carat >= 2.2),
aes(x = table, y = price, colour = cut)) +
geom_point(alpha = 0.7) +
geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
theme_bw() + scale_color_npg()
ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
aes(x = depth, fill = cut)) +
geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
theme_bw() + scale_fill_npg()
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/pal_locuszoom.Rd 0000644 0001762 0000144 00000001626 13221611720 015276 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-locuszoom.R
\name{pal_locuszoom}
\alias{pal_locuszoom}
\title{LocusZoom Color Palette}
\usage{
pal_locuszoom(palette = c("default"), alpha = 1)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"default"}
(7-color palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
}
\description{
Color palettes based on the colors used by LocusZoom.
}
\examples{
library("scales")
show_col(pal_locuszoom("default")(7))
show_col(pal_locuszoom("default", alpha = 0.6)(7))
}
\references{
Pruim, Randall J., et al. (2010). LocusZoom: regional visualization of
genome-wide association scan results. \emph{Bioinformatics},
26(18), 2336--2337.
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/scale_ucscgb.Rd 0000644 0001762 0000144 00000002537 13221611720 015027 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-ucscgb.R
\name{scale_color_ucscgb}
\alias{scale_color_ucscgb}
\alias{scale_colour_ucscgb}
\alias{scale_fill_ucscgb}
\title{UCSC Genome Browser Color Scales}
\usage{
scale_color_ucscgb(palette = c("default"), alpha = 1, ...)
scale_colour_ucscgb(palette = c("default"), alpha = 1, ...)
scale_fill_ucscgb(palette = c("default"), alpha = 1, ...)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"default"}
(26-color palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}}
}
\description{
See \code{\link{pal_ucscgb}} for details.
}
\examples{
library("ggplot2")
data("diamonds")
ggplot(subset(diamonds, carat >= 2.2),
aes(x = table, y = price, colour = cut)) +
geom_point(alpha = 0.7) +
geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
theme_bw() + scale_color_ucscgb()
ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
aes(x = depth, fill = cut)) +
geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
theme_bw() + scale_fill_ucscgb()
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/pal_rickandmorty.Rd 0000644 0001762 0000144 00000001435 13221611720 015750 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-rickandmorty.R
\name{pal_rickandmorty}
\alias{pal_rickandmorty}
\title{Rick and Morty Color Palettes}
\usage{
pal_rickandmorty(palette = c("schwifty"), alpha = 1)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"schwifty"}
(12-color palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
}
\description{
Color palettes inspired by the colors used in \emph{Rick and Morty}.
}
\examples{
library("scales")
show_col(pal_rickandmorty("schwifty")(12))
show_col(pal_rickandmorty("schwifty", alpha = 0.6)(12))
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/scale_rickandmorty.Rd 0000644 0001762 0000144 00000002640 13221611720 016262 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-rickandmorty.R
\name{scale_color_rickandmorty}
\alias{scale_color_rickandmorty}
\alias{scale_colour_rickandmorty}
\alias{scale_fill_rickandmorty}
\title{Rick and Morty Color Scales}
\usage{
scale_color_rickandmorty(palette = c("schwifty"), alpha = 1, ...)
scale_colour_rickandmorty(palette = c("schwifty"), alpha = 1, ...)
scale_fill_rickandmorty(palette = c("schwifty"), alpha = 1, ...)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"schwifty"}
(12-color palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}}
}
\description{
See \code{\link{pal_rickandmorty}} for details.
}
\examples{
library("ggplot2")
data("diamonds")
ggplot(subset(diamonds, carat >= 2.2),
aes(x = table, y = price, colour = cut)) +
geom_point(alpha = 0.7) +
geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
theme_bw() + scale_color_rickandmorty()
ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
aes(x = depth, fill = cut)) +
geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
theme_bw() + scale_fill_rickandmorty()
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/scale_aaas.Rd 0000644 0001762 0000144 00000002535 13221611720 014464 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-aaas.R
\name{scale_color_aaas}
\alias{scale_color_aaas}
\alias{scale_colour_aaas}
\alias{scale_fill_aaas}
\title{AAAS Journal Color Scales}
\usage{
scale_color_aaas(palette = c("default"), alpha = 1, ...)
scale_colour_aaas(palette = c("default"), alpha = 1, ...)
scale_fill_aaas(palette = c("default"), alpha = 1, ...)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"default"}
(10-color palette inspired by \emph{Science}).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}}
}
\description{
See \code{\link{pal_aaas}} for details.
}
\examples{
library("ggplot2")
data("diamonds")
ggplot(subset(diamonds, carat >= 2.2),
aes(x = table, y = price, colour = cut)) +
geom_point(alpha = 0.7) +
geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
theme_bw() + scale_color_aaas()
ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
aes(x = depth, fill = cut)) +
geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
theme_bw() + scale_fill_aaas()
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/rgb_gsea.Rd 0000644 0001762 0000144 00000002261 13221611720 014155 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/continuous-gsea.R
\name{rgb_gsea}
\alias{rgb_gsea}
\title{The GSEA GenePattern Color Palettes}
\usage{
rgb_gsea(palette = c("default"), n = 12, alpha = 1, reverse = FALSE)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"default"}
(continuous palette with 12 base colors).}
\item{n}{Number of individual colors to be generated.}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
\item{reverse}{Logical. Should the order of the colors be reversed?}
}
\description{
Color palette inspired by the colors used in the
heatmaps plotted by GSEA GenePattern.
}
\note{
The 12 base colors used in this palette are derived from
\href{ftp://ftp.broad.mit.edu/pub/genepattern/modules/HeatMapImage/broad.mit.edu:cancer.software.genepattern.module.analysis/00032/6/HeatMapImage.pdf}{this document}.
}
\examples{
library("scales")
show_col(pal_gsea("default")(12))
show_col(pal_gsea("default", n = 30, alpha = 0.6, reverse = TRUE)(30))
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/pal_jama.Rd 0000644 0001762 0000144 00000001431 13221611720 014146 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-jama.R
\name{pal_jama}
\alias{pal_jama}
\title{Journal of the American Medical Association Color Palettes}
\usage{
pal_jama(palette = c("default"), alpha = 1)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"default"}
(7-color palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
}
\description{
Color palette inspired by plots in
\emph{The Journal of the American Medical Association}.
}
\examples{
library("scales")
show_col(pal_jama("default")(7))
show_col(pal_jama("default", alpha = 0.6)(7))
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/scale_futurama.Rd 0000644 0001762 0000144 00000002606 13221611720 015402 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-futurama.R
\name{scale_color_futurama}
\alias{scale_color_futurama}
\alias{scale_colour_futurama}
\alias{scale_fill_futurama}
\title{The Futurama Color Scales}
\usage{
scale_color_futurama(palette = c("planetexpress"), alpha = 1, ...)
scale_colour_futurama(palette = c("planetexpress"), alpha = 1, ...)
scale_fill_futurama(palette = c("planetexpress"), alpha = 1, ...)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"planetexpress"}
(12-color palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}}
}
\description{
See \code{\link{pal_futurama}} for details.
}
\examples{
library("ggplot2")
data("diamonds")
ggplot(subset(diamonds, carat >= 2.2),
aes(x = table, y = price, colour = cut)) +
geom_point(alpha = 0.7) +
geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
theme_bw() + scale_color_futurama()
ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
aes(x = depth, fill = cut)) +
geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
theme_bw() + scale_fill_futurama()
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/scale_gsea.Rd 0000644 0001762 0000144 00000002373 13221611720 014476 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/continuous-gsea.R
\name{scale_color_gsea}
\alias{scale_color_gsea}
\alias{scale_colour_gsea}
\alias{scale_fill_gsea}
\title{The GSEA GenePattern Color Scales}
\usage{
scale_color_gsea(palette = c("default"), alpha = 1, reverse = FALSE, ...)
scale_colour_gsea(palette = c("default"), alpha = 1, reverse = FALSE, ...)
scale_fill_gsea(palette = c("default"), alpha = 1, reverse = FALSE, ...)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"default"}
(continuous palette with 12 base colors).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
\item{reverse}{Logical. Should the order of the colors be reversed?}
\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}}
}
\description{
See \code{\link{pal_gsea}} for details.
}
\examples{
library("ggplot2")
library("reshape2")
data("mtcars")
cor = cor(mtcars)
cor_melt = melt(cor)
ggplot(cor_melt,
aes(x = Var1, y = Var2, fill = value)) +
geom_tile(colour = "black", size = 0.3) +
theme_bw() + scale_fill_gsea()
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/scale_material.Rd 0000644 0001762 0000144 00000004503 13221611720 015352 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/continuous-material.R
\name{scale_color_material}
\alias{scale_color_material}
\alias{scale_colour_material}
\alias{scale_fill_material}
\title{Material Design Color Palettes}
\usage{
scale_color_material(palette = c("red", "pink", "purple", "deep-purple",
"indigo", "blue", "light-blue", "cyan", "teal", "green", "light-green",
"lime", "yellow", "amber", "orange", "deep-orange", "brown", "grey",
"blue-grey"), alpha = 1, reverse = FALSE, ...)
scale_colour_material(palette = c("red", "pink", "purple", "deep-purple",
"indigo", "blue", "light-blue", "cyan", "teal", "green", "light-green",
"lime", "yellow", "amber", "orange", "deep-orange", "brown", "grey",
"blue-grey"), alpha = 1, reverse = FALSE, ...)
scale_fill_material(palette = c("red", "pink", "purple", "deep-purple",
"indigo", "blue", "light-blue", "cyan", "teal", "green", "light-green",
"lime", "yellow", "amber", "orange", "deep-orange", "brown", "grey",
"blue-grey"), alpha = 1, reverse = FALSE, ...)
}
\arguments{
\item{palette}{Palette type.
There are 19 available options:
\itemize{
\item \code{"red"}
\item \code{"pink"}
\item \code{"purple"}
\item \code{"deep-purple"}
\item \code{"indigo"}
\item \code{"blue"}
\item \code{"light-blue"}
\item \code{"cyan"}
\item \code{"teal"}
\item \code{"green"}
\item \code{"light-green"}
\item \code{"lime"}
\item \code{"yellow"}
\item \code{"amber"}
\item \code{"orange"},
\item \code{"deep-orange"}
\item \code{"brown"}
\item \code{"grey"}
\item \code{"blue-grey"}}
See the \href{https://material.io/guidelines/style/color.html}{material
design color guidelines} for details.}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
\item{reverse}{Logical. Should the order of the colors be reversed?}
\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}}
}
\description{
See \code{\link{pal_material}} for details.
}
\examples{
library("ggplot2")
library("reshape2")
data("mtcars")
cor = abs(cor(mtcars))
cor_melt = melt(cor)
ggplot(cor_melt,
aes(x = Var1, y = Var2, fill = value)) +
geom_tile(colour = "black", size = 0.3) +
theme_bw() + scale_fill_material("blue-grey")
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/scale_simpsons.Rd 0000644 0001762 0000144 00000002576 13221611720 015437 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-simpsons.R
\name{scale_color_simpsons}
\alias{scale_color_simpsons}
\alias{scale_colour_simpsons}
\alias{scale_fill_simpsons}
\title{The Simpsons Color Scales}
\usage{
scale_color_simpsons(palette = c("springfield"), alpha = 1, ...)
scale_colour_simpsons(palette = c("springfield"), alpha = 1, ...)
scale_fill_simpsons(palette = c("springfield"), alpha = 1, ...)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"springfield"}
(16-color palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}}
}
\description{
See \code{\link{pal_simpsons}} for details.
}
\examples{
library("ggplot2")
data("diamonds")
ggplot(subset(diamonds, carat >= 2.2),
aes(x = table, y = price, colour = cut)) +
geom_point(alpha = 0.7) +
geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
theme_bw() + scale_color_simpsons()
ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
aes(x = depth, fill = cut)) +
geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
theme_bw() + scale_fill_simpsons()
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/pal_uchicago.Rd 0000644 0001762 0000144 00000001743 13276174440 015043 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-uchicago.R
\name{pal_uchicago}
\alias{pal_uchicago}
\title{The University of Chicago Color Palettes}
\usage{
pal_uchicago(palette = c("default", "light", "dark"), alpha = 1)
}
\arguments{
\item{palette}{Palette type.
There are 3 available options:
\code{"default"} (9-color palette);
\code{"light"} (9-color light palette);
\code{"dark"} (9-color dark palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
}
\description{
Color palettes based on the colors used by the University of Chicago.
}
\examples{
library("scales")
show_col(pal_uchicago("default")(9))
show_col(pal_uchicago("light")(9))
show_col(pal_uchicago("dark")(9))
}
\references{
\url{https://news.uchicago.edu/sites/default/files/attachments/_uchicago.identity.guidelines.pdf}
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/pal_futurama.Rd 0000644 0001762 0000144 00000001421 13221611720 015061 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-futurama.R
\name{pal_futurama}
\alias{pal_futurama}
\title{The Futurama Color Palettes}
\usage{
pal_futurama(palette = c("planetexpress"), alpha = 1)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"planetexpress"}
(12-color palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
}
\description{
Color palettes inspired by the colors used in \emph{Futurama}.
}
\examples{
library("scales")
show_col(pal_futurama("planetexpress")(12))
show_col(pal_futurama("planetexpress", alpha = 0.6)(12))
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/scale_locuszoom.Rd 0000644 0001762 0000144 00000002565 13221611720 015614 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-locuszoom.R
\name{scale_color_locuszoom}
\alias{scale_color_locuszoom}
\alias{scale_colour_locuszoom}
\alias{scale_fill_locuszoom}
\title{LocusZoom Color Scales}
\usage{
scale_color_locuszoom(palette = c("default"), alpha = 1, ...)
scale_colour_locuszoom(palette = c("default"), alpha = 1, ...)
scale_fill_locuszoom(palette = c("default"), alpha = 1, ...)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"default"}
(7-color palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}}
}
\description{
See \code{\link{pal_locuszoom}} for details.
}
\examples{
library("ggplot2")
data("diamonds")
ggplot(subset(diamonds, carat >= 2.2),
aes(x = table, y = price, colour = cut)) +
geom_point(alpha = 0.7) +
geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
theme_bw() + scale_color_locuszoom()
ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
aes(x = depth, fill = cut)) +
geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
theme_bw() + scale_fill_locuszoom()
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/pal_material.Rd 0000644 0001762 0000144 00000003077 13221611720 015044 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/continuous-material.R
\name{pal_material}
\alias{pal_material}
\title{Material Design Color Palettes}
\usage{
pal_material(palette = c("red", "pink", "purple", "deep-purple", "indigo",
"blue", "light-blue", "cyan", "teal", "green", "light-green", "lime",
"yellow", "amber", "orange", "deep-orange", "brown", "grey", "blue-grey"),
n = 10, alpha = 1, reverse = FALSE)
}
\arguments{
\item{palette}{Palette type.
There are 19 available options:
\itemize{
\item \code{"red"}
\item \code{"pink"}
\item \code{"purple"}
\item \code{"deep-purple"}
\item \code{"indigo"}
\item \code{"blue"}
\item \code{"light-blue"}
\item \code{"cyan"}
\item \code{"teal"}
\item \code{"green"}
\item \code{"light-green"}
\item \code{"lime"}
\item \code{"yellow"}
\item \code{"amber"}
\item \code{"orange"},
\item \code{"deep-orange"}
\item \code{"brown"}
\item \code{"grey"}
\item \code{"blue-grey"}}
See the \href{https://material.io/guidelines/style/color.html}{material
design color guidelines} for details.}
\item{n}{Number of individual colors to be generated.}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
\item{reverse}{Logical. Should the order of the colors be reversed?}
}
\description{
The Material Design color palettes.
}
\examples{
library("scales")
show_col(pal_material("indigo")(10))
show_col(pal_material("indigo", n = 30, alpha = 0.6, reverse = TRUE)(30))
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/scale_startrek.Rd 0000644 0001762 0000144 00000002552 13221611720 015415 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-startrek.R
\name{scale_color_startrek}
\alias{scale_color_startrek}
\alias{scale_colour_startrek}
\alias{scale_fill_startrek}
\title{Star Trek Color Scales}
\usage{
scale_color_startrek(palette = c("uniform"), alpha = 1, ...)
scale_colour_startrek(palette = c("uniform"), alpha = 1, ...)
scale_fill_startrek(palette = c("uniform"), alpha = 1, ...)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"uniform"}
(7-color palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}}
}
\description{
See \code{\link{pal_startrek}} for details.
}
\examples{
library("ggplot2")
data("diamonds")
ggplot(subset(diamonds, carat >= 2.2),
aes(x = table, y = price, colour = cut)) +
geom_point(alpha = 0.7) +
geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
theme_bw() + scale_color_startrek()
ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
aes(x = depth, fill = cut)) +
geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
theme_bw() + scale_fill_startrek()
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/scale_uchicago.Rd 0000644 0001762 0000144 00000003463 13276174440 015357 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-uchicago.R
\name{scale_color_uchicago}
\alias{scale_color_uchicago}
\alias{scale_colour_uchicago}
\alias{scale_fill_uchicago}
\title{The University of Chicago Color Scales}
\usage{
scale_color_uchicago(palette = c("default", "light", "dark"), alpha = 1,
...)
scale_colour_uchicago(palette = c("default", "light", "dark"), alpha = 1,
...)
scale_fill_uchicago(palette = c("default", "light", "dark"), alpha = 1, ...)
}
\arguments{
\item{palette}{Palette type.
There are 3 available options:
\code{"default"} (9-color palette);
\code{"light"} (9-color light palette);
\code{"dark"} (9-color dark palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}}
}
\description{
See \code{\link{pal_uchicago}} for details.
}
\examples{
library("ggplot2")
data("diamonds")
p1 = ggplot(subset(diamonds, carat >= 2.2),
aes(x = table, y = price, colour = cut)) +
geom_point(alpha = 0.7) +
geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
theme_bw()
p2 = ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
aes(x = depth, fill = cut)) +
geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
theme_bw()
p1 + scale_color_uchicago()
p2 + scale_fill_uchicago()
p1 + scale_color_uchicago(palette = "light")
p2 + scale_fill_uchicago(palette = "light")
p1 + scale_color_uchicago(palette = "dark")
p2 + scale_fill_uchicago(palette = "dark")
}
\references{
\url{https://news.uchicago.edu/sites/default/files/attachments/_uchicago.identity.guidelines.pdf}
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/pal_aaas.Rd 0000644 0001762 0000144 00000001565 13221611720 014153 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-aaas.R
\name{pal_aaas}
\alias{pal_aaas}
\title{AAAS Journal Color Palettes}
\usage{
pal_aaas(palette = c("default"), alpha = 1)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"default"}
(10-color palette inspired by \emph{Science}).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
}
\description{
Color palettes inspired by plots in journals published by
American Association for the Advancement of Science (AAAS),
such as \emph{Science} and \emph{Science Translational Medicine}.
}
\examples{
library("scales")
show_col(pal_aaas("default")(10))
show_col(pal_aaas("default", alpha = 0.6)(10))
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/scale_d3.Rd 0000644 0001762 0000144 00000003660 13221611720 014065 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-d3.R
\name{scale_color_d3}
\alias{scale_color_d3}
\alias{scale_colour_d3}
\alias{scale_fill_d3}
\title{D3.js Color Scales}
\usage{
scale_color_d3(palette = c("category10", "category20", "category20b",
"category20c"), alpha = 1, ...)
scale_colour_d3(palette = c("category10", "category20", "category20b",
"category20c"), alpha = 1, ...)
scale_fill_d3(palette = c("category10", "category20", "category20b",
"category20c"), alpha = 1, ...)
}
\arguments{
\item{palette}{Palette type.
There are 4 available options:
\code{"category10"} (10-color palette);
\code{"category20"} (20-color palette);
\code{"category20b"} (20-color palette);
\code{"category20c"} (20-color palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}}
}
\description{
See \code{\link{pal_d3}} for details.
}
\examples{
library("ggplot2")
data("diamonds")
p1 = ggplot(subset(diamonds, carat >= 2.2),
aes(x = table, y = price, colour = cut)) +
geom_point(alpha = 0.7) +
geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
theme_bw()
p2 = ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
aes(x = depth, fill = cut)) +
geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
theme_bw()
p1 + scale_color_d3()
p2 + scale_fill_d3()
p1 + scale_color_d3(palette = "category20")
p2 + scale_fill_d3(palette = "category20")
p1 + scale_color_d3(palette = "category20b")
p2 + scale_fill_d3(palette = "category20b")
p1 + scale_color_d3(palette = "category20c")
p2 + scale_fill_d3(palette = "category20c")
}
\references{
\url{https://github.com/d3/d3-3.x-api-reference/blob/master/Ordinal-Scales.md}
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/pal_startrek.Rd 0000644 0001762 0000144 00000001364 13221611720 015102 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-startrek.R
\name{pal_startrek}
\alias{pal_startrek}
\title{Star Trek Color Palettes}
\usage{
pal_startrek(palette = c("uniform"), alpha = 1)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"uniform"}
(7-color palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
}
\description{
Color palettes inspired by the colors used in \emph{Star Trek}.
}
\examples{
library("scales")
show_col(pal_startrek("uniform")(7))
show_col(pal_startrek("uniform", alpha = 0.6)(7))
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/pal_gsea.Rd 0000644 0001762 0000144 00000001710 13221611720 014155 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/continuous-gsea.R
\name{pal_gsea}
\alias{pal_gsea}
\title{The GSEA GenePattern Color Palettes}
\usage{
pal_gsea(palette = c("default"), n = 12, alpha = 1, reverse = FALSE)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"default"}
(continuous palette with 12 base colors).}
\item{n}{Number of individual colors to be generated.}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
\item{reverse}{Logical. Should the order of the colors be reversed?}
}
\description{
Color palette inspired by the colors used in the
heatmaps plotted by GSEA GenePattern.
}
\examples{
library("scales")
show_col(pal_gsea("default")(12))
show_col(pal_gsea("default", n = 30, alpha = 0.6, reverse = TRUE)(30))
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/scale_jama.Rd 0000644 0001762 0000144 00000002540 13221611720 014463 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-jama.R
\name{scale_color_jama}
\alias{scale_color_jama}
\alias{scale_colour_jama}
\alias{scale_fill_jama}
\title{Journal of the American Medical Association Color Scales}
\usage{
scale_color_jama(palette = c("default"), alpha = 1, ...)
scale_colour_jama(palette = c("default"), alpha = 1, ...)
scale_fill_jama(palette = c("default"), alpha = 1, ...)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"default"}
(7-color palette).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}}
}
\description{
See \code{\link{pal_jama}} for details.
}
\examples{
library("ggplot2")
data("diamonds")
ggplot(subset(diamonds, carat >= 2.2),
aes(x = table, y = price, colour = cut)) +
geom_point(alpha = 0.7) +
geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
theme_bw() + scale_color_jama()
ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
aes(x = depth, fill = cut)) +
geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
theme_bw() + scale_fill_jama()
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/scale_lancet.Rd 0000644 0001762 0000144 00000002570 13221611720 015024 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-lancet.R
\name{scale_color_lancet}
\alias{scale_color_lancet}
\alias{scale_colour_lancet}
\alias{scale_fill_lancet}
\title{Lancet Journal Color Scales}
\usage{
scale_color_lancet(palette = c("lanonc"), alpha = 1, ...)
scale_colour_lancet(palette = c("lanonc"), alpha = 1, ...)
scale_fill_lancet(palette = c("lanonc"), alpha = 1, ...)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"lanonc"}
(9-color palette inspired by \emph{Lancet Oncology}).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
\item{...}{additional parameters for \code{\link[ggplot2]{discrete_scale}}}
}
\description{
See \code{\link{pal_lancet}} for details.
}
\examples{
library("ggplot2")
data("diamonds")
ggplot(subset(diamonds, carat >= 2.2),
aes(x = table, y = price, colour = cut)) +
geom_point(alpha = 0.7) +
geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
theme_bw() + scale_color_lancet()
ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
aes(x = depth, fill = cut)) +
geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
theme_bw() + scale_fill_lancet()
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/man/pal_npg.Rd 0000644 0001762 0000144 00000001455 13221611720 014030 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/discrete-npg.R
\name{pal_npg}
\alias{pal_npg}
\title{NPG Journal Color Palettes}
\usage{
pal_npg(palette = c("nrc"), alpha = 1)
}
\arguments{
\item{palette}{Palette type.
Currently there is one available option: \code{"nrc"}
(10-color palette inspired by \emph{Nature Reviews Cancer}).}
\item{alpha}{Transparency level, a real number in (0, 1].
See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
}
\description{
Color palettes inspired by plots in journals published by
Nature Publishing Group, such as \emph{Nature Reviews Cancer}.
}
\examples{
library("scales")
show_col(pal_npg("nrc")(10))
show_col(pal_npg("nrc", alpha = 0.6)(10))
}
\author{
Nan Xiao <\email{me@nanx.me}> |
<\href{https://nanx.me}{https://nanx.me}>
}
ggsci/LICENSE 0000644 0001762 0000144 00000104513 13221611720 012352 0 ustar ligges users GNU GENERAL PUBLIC LICENSE
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How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
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You should have received a copy of the GNU General Public License
along with this program. If not, see .
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short
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Copyright (C)
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
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The hypothetical commands `show w' and `show c' should show the appropriate
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if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
.
The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
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.