yulab.utils/ 0000755 0001762 0000144 00000000000 14746344222 012535 5 ustar ligges users yulab.utils/MD5 0000644 0001762 0000144 00000005663 14746344222 013057 0 ustar ligges users bdbc33686bbff396223a63f41200cd00 *DESCRIPTION
be784f9d486c3b3f632918b731441edd *NAMESPACE
ebafcb7aa06a2ae6e92e851ac2794f9e *NEWS.md
007e3de7a11b71539e2d8617ebc295c5 *R/bib-ggtree.R
53a06eaae05f939981d43ffbe9b636c8 *R/bib-knownledge.R
8c817a90acb8deb76024a36d5662c824 *R/biorxiv.R
09a18d0b822d2e29ca10ba3e76fb7485 *R/cache.R
95effca842167b8d4ab1d11056e3e84e *R/combinations.R
664948f3ab8aa48e35c8dd268bcdf822 *R/concat.r
135705b0f129acd7f0418127a17e8994 *R/download.R
5e45a091afcc9573f8c2eef871845044 *R/file.R
a88f332cc523f835302372eb330808c1 *R/install_zip.R
29332963a97b933d165880d14b5a926f *R/list.R
c9d9db73e55f3aadfa2a3cde09cd51c6 *R/matrix-utils.R
e703f7689d1b0a0d7ea2dcaed9fa1038 *R/os.R
bc5a9393353846510cf4f532137aa7d0 *R/pkg-utils.R
522473cababc10ee439a582555d821cb *R/regexpr.R
0db1a99ecdc6501760d342d82da783a8 *R/scale.R
8b2467b550b0debf2161c3ffa984f73c *R/scihub-dl.R
5b32966c3e9170d5ab3207e9ea07211a *R/str-utils.R
a33656388df140e42f096042e4d94c4f *R/sudo-install.R
ee2efad4700779e729634304bc862ee5 *R/utilities.R
2bcf5d590c3a9828af87f6ebcf4113a6 *R/yulab-msg.R
da7bac5323d313dfbcdb38f8fbf613f0 *R/yulab-utils-package.R
81128a8e2c6dac0484310aefb614e6c3 *R/zzz.R
e102b8ef2ffb9aafef52223a22e88753 *inst/prototype/GEO.r
fe6013508f10ad5584815759267861f0 *inst/prototype/sra.r
d611cc86140e279caf3e3acb788b6153 *man/c2.Rd
438fff93f806ab18e9db99060cbabb1b *man/check_pkg.Rd
740f5276df44ad1e6766f7a37fe1d21a *man/combinations.Rd
db93bb4ab3c70d03ce07c3a35f237cdd *man/cran-bioc-pkg.Rd
aeaacad247b828ca4591480b2015c198 *man/exec.Rd
e729417aa83b01b31ac177ed6f6c3a14 *man/get_dependencies.Rd
feeda9894ca366d3cecd321a26b1c757 *man/get_fun_from_pkg.Rd
4037c412514457e4aa46f4ae2e87a25d *man/github-pkg.Rd
e0532e636b9a265f753170bf7ad77605 *man/has_internet.Rd
dfbc4e67550a8ff93dd167f828333c0a *man/install_zip.Rd
27416a715194cdda190410318907fcb7 *man/install_zip_gh.Rd
f1fb5a178766a681c0ee36d3ee16f50f *man/is.installed.Rd
7429eb4c6b9f62553ecae5e16edc4824 *man/ls2df.Rd
6ad39ca2459889f1cdd3f10b50cca2b1 *man/mat2df.Rd
035dbcab8d8db17527a76278426722ca *man/mat2list.Rd
5de5c1a676be17dc7fbe1de44a430b38 *man/mypkg.Rd
350771e856ec3d6a012327e9f9a7661c *man/o.Rd
e101a49107b31f0d3bedef24de40e2a5 *man/packageTitle.Rd
8317241089ca88b826c9fab73d536d8e *man/pload.Rd
340d383c001465de8a3773b6cd1db10b *man/rbindlist.Rd
0e20524bfebe8e2ef91eea11dbb62ccb *man/read.cb.Rd
94015f38ecbf2eeb9f295345d938b702 *man/regexpr-style.Rd
e4439fe352c1817015d3bc28bd4f5abf *man/scale_range.Rd
7ca4626445edad5c55b084c9a360cff2 *man/scihub-dl.Rd
376e2961dcdfc973c2449512a05eb2a3 *man/show_in_excel.Rd
ea0c0f3acb8187602161ff2a7bc5d1ac *man/str-detect.Rd
0ee359877a2bc4bd14136104fd61d24f *man/str-extract.Rd
be70aa2c7a2cc288386c27b41a1d122a *man/str-starts-ends.Rd
3aade7406ca5eaadbc07b0c5679b063b *man/str_wrap.Rd
4ced4ba5fc9eca943c92574732a1b205 *man/yread.Rd
0c88c99a76427c4980cf90320e9c3057 *man/yulab-cache.Rd
eedc7b6680597a4df3d869fe84f9ca5c *man/yulab.utils-package.Rd
376b3e7335587d2531cd9360557fcc9d *man/yulab_msg.Rd
yulab.utils/R/ 0000755 0001762 0000144 00000000000 14723463462 012741 5 ustar ligges users yulab.utils/R/cache.R 0000644 0001762 0000144 00000005471 14543172714 014133 0 ustar ligges users ##' @rdname yulab-cache
##' @export
initial_cache <- function() {
pos <- 1
envir <- as.environment(pos)
assign(".yulabCache", new.env(), envir = envir)
}
##' @rdname yulab-cache
##' @export
get_cache <- function() {
if (!exists(".yulabCache", envir = .GlobalEnv)) {
initial_cache()
}
get(".yulabCache", envir = .GlobalEnv)
}
##' @rdname yulab-cache
##' @export
rm_cache <- function() {
if (exists(".yulabCache", envir = .GlobalEnv)) {
rm(".yulabCache", envir = .GlobalEnv)
}
}
##' @rdname yulab-cache
##' @export
initial_cache_item <- function(item) {
env <- get_cache()
assign(item, list(), envir = env)
}
##' @rdname yulab-cache
##' @export
get_cache_item <- function(item) {
env <- get_cache()
if (!exists(item, envir = env)) {
initial_cache_item(item)
}
get(item, envir = env, inherits = FALSE)
}
##' @rdname yulab-cache
##' @export
rm_cache_item <- function(item) {
env <- get_cache()
if (exists(item, envir = env)) {
rm(list = item, envir = env)
}
}
##' cache intermediate data
##'
##' Yulab provides a set of utilities to cache intermediate data,
##' including initialize the cached item, update cached item and rmove the cached item, etc.
##'
##' @rdname yulab-cache
##' @param item the name of the cached item
##' @param elements elements to be cached in the item
##' @return return the cache environment, item or selected elements, depends on the functions.
##' @importFrom utils modifyList
##' @export
##' @examples
##' \dontrun{
##' slow_fib <- function(x) {
##' if (x < 2) return(1)
##' slow_fib(x-2) + slow_fib(x-1)
##' }
##'
##' fast_fib <- function(x) {
##' if (x < 2) return(1)
##' res <- get_cache_element('fibonacci', as.character(x))
##' if (!is.null(res)) {
##' return(res)
##' }
##' res <- fast_fib(x-2) + fast_fib(x-1)
##' e <- list()
##' e[[as.character(x)]] <- res
##' update_cache_item('fibonacci', e)
##' return(res)
##' }
##'
##' system.time(slow_fib(30))
##' system.time(fast_fib(30))
##'
##' }
update_cache_item <- function(item, elements) {
msg <- "new elements should be stored as a named list"
if (!inherits(elements, 'list')) {
stop(msg)
}
if (is.null(names(elements))) {
stop(msg)
}
if(any(names(elements) == "")) {
stop(msg)
}
env <- get_cache()
res <- get_cache_item(item)
res <- modifyList(res, elements)
assign(item, res, envir = env)
}
##' @rdname yulab-cache
##' @export
get_cache_element <- function(item, elements) {
x <- get_cache_item(item)
n <- length(elements)
if (n == 1) return(x[[elements]])
return(x[elements])
}
yulab.utils/R/pkg-utils.R 0000644 0001762 0000144 00000015355 14712620134 015001 0 ustar ligges users ##' loading a package
##'
##' The function use 'library()' to load the package.
##' If the package is not installed, the function will try to install it before loading it.
##' @title pload
##' @param package package name
##' @param action function used to install package.
##' If 'action = "auto"', it will try to use 'BiocManager::install()' if it is available.
##' @return the selected package loaded to the R session
##' @importFrom rlang as_name
##' @importFrom rlang enquo
##' @importFrom rlang check_installed
##' @importFrom cli cli_h2
##' @importFrom utils getFromNamespace
##' @export
##' @author Guangchuang Yu
pload <- function(package, action = "auto") {
pkg <- as_name(enquo(package))
if (action == "auto") {
if (is.installed("BiocManager")) {
install <- getFromNamespace("install", "BiocManager")
action <- function(package, ask=FALSE, update=FALSE, ...) {
install(package, ask=ask, update = update, ...)
}
} else {
action <- NULL
}
}
check_installed(pkg, action = action)
pkg <- sub("\\w+/", "", pkg) # for github pkg: repo/pkg
cli::cli_h2(sprintf("loading the package: %s", pkg))
library(pkg, character.only = TRUE)
}
##' get reverse dependencies
##'
##'
##' @title get_dependencies
##' @param pkg package name
##' @param repo 'CRAN' and/or 'BioC'
##' @return reverse dependencies
## @importFrom BiocInstaller biocinstallRepos
##' @importFrom tools package_dependencies
##' @export
##' @author Guangchuang Yu
get_dependencies <- function(pkg, repo=c("CRAN", "BioC")) {
rp <- get_repo(repo)
db <- utils::available.packages(repo=rp)
tools::package_dependencies(pkg, db=db, reverse=TRUE)
}
get_repo <- function(repo = c("CRAN", "BioC")) {
rp <- c()
if ('CRAN' %in% repo) {
cran <- getOption("repos")["CRAN"]
if (is.null(cran)) {
cran <- "http://cloud.r-project.org/"
}
rp <- c(rp, cran)
}
if ('BioC' %in% repo) {
bioc <- getOption("BioC_mirror")
if (is.null(bioc)) {
bioc <- "https://mirrors.tuna.tsinghua.edu.cn/bioconductor/"
}
rp <- c(rp, bioc)
}
## options(repos = biocinstallRepos())
sub("/$", "", rp)
}
##' Extract package title
##'
##'
##' @title packageTitle
##' @param pkg package name
##' @param repo 'CRAN' and/or 'BioC'
##' @return reverse dependencies
##' @importFrom utils packageDescription
##' @export
##' @author Guangchuang Yu
packageTitle <- function(pkg, repo='CRAN') {
title <- tryCatch(packageDescription(pkg)$Title, error=function(e) NULL)
if (is.null(title)) {
repo_url <- get_repo(repo)
if (repo == "CRAN") {
url <- sprintf("%s/package=%s", repo_url, pkg)
} else {
bioc_type <- c("bioc", "workflows", "data/annotation", "data/experiment")
url <- sprintf("%s/packages/release/%s/html/%s.html", repo_url, bioc_type, pkg)
}
## x <- tryCatch(readLines(url), error = function(e) NULL)
## if (is.null(x)) return("")
for (u in url) {
x <- tryCatch(yread(u), error = function(e) NULL)
if (!is.null(x)) {
break()
}
}
if (is.null(x)) {
return(NA)
}
i <- grep('^\\s*', x)
if (grepl("
$", x[i])) {
xx <- x[i]
} else {
j <- grep('$', x)
xx <- paste(x[i:j], collapse=" ")
}
title <- gsub('$', '', gsub('\\s*', '', xx))
}
sub("^\\w+\\s*:\\s*", "", gsub("\n", " ", title))
}
##' Check whether the input packages are installed
##'
##' This function check whether the input packages are installed
##' @title is.installed
##' @param packages package names
##' @return logical vector
##' @export
##' @examples
##' is.installed(c("dplyr", "ggplot2"))
##' @author Guangchuang Yu
is.installed <- function(packages) {
vapply(packages, function(package) {
system.file(package=package) != ""
}, logical(1))
}
##' Check whether the input packages are installed
##'
##' This function check whether the input packages are installed. If not, it asks the user whether to install the missing packages.
##' @title check_pkg
##' @param pkg package names
##' @param reason the reason to check the pkg. If NULL, it will set the reason to the parent call.
##' @param ... additional parameters that passed to `rlang::check_installed()`
##' @return see also [check_installed][rlang::check_installed]
##' @export
##' @importFrom rlang check_installed
##' @author Guangchuang Yu
check_pkg <- function(pkg, reason=NULL, ...) {
# v1
#
# if (!is.installed(pkg)) {
# msg <- sprintf("%s is required, please install it first", pkg)
# stop(msg)
# }
if (is.null(reason)) {
call <- sys.call(1L)
reason <- sprintf("for %s()", as.character(call)[1])
}
rlang::check_installed(pkg, reason, ...)
}
##' load function from package
##'
##'
##' @title get_fun_from_pkg
##' @param pkg package
##' @param fun function
##' @return function
##' @export
##' @examples
##' get_fun_from_pkg('utils', 'zip')
##' @author Guangchuang Yu
get_fun_from_pkg <- function(pkg, fun) {
## v1
##
## requireNamespace(pkg)
## eval(parse(text=paste0(pkg, "::", fun)))
## v2
##
## require(pkg, character.only = TRUE)
## eval(parse(text = fun))
# check_pkg(pkg)
utils::getFromNamespace(fun, pkg)
}
##' print md text of package with link to homepage (CRAN or Bioconductor)
##'
##'
##' @rdname cran-bioc-pkg
##' @param pkg package name
##' @return md text string
##' @export
##' @author Guangchuang Yu
CRANpkg <- function(pkg) {
cran <- "https://CRAN.R-project.org/package"
fmt <- "[%s](%s=%s)"
sprintf(fmt, pkgfmt(pkg), cran, pkg)
}
##' @rdname cran-bioc-pkg
##' @export
Biocpkg <- function(pkg) {
sprintf("[%s](http://bioconductor.org/packages/%s)", pkgfmt(pkg), pkg)
}
##' print md text of package with link to github repo
##'
##'
##' @rdname github-pkg
##' @param user github user
##' @param pkg package name
##' @return md text string
##' @export
##' @author Guangchuang Yu
Githubpkg <- function(user, pkg) {
gh <- "https://github.com"
fmt <- "[%s](%s/%s/%s)"
sprintf(fmt, pkgfmt(pkg), gh, user, pkg)
}
##' print md text of link to a pakcage
##'
##'
##' @title mypkg
##' @param pkg package name
##' @param url package url
##' @return md text string
##' @export
##' @author Guangchuang Yu
mypkg <- function(pkg, url) {
fmt <- "[%s](%s)"
sprintf(fmt, pkgfmt(pkg), url)
}
pkgfmt <- function(pkg) {
fmt <- getOption('yulab.utils_pkgfmt', default="%s")
sprintf(fmt, pkg)
}
yulab.utils/R/download.R 0000644 0001762 0000144 00000000451 14660652063 014670 0 ustar ligges users mydownload <- function(url, destfile) {
if (is.installed('httr2')) {
req <- httr2::request(url) |>
httr2::req_progress()
req |> httr2::req_perform(path = destfile)
} else {
download.file(url = url, destfile = destfile)
}
}
yulab.utils/R/os.R 0000644 0001762 0000144 00000002700 14663004004 013466 0 ustar ligges users ##' run system command
##'
##'
##' @title exec
##' @param command system command to run
##' @return An `exec` instance that stores system command outputs
##' @export
##' @author Guangchuang Yu
exec <- function(command) {
res <- system(command, intern=TRUE)
structure(res, class = "exec")
}
##' @method print exec
##' @export
print.exec <- function(x, ...) {
cat(x, sep='\n')
}
has_bin <- function(bin) {
os <- which_os()
which <- "which"
if (os == "Windows") {
which <- "where"
}
command <- sprintf("%s %s", which, bin)
exit_code <- system(command,
ignore.stdout = TRUE,
ignore.stderr = TRUE)
return(exit_code == 0)
}
##' test for internect connection via reading lines from a URL
##'
##'
##' @title has_internet
##' @param site URL to test connection
##' @return logical value
##' @export
##' @author Guangchuang Yu
has_internet <- function(site = "https://www.baidu.com/") {
ret <- tryCatch(
suppressWarnings(readLines(site, n = 1)),
error = function(e) NULL
)
return(!is.null(ret))
}
which_os <- function() {
Sys.info()[1]
}
user_dir <- function(appname = NULL, appauthor = NULL, ...) {
dir <- rappdirs::user_data_dir(
appname = appname,
appauthor=appauthor,
...)
if (!dir.exists(dir)) dir.create(dir, recursive = TRUE)
return(dir)
}
yulab.utils/R/combinations.R 0000644 0001762 0000144 00000000500 14471060615 015535 0 ustar ligges users #' all possible combinations of n sets
#'
#' @title combinations
#' @param n number of sets
#' @return a list of all combinations
#' @importFrom utils combn
#' @export
combinations <- function(n){
l <- lapply(seq_len(n), function(x){
m <- combn(n,x)
mat2list(m)
})
unlist(l, recursive = F)
}
yulab.utils/R/list.R 0000644 0001762 0000144 00000001476 14474263164 014047 0 ustar ligges users ##' rbind a list
##'
##'
##' @title rbindlist
##' @param x a list that have similar elements that can be rbind to a data.frame
##' @return data.frame
##' @author Guangchuang Yu
##' @export
rbindlist <- function(x) {
do.call('rbind', x)
}
##' Convert a list of vector to a data.frame object.
##'
##'
##' @title Convert a list of vector (e.g, gene IDs) to a data.frame object
##' @param inputList A list of vector
##' @return a data.frame object.
##' @export
ls2df <- function(inputList) {
# ldf <- lapply(1:length(inputList), function(i) {
ldf <- lapply(seq_len(length(inputList)), function(i) {
data.frame(category=rep(names(inputList[i]),
length(inputList[[i]])),
value=inputList[[i]])
})
do.call('rbind', ldf)
}
yulab.utils/R/bib-ggtree.R 0000644 0001762 0000144 00000023053 14656277555 015111 0 ustar ligges users bib_ggtree <- function(id) {
bib <- c(
jgg2024 = bib_shinyTempSignal_jgg2024,
bib2022 = bib_ggmsa_bib2022,
book = bib_ggtree_book2022,
imeta2022 = bib_ggtree_imeta2022,
cpb2020 = bib_ggtree_cpb2020,
mbe2020 = bib_treeio_mbe2020,
mbe2018 = bib_ggtree_mbe2018,
mee2017 = bib_ggtree_mee2017
)
if (!id %in% names(bib)) return(NULL)
bib[id]
}
ref_ggtree <- function() {
refs <- c(
shinyTempSignal = paste(
"L Zhan, X Luo, W Xie, XA Zhu, Z Xie, J Lin, L Li, W Tang, R Wang, L Deng, Y Liao, B Liu, Y Cai, Q Wang, S Xu, G Yu.",
"shinyTempSignal: an R shiny application for exploring temporal and other phylogenetic signals.",
"Journal of Genetics and Genomics 2024, 51(7):762-768. doi: 10.1016/j.jgg.2024.02.004"),
ggtreeBook = paste(
"Guangchuang Yu. ",
"Data Integration, Manipulation and Visualization of Phylogenetic Trees (1st edition).",
"Chapman and Hall/CRC. 2022, doi:10.1201/9781003279242, ISBN: 9781032233574\n"),
ggtreeCPB = paste0(
"Guangchuang Yu. ",
"Using ggtree to visualize data on tree-like structures. ",
"Current Protocols in Bioinformatics. 2020, 69:e96. doi:10.1002/cpbi.96\n"
),
ggtree_imeta = paste0(
"Shuangbin Xu, Lin Li, Xiao Luo, Meijun Chen, Wenli Tang, Li Zhan, Zehan Dai, Tommy T. Lam, Yi Guan, Guangchuang Yu. ",
"Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data. ",
"iMeta 2022, 1(4):e56. doi:10.1002/imt2.56\n"),
ggtreeMBE = paste0(
"Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. ",
"Two methods for mapping and visualizing associated data on phylogeny using ggtree. ",
"Molecular Biology and Evolution. 2018, 35(12):3041-3043. doi:10.1093/molbev/msy194\n"
),
ggtree = paste0(
"Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ",
"ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ",
"Methods in Ecology and Evolution. 2017, 8(1):28-36. doi:10.1111/2041-210X.12628\n"
),
treeio = paste0(
"LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu. ",
"treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. ",
"Molecular Biology and Evolution. 2020, 37(2):599-603. doi: 10.1093/molbev/msz240\n"
),
ggtreeExtra = paste0(
"S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L Zhan, T Wu, E Hu, Y Jiang, X Bo, G Yu. ",
"ggtreeExtra: Compact visualization of richly annotated phylogenetic data. ",
"Molecular Biology and Evolution. 2021, 38(9):4039-4042. doi: 10.1093/molbev/msab166\n"
),
ggmsa = paste(
"L Zhou, T Feng, S Xu, F Gao, TT Lam, Q Wang, T Wu, H Huang, L Zhan, L Li, Y Guan, Z Dai, G Yu.",
"ggmsa: a visual exploration tool for multiple sequence alignment and associated data.",
"Bioinformatics. 2022, 23(4):bbac222. 10.1093/bib/bbac222"
)
)
return(refs)
}
refs <- ref_ggtree()
bib_ggtree_book2022 <- bibentry(
bibtype = "book",
title = "Data Integration, Manipulation and Visualization of Phylogenetic Treess",
author = person("Guangchuang", "Yu"),
publisher = "Chapman and Hall/{CRC}",
year = "2022",
edition = "1st edition",
doi = "10.1201/9781003279242",
url = "https://www.amazon.com/Integration-Manipulation-Visualization-Phylogenetic-Computational-ebook/dp/B0B5NLZR1Z/",
textVersion = refs['ggtreeBook']
)
bib_ggtree_imeta2022 <- bibentry(
bibtype = "article",
title = "Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data",
author = personList(
person("Shuangbin", "Xu"),
person("Lin", "Li"),
person("Xiao", "Luo"),
person("Meijun", "Chen"),
person("Wenli", "Tang"),
person("Li", "Zhan"),
person("Zehan", "Dai"),
person("Tommy T. Lam"),
person("Yi", "Guan"),
person("Guangchuang", "Yu")
),
year = "2022",
journal = "iMeta",
volume = "1",
number = "4",
pages = "e56",
doi = "10.1002/imt2.56",
url = "https://onlinelibrary.wiley.com/doi/full/10.1002/imt2.56",
textVersion = refs['ggtree_imeta']
)
bib_ggtree_cpb2020 <- bibentry(
bibtype = "article",
title = "Using ggtree to Visualize Data on Tree-Like Structures",
author = person("Guangchuang", "Yu"),
year = "2020",
journal = "Current Protocols in Bioinformatics",
volume = "69",
pages = "e96",
number = "1",
url = "https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpbi.96",
doi = "10.1002/cpbi.96",
textVersion = refs['ggtreeCPB']
)
bib_ggtree_mbe2018 <- bibentry(
bibtype = "article",
title = "Two methods for mapping and visualizing associated data on phylogeny using ggtree.",
author = personList(
as.person("Guangchuang Yu"),
as.person("Tommy Tsan-Yuk Lam"),
as.person("Huachen Zhu"),
as.person("Yi Guan")
),
year = "2018",
journal = "Molecular Biology and Evolution",
volume = "35",
issue = "2",
number = "",
pages = "3041-3043",
doi = "10.1093/molbev/msy194",
PMID = "",
url = "https://academic.oup.com/mbe/article/35/12/3041/5142656",
textVersion = refs['ggtreeMBE']
)
bib_ggtree_mee2017 <- bibentry(
bibtype = "article",
title = "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.",
author = personList(
as.person("Guangchuang Yu"),
as.person("David Smith"),
as.person("Huachen Zhu"),
as.person("Yi Guan"),
as.person("Tommy Tsan-Yuk Lam")
),
year = "2017",
journal = "Methods in Ecology and Evolution",
volume = "8",
issue = "1",
number = "",
pages = "28-36",
doi = "10.1111/2041-210X.12628",
PMID = "",
url = "http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract",
textVersion = refs['ggtree']
)
bib_shinyTempSignal_jgg2024 <-bibentry(
bibtype = "article",
title = "shinyTempSignal: an R shiny application for exploring temporal and other phylogenetic signals.",
author = c(
person("Li", "Zhan"),
person("Xiao", "Luo"),
person("Wenqin", "Xie"),
person("Xuan-An", "Zhu"),
person("Zijing", "Xie"),
person("Jianfeng", "Lin"),
person("Lin", "Li"),
person("Wenli", "Tang"),
person("Rui", "Wang"),
person("Lin", "Deng"),
person("Yufan", "Liao"),
person("Bingdong", "Liu"),
person("Yantong", "Cai"),
person("Qianwen", "Wang"),
person("Shuangbin", "Xu"),
person("Guangchuang", "Yu")
),
year = "2024",
journal = "Journal of Genetics and Genomics",
volume = "51",
issue = "7",
number = "",
pages = "762-768",
doi = "10.1016/j.jgg.2024.02.004",
PMID = "",
url = "https://www.sciencedirect.com/science/article/pii/S167385272400033X",
textVersion = refs['shinyTempSignal']
)
bib_treeio_mbe2020 <- bibentry(
bibtype = "article",
title = "treeio: an R package for phylogenetic tree input and output with richly annotated and associated data.",
author = c(
person("Li-Gen", "Wang"),
person("Tommy Tsan-Yuk", "Lam"),
person("Shuangbin", "Xu"),
person("Zehan", "Dai"),
person("Lang", "Zhou"),
person("Tingze", "Feng"),
person("Pingfan", "Guo"),
person("Casey W.", "Dunn"),
person("Bradley R.", "Jones"),
person("Tyler", "Bradley"),
person("Huachen", "Zhu"),
person("Yi", "Guan"),
person("Yong", "Jiang"),
person("Guangchuang", "Yu")
),
year = "2020",
journal = "Molecular Biology and Evolution",
volume = "37",
issue = "2",
number = "",
pages = "599-603",
doi = "10.1093/molbev/msz240",
PMID = "",
url = "",
textVersion = refs['treeio']
)
bib_ggmsa_bib2022 <- citEntry(
entry = "article",
title = "ggmsa: a visual exploration tool for multiple sequence alignment and associated data ",
author = personList(
as.person("Lang Zhou"),
as.person("Tingze Feng"),
as.person("Shuangbin Xu"),
as.person("Fangluan Gao"),
as.person("Tommy T Lam"),
as.person("Qianwen Wang"),
as.person("Tianzhi Wu"),
as.person("Huina Huang"),
as.person("Li Zhan"),
as.person("Lin Li"),
as.person("Yi Guan"),
as.person("Zehan Dai"),
as.person("Guangchuang Yu")
),
journal = "BRIEFINGS IN BIOINFORMATICS",
volume = "23",
issue = "4",
year = "2022",
month = "06",
ISSN = "1467-5463",
doi = "10.1093/bib/bbac222",
PMID = "35671504",
url = "https://academic.oup.com/bib/article-abstract/23/4/bbac222/6603927",
textVersion = refs['ggmsa']
)
yulab.utils/R/biorxiv.R 0000644 0001762 0000144 00000002647 14404503310 014536 0 ustar ligges users ## biorxiv_get_publication <- function(url) {
## # url <- "https://www.biorxiv.org/search/visualization%20numresults%3A75%20sort%3Arelevance-rank"
## x <- readLines(url)
## pub <- x[grep("/content/10.1101", x)]
## pub_url <- gsub(".*(/content/[[:digit:]\\.v/]+).*", "\\1", pub)
## pub_url <- paste0("https://www.biorxiv.org", pub_url)
## pub_title <- gsub("<[^>]+>", "", pub) %>%
## sub("^\\s+", "", .) %>%
## sub("\\s+$", "", .)
## data.frame(url = pub_url,
## title = pub_title)
## }
## biorxiv_get_correspondance <- function(url) {
## # url <- "https://www.biorxiv.org/content/10.1101/701680v3"
## x <- readLines(url)
## i <- grep("citation_author\"", x)
## j <- grep("citation_author_email", x)
## idx <- vapply(j, function(ii) {
## jj <- ii - i
## i[which(jj == min(jj[jj >0]))]
## }, numeric(1))
## author <- x[idx] %>% unique %>%
## sub(".*content=\"([^\"]+).*", "\\1", .)
## email <- x[j] %>% unique %>%
## sub(".*content=\"([^\"]+).*", "\\1", .)
## data.frame(author = author, email = email) %>% unique
## }
## url <- "https://www.biorxiv.org/search/visualization%20numresults%3A75%20sort%3Arelevance-rank"
## y <- biorxiv_get_publication(url)
## xx <- lapply(y$url, function(x) {
## cat("parsing", x, "\n")
## biorxiv_get_correspondance(x)
## })
yulab.utils/R/file.R 0000644 0001762 0000144 00000010653 14660051033 013773 0 ustar ligges users #' @rdname yread
#' @export
yread_tsv <- function(file, reader = utils::read.delim,
params = list(),
cache_dir = tempdir()
) {
# e.g. params = list(sep = "\t", header = FALSE)
yread(file,
reader = reader,
params = params,
cache_dir = cache_dir
)
}
#' read file with caching
#'
#' This function read a file (local or url) and cache the content.
#' @title yread
#' @rdname yread
#' @param file a file or url
#' @param reader a function to read the 'file_url'
#' @param params a list of parameters that passed to the 'reader'
#' @param cache_dir a folder to store cache files. If set to NULL will disable cache.
#' @return the output of using the 'reader' to read the 'file_url' with parameters specified by the 'params'
#' @author Yonghe Xia and Guangchuang Yu
#' @importFrom fs path_join
#' @importFrom digest digest
#' @export
yread <- function(file, reader = readLines, params = list(),
cache_dir = NULL) {
if (!is.null(cache_dir)) {
# Generate a unique cache filename based on the file URL
cache_filename <- fs::path_join(c(cache_dir, paste0(digest::digest(file), ".rds")))
} else {
cache_filename <- NULL
}
# Check if the cached file exists
if (!is.null(cache_filename) && file.exists(cache_filename)) {
# If cached file exists, load and return the cached data
cached_data <- readRDS(cache_filename)
return(cached_data)
} else {
# If cached file does not exist, read and cache the data
data <- do.call(reader, args = c(file, params))
if (!is.null(cache_filename)) {
saveRDS(data, cache_filename)
}
return(data)
}
}
##' read clipboard
##'
##'
##' @title read.cb
##' @param reader function to read the clipboard
##' @param ... parameters for the reader
##' @return clipboard content, output type depends on the output of the reader
##' @author Guangchuang Yu
##' @importFrom utils read.table
##' @export
read.cb <- function(reader = read.table, ...) {
os <- which_os()
if (os == "Darwin") {
clip <- pipe("pbpaste")
} else {
clip <- "clipboard"
}
reader(clip, ...)
}
##' open selected directory or file
##'
##'
##' @title o
##' @param file to be open; open working directory by default
##' @return No return value, called for opening specific directory or file
##' @examples
##' \dontrun{
##' ## to open current working directory
##' o()
##' }
##' @export
##' @author Guangchuang Yu
o <- function(file=".") {
file <- normalizePath(file)
os <- which_os()
if (is.rserver()) {
if (dir.exists(file)) {
stop("open directory in RStudio Server is not supported.")
}
rserver_ip <- getOption("rserver_ip")
if (!is.null(rserver_ip)) {
rserver_port <- getOption("rserver_port") %||% '8787'
if (!startsWith(rserver_ip, "http")) {
rserver_ip <- paste0("http://", rserver_ip)
}
utils::browseURL(
paste0(
paste(rserver_ip, rserver_port, sep=":"),
"/file_show?path=",
file
))
} else {
file.edit <- get("file.edit")
file.edit(file)
}
} else if (os == "Darwin") {
cmd <- paste("open", file)
system(cmd)
} else if (os == "Linux") {
cmd <- paste("xdg-open", file, "&")
system(cmd)
} else if (os == "Windows") {
## wd <- sub("/", "\\", getwd())
## cmd <- paste("explorer", wd)
## suppressWarnings(shell(cmd))
cmd <- paste("start", file)
shell(cmd)
}
}
is.rserver <- function(){
RStudio.Version <- tryCatch(get("RStudio.Version"), error = function(e) NULL)
if(is.null(RStudio.Version)) return(FALSE)
if(!is.function(RStudio.Version)) return(FALSE)
RStudio.Version()$mode == 'server'
}
##' Open data frame in Excel. It can be used in pipe.
##'
##'
##' @title show_in_excel
##' @param .data a data frame to be open
##' @return original .data
##' @export
##' @author Guangchuang Yu
show_in_excel <- function(.data) {
f <- tempfile(fileext = '.csv')
utils::write.csv(.data, file=f)
o(f)
invisible(.data)
}
yulab.utils/R/sudo-install.R 0000644 0001762 0000144 00000001132 14444013464 015470 0 ustar ligges users sudo_install <- function(pkgs) {
## pkgs_str <- paste0('"', pkgs, '"') %>%
## paste(collapse=',') %>%
## paste("c(", ., ")")
## rcmd0 <- 'options(repos = c(CRAN = "https://mirrors.e-ducation.cn/CRAN/"));'
os <- Sys.info()[1]
if (os == "Windows") {
sudo <- ""
} else {
sudo <- "sudo"
}
for (pkg in pkgs) {
pkg <- paste0('"', pkg, '"')
rcmd <- paste0('install.packages(', pkg, ')')
## rcmd <- paste0(rcmd0, rcmd)
cmd <- paste0(sudo, " Rscript -e '", rcmd, "'")
system(cmd)
}
}
yulab.utils/R/install_zip.R 0000644 0001762 0000144 00000004130 14660013201 015370 0 ustar ligges users ##' install github package
##'
##' it download the zip file first and use `install_zip` to install it
##' @title install_zip_gh
##' @param repo github repo
##' @param ref github branch, default is HEAD, which means the default branch of the GitHub repo
##' @param args argument to build package
##' @return No return value, called for installing github package
##' @importFrom utils download.file
##' @export
##' @author Guangchuang Yu
install_zip_gh <- function(repo, ref = "HEAD", args = "--no-build-vignettes") {
## repo <- 'GuangchuangYu/nCov2019'
url <- paste0('https://codeload.github.com/', repo, '/zip/', ref)
f <- tempfile(fileext=".zip")
mydownload(url, destfile = f)
if (!is_valid_zip(f)) {
stop("Invalid zip file downloaded, please check the 'ref' parameter to set a correct github branch.")
}
install_zip(f, args=args)
}
##' install R package from zip file of source codes
##'
##'
##' @title install_zip
##' @param file zip file
##' @param args argument to build package
##' @return No return value, called for install R package from zip file of source codes
##' @export
##' @author Guangchuang Yu
install_zip <- function(file, args = "--no-build-vignettes") {
dir <- tempfile()
utils::unzip(file, exdir=dir)
fs <- list.files(path=dir, full.names=T)
#if (length(fs) == 1 && dir.exists(fs)) {
# dir <- fs
#}
## dir <- paste0(dir, '/', basename(repo), '-master')
dir <- fs[which.max(file.info(fs)$atime)]
if ("INDEX" %in% list.files(dir)) {
# file is binary package
pkg <- file
} else {
# file is zip of package source
## remotes::install_local(path=dir, ..., force=TRUE)
## pkg <- pkgbuild::build(dir, args=args)
build <- get_fun_from_pkg('pkgbuild', 'build')
pkg <- build(dir, args=args)
}
utils::install.packages(pkg, repos=NULL)
}
is_valid_zip <- function(zipfile) {
fs <- tryCatch(utils::unzip(zipfile, list=TRUE), error = function(e) NULL)
if (is.null(fs)) return(FALSE)
return(TRUE)
}
yulab.utils/R/bib-knownledge.R 0000644 0001762 0000144 00000026626 14713050757 015765 0 ustar ligges users bib_knownledge <- function(id) {
bib <- c(
innovation2024 = bib_clusterProfiler_innovation2024,
np2024 = bib_clusterProfiler_np2024,
innovation2021 = bib_clusterProfiler_innovation2021,
omics2012 = bib_clusterProfiler_omics2012,
chipseeker2022 = bib_chipseeker_cp2022,
chipseeker2015 = bib_chipseeker_bioinfo2015,
gosemsim2020 = bib_gosemsim_mmb2020,
gosemsim2010 = bib_gosemsim_bioinfo2010,
meshes2018 = bib_meshes_bioinfo2018,
reactome2016 = bib_reactomepa_mbs20016,
dose2015 = bib_dose_bioinfo2015
)
if (!id %in% names(bib)) return(NULL)
bib[id]
}
ref_knownledge <- function() {
refs <- c(
ChIPseeker_CP = paste(
"Qianwen Wang, Ming Li, Tianzhi Wu, Li Zhan, Lin Li, Meijun Chen, Wenqin Xie, Zijing Xie, Erqiang Hu, Shuangbin Xu, Guangchuang Yu.",
"Exploring epigenomic datasets by ChIPseeker.",
"Current Protocols. 2022, 2(10): e585"),
ChIPseeker = paste(
"Guangchuang Yu, Li-Gen Wang, and Qing-Yu He.",
"ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization.",
"Bioinformatics. 2015, 31(14):2382-2383"),
GOSemSim_MMB = paste(
"Guangchuang Yu.",
"Gene Ontology Semantic Similarity Analysis Using GOSemSim.",
"In: Kidder B. (eds) Stem Cell Transcriptional Networks.",
"Methods in Molecular Biology. 2020, 2117:207-215.",
"Humana, New York, NY."),
GOSemSim = paste(
"Guangchuang Yu, Fei Li, Yide Qin, Xiaochen Bo, Yibo Wu and Shengqi Wang.",
"GOSemSim: an R package for measuring semantic similarity among GO terms and gene products.",
"Bioinformatics. 2010, 26(7):976-978"),
DOSE = paste(
"Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He.",
"DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis.",
"Bioinformatics. 2015, 31(4):608-609"),
ReactomePA = paste(
"Guangchuang Yu, Qing-Yu He.",
"ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization.",
"Molecular BioSystems. 2016, 12(2):477-479"),
clusterProfiler_NP = paste(
"S Xu, E Hu, Y Cai, Z Xie, X Luo, L Zhan, W Tang,",
"Q Wang, B Liu, R Wang, W Xie, T Wu, L Xie, G Yu.",
"Using clusterProfiler to characterize multiomics data.",
"Nature Protocols. 2024, 19(11):3292-3320"),
clusterProfiler_Innovation2024 = paste(
"G Yu.",
"Thirteen years of clusterProfiler.",
"The Innovation. 2024, 5(6):100722"),
clusterProfiler_Innovation = paste(
"T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou,",
"W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu.",
"clusterProfiler 4.0: A universal enrichment tool for interpreting omics data.",
"The Innovation. 2021, 2(3):100141"),
clusterProfiler = paste(
"Guangchuang Yu, Li-Gen Wang, Yanyan Han and Qing-Yu He.",
"clusterProfiler: an R package for comparing biological themes among gene clusters.",
"OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287"),
meshes = paste(
"Guangchuang Yu.",
"Using meshes for MeSH term enrichment and semantic analyses.",
"Bioinformatics. 2018, 34(21):3766-3767, doi:10.1093/bioinformatics/bty410")
)
return(refs)
}
ref2 <- ref_knownledge()
bib_clusterProfiler_innovation2024 <- citEntry(
entry ="ARTICLE",
title = "Thirteen years of clusterProfiler",
author = c(person("Guangchuang", "Yu")),
url = "https://doi.org/10.1016/j.xinn.2024.100722",
doi = "10.1016/j.xinn.2024.100722",
journal = "The Innovation",
month = "Nov",
year = "2024",
volume = "5",
number = "6",
pages = "100722",
textVersion = ref2['clusterProfiler_Innovation2024']
)
bib_clusterProfiler_np2024 <- citEntry(
entry ="ARTICLE",
title = "Using clusterProfiler to characterize multiomics data",
author = c(
person("Shuangbin", "Xu"),
person("Erqiang", "Hu"),
person("Yantong", "Cai"),
person("Zijing", "Xie"),
person("Xiao", "Luo"),
person("Li", "Zhan"),
person("Wenli", "Tang"),
person("Qianwen", "Wang"),
person("Bingdong", "Liu"),
person("Rui", "Wang"),
person("Wenqin", "Xie"),
person("Tianzhi", "Wu"),
person("Liwei", "Xie"),
person("Guangchuang", "Yu")
),
issn = "1750-2799",
url = "https://www.nature.com/articles/s41596-024-01020-z",
doi = "10.1038/s41596-024-01020-z",
journal = "Nature Protocols",
month = "Nov",
year = "2024",
volume = "19",
number = "11",
pages = "3292-3320",
textVersion = ref2['clusterProfiler_NP']
)
bib_clusterProfiler_innovation2021 <- citEntry(entry ="ARTICLE",
title = "clusterProfiler 4.0: A universal enrichment tool for interpreting omics data",
author = c(
person("Tianzhi", "Wu"),
person("Erqiang", "Hu"),
person("Shuangbin", "Xu"),
person("Meijun", "Chen"),
person("Pingfan", "Guo"),
person("Zehan", "Dai"),
person("Tingze", "Feng"),
person("Lang", "Zhou"),
person("Wenli", "Tang"),
person("Li", "Zhan"),
person("xiaochong", "Fu"),
person("Shanshan", "Liu"),
person("Xiaochen", "Bo"),
person("Guangchuang", "Yu")
),
journal = "The Innovation",
year = "2021",
volume = "2",
number = "3",
pages = "100141",
PMID = "",
doi = "10.1016/j.xinn.2021.100141",
textVersion = ref2['clusterProfiler_Innovation']
)
bib_clusterProfiler_omics2012 <- citEntry(entry ="ARTICLE",
title = "clusterProfiler: an R package for comparing biological themes among gene clusters",
author = personList(
as.person("Guangchuang Yu"),
as.person("Li-Gen Wang"),
as.person("Yanyan Han"),
as.person("Qing-Yu He")
),
journal = "OMICS: A Journal of Integrative Biology",
year = "2012",
volume = "16",
number = "5",
pages = "284-287",
PMID = "22455463",
doi = "10.1089/omi.2011.0118",
textVersion = ref2['clusterProfiler']
)
bib_meshes_bioinfo2018 <- citEntry(entry ="ARTICLE",
title = "Using meshes for MeSH term enrichment and semantic analyses ",
author = as.person("Guangchuang Yu"),
journal = "Bioinformatics",
year = "2018",
volume = "34",
number = "21",
pages = "3766-3767",
PMID = "29790928",
doi = "10.1093/bioinformatics/bty410",
textVersion = ref2["meshes"]
)
bib_reactomepa_mbs20016 <- citEntry(entry = "ARTICLE",
title = "ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization",
author = c(
person("Guangchuang", "Yu"),
person("Qing-Yu", "He")
),
journal = "Molecular BioSystems",
year = "2016",
volume = "12",
number = "12",
pages = "477-479",
PMID = "26661513",
url = "http://pubs.rsc.org/en/Content/ArticleLanding/2015/MB/C5MB00663E",
doi = "10.1039/C5MB00663E",
textVersion = ref2['ReactomePA']
)
bib_dose_bioinfo2015 <- citEntry(entry = "ARTICLE",
title = "DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis",
author = c(
person("Guangchuang", "Yu"),
person("Li-Gen", "Wang"),
person("Guang-Rong", "Yan"),
person("Qing-Yu", "He")
),
journal = "Bioinformatics",
year = "2015",
volume = "31",
number = "4",
pages = "608-609",
PMID = "",
url = "http://bioinformatics.oxfordjournals.org/content/31/4/608",
doi = "10.1093/bioinformatics/btu684",
textVersion = ref2['DOSE']
)
bib_chipseeker_cp2022 <- citEntry(entry ="ARTICLE",
title = "Exploring epigenomic datasets by ChIPseeker",
author = c(
person("Qianwen", "Wang"),
person("Ming", "Li"),
person("Tianzhi", "Wu"),
person("Li", "Zhan"),
person("Lin", "Li"),
person("Meijun", "Chen"),
person("Wenqin", "Xie"),
person("Zijing", "Xie"),
person("Erqiang", "Hu"),
person("Shuangbin", "Xu"),
person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com")
),
journal = "Current Protocols",
year = "2022",
volume = "2",
number = "10",
pages = "e585",
PMID = "36286622",
doi = "10.1002/cpz1.585",
url = "https://onlinelibrary.wiley.com/share/author/GYJGUBYCTRMYJFN2JFZZ?target=10.1002/cpz1.585",
textVersion = ref2['ChIPseeker_CP']
)
bib_chipseeker_bioinfo2015 <- citEntry(entry ="ARTICLE",
title = "ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization",
author = personList(
as.person("Guangchuang Yu"),
as.person("Li-Gen Wang"),
as.person("Qing-Yu He")
),
journal = "Bioinformatics",
year = "2015",
volume = "31",
number = "14",
pages = "2382-2383",
PMID = "25765347",
doi = "10.1093/bioinformatics/btv145",
textVersion = ref2['ChIPseeker']
)
bib_gosemsim_mmb2020 <- citEntry(entry ="ARTICLE",
title = "Gene Ontology Semantic Similarity Analysis Using GOSemSim",
author = person("Guangchuang", "Yu"),
journal = "Methods in Molecular Biology",
shortjournal = "Methods Mol. Biol.",
year = "2020",
volume = "2117",
pages = "207-215",
PMID = "31960380",
issn = "1940-6029",
doi = "10.1007/978-1-0716-0301-7_11",
textVersion = ref2['GOSemSim_MMB']
)
bib_gosemsim_bioinfo2010 <- citEntry(entry ="ARTICLE",
title = "GOSemSim: an R package for measuring semantic similarity among GO terms and gene products",
author = personList(
as.person("Guangchuang Yu"),
as.person("Fei Li"),
as.person("Yide Qin"),
as.person("Xiaochen Bo"),
as.person("Yibo Wu"),
as.person("Shengqi Wang")
),
journal = "Bioinformatics",
year = "2010",
volume = "26",
number = "7",
pages = "976-978",
PMID = "20179076",
doi = "10.1093/bioinformatics/btq064",
textVersion = ref2['GOSemSim']
)
yulab.utils/R/utilities.R 0000644 0001762 0000144 00000001241 14741745041 015071 0 ustar ligges users `%||%` <- function(a, b) ifelse(is.null(a), b, a)
.hi <- function(package = NULL, n=2L) {
env <- sys.parent(n)
if (!is.null(env)) {
caller <- deparse(sys.call(env))
caller <- sub("(\\w+)\\(.*", "\\1", caller)
if (is.null(package)) return(FALSE)
if (get_caller_package(caller) %in% package) return(TRUE)
}
return(FALSE)
}
get_caller_package <- function(caller) {
if (is.character(caller)) {
fn <- tryCatch(eval(parse(text=caller)), error=function(e) NULL)
if (is.null(fn)) return("")
} else {
fn <- caller
}
return(environmentName(environment(fn)))
}
yulab.utils/R/zzz.R 0000644 0001762 0000144 00000000341 14651121636 013711 0 ustar ligges users ## @importFrom memoise memoise
.onLoad <- function(libname, pkgname) {
# yread <<- memoise::memoise(yread)
# yread_tsv <<- memoise::memoise(yread_tsv)
# packageStartupMessage(yulab_msg(pkgname))
}
yulab.utils/R/scale.R 0000644 0001762 0000144 00000000566 14443621642 014155 0 ustar ligges users ##' normalized data by range
##'
##'
##' @title scale-range
##' @param data the input data.
##' @return normalized data
##' @export
##' @author Guangchuang Yu
scale_range <- function(data) {
normalized_data <- apply(data, 2, function(x) {
(x - min(x, na.rm = TRUE)) / (max(x, na.rm = TRUE) - min(x, na.rm = TRUE))
})
as.data.frame(normalized_data)
}
yulab.utils/R/yulab-utils-package.R 0000644 0001762 0000144 00000000045 14560213723 016716 0 ustar ligges users #' @keywords internal
"_PACKAGE"
yulab.utils/R/matrix-utils.R 0000644 0001762 0000144 00000001713 14471061074 015521 0 ustar ligges users ##' convert a matrix to a tidy data frame
##' (from wide to long format as described in the tidyverse concept)
##'
##'
##' @title mat2df
##' @param x the input matrix
##' @return a data.frame in long format with the 'value' column stores the original values
##' and 'row' and 'col' columns stored in row and column index as in x
##' @examples
##' x <- matrix(1:15, nrow = 3)
##' mat2df(x)
##' @export
##' @author Guangchuang Yu
mat2df <- function(x) {
nr <- nrow(x)
nc <- ncol(x)
d <- data.frame(
value = as.vector(x),
row = rep(1:nr, times = nc),
col = rep(1:nc, each = nr)
)
return(d)
}
##' convert a matrix to a list
##'
##'
##' @title mat2list
##' @param x the input matrix
##' @return a list that contains matrix columns as its elements
##' @examples
##' x <- matrix(1:15, nrow = 3)
##' mat2list(x)
##' @export
mat2list <- function(x){
lapply(seq_len(ncol(x)), function(i) x[,i])
}
yulab.utils/R/concat.r 0000644 0001762 0000144 00000004563 14723520003 014364 0 ustar ligges users #' chunked array
#'
#' concate two vector/chunked_array into a chunked_array object
#' @title c2
#' @param x a vector or chunked_array object
#' @param y a vector or chunked_array object
#' @return chunked_array object
#' @author Guangchuang Yu
#' @export
c2 <- function(x, y) {
if (length(x) == 0) return(y)
if (length(y) == 0) return(x)
same_mode <- (is.numeric(x) && is.numeric(y)) ||
(is.character(x) && is.character(y))
if (!same_mode) stop("x and y should be both numeric or character vector.")
X <- as_chunked_array(x)
Y <- as_chunked_array(y)
res <- structure(
list(
vector_list = c(X$vector_list, Y$vector_list),
idx = c(X$idx, Y$idx + length(X))
),
class = "chunked_array"
)
return(res)
}
as_chunked_array <- function(x) {
if (inherits(x, "chunked_array")) return(x)
if (!is.numeric(x) && !is.character(x)) {
stop("only numeric/character vector supported")
}
structure(
list(
vector_list = list(x),
idx = 0
),
class = "chunked_array"
)
}
#' @method as.vector chunked_array
#' @export
as.vector.chunked_array <- function(x, mode = "any") {
unlist(x$vector_list)
}
#' @method print chunked_array
#' @export
print.chunked_array <- function(x, ...) {
n <- length(x)
msg <- sprintf("chunked array with size of %d\n", n)
cat(msg)
}
#' @method length chunked_array
#' @export
length.chunked_array <- function(x) {
last_item(x$idx) + length(last_item(x$vector_list))
}
last_item <- function(x) {
if (is.list(x)) return(x[[length(x)]])
x[length(x)]
}
#' @method [ chunked_array
#' @export
`[.chunked_array` <- function(x, i, ...) {
# array_idx <- vapply(i, \(ii) last_item(which(ii > x$idx)), numeric(1))
#
# pos <- i - x$idx[array_idx]
#
# output <- ifelse(is.numeric(x), numeric(1), character(1))
# vapply(seq_along(i), \(j) x$vector_list[[array_idx[j]]][pos[j]], output)
as.vector(x)[i] # faster :)
}
#' @method is.numeric chunked_array
#' @export
is.numeric.chunked_array <- function(x) {
is.numeric(x$vector_list[[1]])
}
#' @method is.character chunked_array
#' @export
is.character.chunked_array <- function(x) {
is.character(x$vector_list[[1]])
}
yulab.utils/R/regexpr.R 0000644 0001762 0000144 00000004021 14660772537 014543 0 ustar ligges users ##' @rdname regexpr-style
##' @export
set_PCRE <- function() {
options(regexpr_use_perl = TRUE)
}
##' @rdname regexpr-style
##' @export
set_TRE <- function() {
options(regexpr_use_perl = FALSE)
}
##' @rdname regexpr-style
##' @export
use_perl <- function() {
res <- getOption("regexpr_use_perl", default = auto_set_regexpr_style())
return(res)
}
##' switch regular expression style (PCRE vs TRE)
##'
##' The `set_regexpr_style()` allows user to specify which style to be used,
##' while the `auto_set_regexpr_style()` automatically set the style depdending on
##' the operating system (TRE for Windows and PCRE for other OSs (Linux and Mac)).
##'
##' `set_PCRE()` force to use PCRE style while `set_TRE()` force to use TRE.
##'
##' Note that all these functions are not change the behavior of `gsub()` and `regexpr()`.
##' The functions are just set a global option to store the user's choice of whether using `perl = TRUE`.
##'
##' Users can access the option via `use_perl()` and pass the return value to `gusb()` or `regexpr()` to specify the style in use.
##'
##' @rdname regexpr-style
##' @param style one of 'PCRE' or 'TRE'
##' @return logical value of whether use perl
##' @references
##' @export
##' @author Guangchuang Yu
set_regexpr_style <- function(style) {
if (missing(style)) {
message("style is not specific, set automatically.")
auto_set_regexpr_style()
} else {
style <- match.arg(style, c("PCRE", "TRE"))
if (style == "PCRE") {
set_PCRE()
} else {
set_TRE()
}
}
res <- getOption("regexpr_use_perl")
invisible(res)
}
##' @rdname regexpr-style
##' @export
auto_set_regexpr_style <- function() {
if (which_os() == "Windows") {
set_TRE()
res <- FALSE
} else {
set_PCRE()
res <- TRUE
}
invisible(res)
}
yulab.utils/R/scihub-dl.R 0000644 0001762 0000144 00000001300 14404503310 014707 0 ustar ligges users ##' download publication via scihub
##'
##' using scihub to download publication using doi
##' @rdname scihub-dl
##' @name scihub_dl
##' @param doi doi
##' @param scihub scihub website
##' @param download whether download the pdf file
##' @return pdf url
##' @author Guangchuang Yu
##' @export
scihub_dl <- function(doi, scihub = 'sci-hub.tw', download=TRUE) {
url <- paste0('https://', scihub, '/', doi)
x <- readLines(url)
i <- grep('id = "pdf"', x)
pdf_url <-sub(".*(//.*\\.pdf).*", "https:\\1", x[i])
if (download) {
outfile <- sub(".*/", "", pdf_url)
utils::download.file(pdf_url, destfile = outfile)
}
invisible(pdf_url)
}
yulab.utils/R/str-utils.R 0000644 0001762 0000144 00000006460 14660652642 015040 0 ustar ligges users ##' wraping long string to multiple lines
##'
##'
##' @title str_wrap
##' @param string input string
##' @param width the maximum number of characters before wrapping to a new line
##' @return update strings with new line character inserted
##' @export
##' @author Guangchuang Yu
str_wrap <- function(string, width = getOption("width")) {
##
## speed comparison
## str_wrap() > stringr::str_wrap() > paste0(base::strwrap(), collapse = "\n")
##
result <- vapply(string,
FUN = function(st) {
words <- list()
i <- 1
while(nchar(st) > width) {
if (length(grep(pattern = " ", x = st, perl = use_perl())) == 0) break
y <- gregexpr(pattern = ' ', text = st, perl = use_perl())
y <- y[[1]]
n <- nchar(st)
y <- c(y,n)
idx <- which(y < width)
# When the length of first word > width
if (length(idx) == 0) idx <- 1
# Split the string into two pieces
# The length of first piece is small than width
words[[i]] <- substring(st, 1, y[idx[length(idx)]] - 1)
st <- substring(st, y[idx[length(idx)]] + 1, n)
i <- i + 1
}
words[[i]] <- st
paste0(unlist(words), collapse="\n")
},
FUN.VALUE = character(1)
)
names(result) <- NULL
result
}
##' Detect the presence or absence of a pattern at the beginning or end of a string or string vector.
##'
##'
##' @title str_starts
##' @rdname str-starts-ends
##' @param string input string
##' @param pattern pattern with which the string starts or ends
##' @param negate if TRUE, return non-matching elements
##' @return a logical vector
##' @export
##' @author Guangchuang Yu
str_starts <- function(string, pattern, negate=FALSE) {
pattern <- paste0('^', pattern)
str_detect(string, pattern, negate)
}
##' @rdname str-starts-ends
##' @export
str_ends <- function(string, pattern, negate=FALSE) {
pattern <- paste0(pattern, '$')
str_detect(string, pattern, negate)
}
##' Detect the presentce/absence of a match
##'
##'
##' @title str_detect
##' @rdname str-detect
##' @param string input string
##' @param pattern pattern to look for
##' @param negate if TRUE, inverts the resulting boolen vector
##' @return logical vector
##' @export
##' @author Guangchuang Yu
str_detect <- function(string, pattern, negate = FALSE) {
## faster than stringr::str_detect
res <- grepl(pattern = pattern, x = string, perl = use_perl())
if (negate) res <- !res
return(res)
}
##' Extract a substring using a pattern
##'
##'
##' @title str_extract
##' @rdname str-extract
##' @param string input string
##' @param pattern a regular expression to describe the pattern to extracted from the 'string'
##' @return substring
##' @export
##' @author Guangchuang Yu
str_extract <- function(string, pattern) {
i <- regexpr(pattern = pattern, text = string, perl = use_perl())
j <- attr(i, 'match.length')
res <- substring(string, i, i+j-1)
res[res == ""] <- NA
return(res)
}
yulab.utils/R/yulab-msg.R 0000644 0001762 0000144 00000005546 14663031420 014762 0 ustar ligges users ##' Messages for R package developed by YuLab
##'
##'
##' @title yulab_msg
##' @param pkgname package name
##' @param n number of citation messages
##' @return package message
##' @export
##' @author Guangchuang Yu
yulab_msg <- function(pkgname = NULL, n = 1) {
pkgs_knownledge <- c("GOSemSim",
"DOSE",
"clusterProfiler",
"meshes",
"ReactomePA",
"MicrobiomeProfiler",
"enrichplot",
"ChIPseeker")
pkgs_tree <- c("tidytree",
"treeio",
"ggtree",
"ggtreeExtra",
"ggtreeSpace",
"shinyTempSignal")
if (pkgname %in% pkgs_knownledge) {
id <- 1
} else if (pkgname %in% pkgs_tree) {
id <- 2
} else {
id <- 3
}
header_msg <- yulab_msg_header(pkgname, id)
if (id == 1) {
citation_msg <- random_ref(pkgname, ref_knownledge(), random_n = n)
} else if (id == 2) {
citation_msg <- random_ref(pkgname, ref_ggtree(), random_n = n)
} else {
citation_msg <- pkg_ref(pkgname)
}
if (is.null(citation_msg)) return(header_msg)
sprintf("%s%s", header_msg, citation_msg)
}
##' @importFrom utils packageDescription
yulab_msg_header <- function(pkgname = NULL, id = 3) {
if (is.null(pkgname)) return(NULL)
pages <- c("contribution-knowledge-mining/",
"contribution-tree-data/",
"")
urls <- sprintf("https://yulab-smu.top/%s", pages)
pkgVersion <- packageDescription(pkgname, fields = "Version")
sprintf("%s v%s Learn more at %s\n\n", pkgname, pkgVersion, urls[id])
}
random_ref <- function(pkgname, refs, random_n) {
msg <- "Please cite:\n\n"
indx <- grep(pkgname, names(refs))
if (length(indx) == 0) {
refs <- sample(refs, random_n)
} else if (length(indx) > random_n) {
refs <- sample(refs[indx], random_n)
} else {
refs <- c(refs[indx], sample(refs[-indx], random_n - length(indx)))
}
refs <- paste0(refs, collapse="\n")
if (nchar(refs) <= 0) return(NULL)
paste(strwrap(paste0(msg, refs)), collapse = "\n")
}
pkg_ref <- function(pkgname) {
refs <- c(
fanyi =
paste("D Wang, G Chen, L Li, S Wen, Z Xie, X Luo, L Zhan, S Xu, J Li, R Wang, Q Wang, G Yu.",
"Reducing language barriers, promoting information absorption, and communication using fanyi.",
"Chinese Medical Journal. 2024, 137(16):1950-1956. doi: 10.1097/CM9.0000000000003242")
)
ref <- refs[pkgname]
if (is.null(ref) || is.na(ref)) return(NULL)
msg <- "Please cite:\n\n"
str_wrap(paste0(msg, refs, "\n"))
}
yulab.utils/NAMESPACE 0000644 0001762 0000144 00000003066 14723464027 013762 0 ustar ligges users # Generated by roxygen2: do not edit by hand
S3method("[",chunked_array)
S3method(as.vector,chunked_array)
S3method(is.character,chunked_array)
S3method(is.numeric,chunked_array)
S3method(length,chunked_array)
S3method(print,chunked_array)
S3method(print,exec)
export(Biocpkg)
export(CRANpkg)
export(Githubpkg)
export(auto_set_regexpr_style)
export(c2)
export(check_pkg)
export(combinations)
export(exec)
export(get_cache)
export(get_cache_element)
export(get_cache_item)
export(get_dependencies)
export(get_fun_from_pkg)
export(has_internet)
export(initial_cache)
export(initial_cache_item)
export(install_zip)
export(install_zip_gh)
export(is.installed)
export(ls2df)
export(mat2df)
export(mat2list)
export(mypkg)
export(o)
export(packageTitle)
export(pload)
export(rbindlist)
export(read.cb)
export(rm_cache)
export(rm_cache_item)
export(scale_range)
export(scihub_dl)
export(set_PCRE)
export(set_TRE)
export(set_regexpr_style)
export(show_in_excel)
export(str_detect)
export(str_ends)
export(str_extract)
export(str_starts)
export(str_wrap)
export(update_cache_item)
export(use_perl)
export(yread)
export(yread_tsv)
export(yulab_msg)
importFrom(cli,cli_h2)
importFrom(digest,digest)
importFrom(fs,path_join)
importFrom(rlang,as_name)
importFrom(rlang,check_installed)
importFrom(rlang,enquo)
importFrom(tools,package_dependencies)
importFrom(utils,combn)
importFrom(utils,download.file)
importFrom(utils,getFromNamespace)
importFrom(utils,modifyList)
importFrom(utils,packageDescription)
importFrom(utils,read.table)
yulab.utils/NEWS.md 0000644 0001762 0000144 00000007105 14745456475 013653 0 ustar ligges users # yulab.utils 0.2.0
+ bug fixed in `get_caller_package()` (2025-01-08, Wed)
# yulab.utils 0.1.9
+ `c2()` to concate two vectors into a 'chunked_array' object (2024-12-03, Tue)
# yulab.utils 0.1.8
+ add new citation (The Innovation 2024) (2024-11-07, Thu)
+ `pload()` now supports github package (2024-11-06, Wed)
+ bug fixed in `pkg_ref()` (2024-08-26, Mon)
# yulab.utils 0.1.7
+ `has_internet()` for testing internet connection (2024-08-26, Mon)
+ `pkg_ref()` to access textVersion of package reference (2024-08-21, Wed)
+ export `str_detect()` (20024-08-19, Mon)
+ `user_dir()` to setup user data dir (20024-08-17, Sat)
+ `which_os()` to return the system name
+ `has_bin()` to check whether a command is exist in the system
# yulab.utils 0.1.6
+ `mydownload()` for downloading online file (2024-08-17, Sat)
- internally use 'httr2' and is 'https' friendly
+ update `bib_ggtree()` and `bib_knowledge()` with all previous related publications (2024-08-12, Mon)
+ remove memory caching and disable file cache by default in `yread()` and `yread_tsv()` (2024-07-27, Sat)
+ `bib_ggtree()` and `bib_knowledge()` (2024-07-27, Sat)
# yulab.utils 0.1.5
+ `yulab_msg()` for startup message of packages developed by YuLab (2024-07-26, Fri)
# yulab.utils 0.1.4
+ `str_extract()` to extract substring using a regular expression pattern (2024--01-25, Thu)
# yulab.utils 0.1.3
+ with cache ability (2023-12-27, Wed)
- `initial_cache()`
- `initial_cache_item()`
- `get_cache()`
- `get_cache_item()`
- `get_cache_element()`
- `rm_cache_item()`
- `rm_cache()`
# yulab.utils 0.1.2
+ mv translate functions to the 'fanyi' package (2023-12-14, Thu)
+ tools to switch from PCRE or TRE in regular expression (2023-12-13, Wed)
# yulab.utils 0.1.1
+ use `normalizePath()` in `o()` to convert file paths to canonical form (2023-10-06, Fri, #4)
+ change the default parameter, `ref = "master"` to `ref = "HEAD"` in the `install_zip_gh()` function to use the default branch of the GitHub repo (2023-10-02, Mon)
# yulab.utils 0.1.0
+ `install_zip()` allows both binary and source zip files (2023-09-20, Wed)
+ `pload()` for loading package with the ability to install it if not available (2023-09-16, Sat)
+ `get_dependencies()` and `packageTitle()` (2023-09-11, Mon)
+ import 'fs' and 'digest' (2023-09-07, Thu)
# yulab.utils 0.0.9
+ `ls2df()` convert list of vector to a data.frame (2023-09-01, Fri)
# yulab.utils 0.0.8
+ `mat2list()` and `combinations()` (2023-08-22, Tue)
+ remove default 'params' setting in `yread_tsv()` (2023-08-15, Tue)
# yulab.utils 0.0.7
+ update `check_pkg()` to call `rlang::check_installed()` with reason set automatically (2023-08-03, Thu)
+ `yread()` and `yread_tsv()` that read file with caching (2023-08-02, Wed)
+ `rbindlist()` to rbind a list (2023-08-01, Tue)
+ `exec()` to run system command (2023-06-19, Mon)
+ `scale_range()` to normalize data by range (2023-06-18, Sun)
# yulab.utils 0.0.6
+ `mat2df()` to convert matrix to a tidy data frame (2022-12-20, Tue)
+ `str_starts()` and `str_ends()` (2022-07-29, Fri)
# yulab.utils 0.0.5
+ `get_fun_from_pkg()` outputs friendly message if the pkg is not installed (2022-06-08, Wed)
+ `show_in_excel()`, `CRANpkg()`, `Biocpkg()`, `Githubpkg()`, `mypkg()` (2021-10-13, Wed)
# yulab.utils 0.0.4
+ `str_wrap()` (2021-10-09, Sat)
# yulab.utils 0.0.3
+ `read.cb()` (2021-08-17)
# yulab.utils 0.0.2
+ `o()`, `install_zip()`, `get_fun_from_pkg()`
# yulab.utils 0.0.1
+ `is.installed()`, `scihub_dl()`, `sudo_install()`
yulab.utils/inst/ 0000755 0001762 0000144 00000000000 14660651434 013513 5 ustar ligges users yulab.utils/inst/prototype/ 0000755 0001762 0000144 00000000000 14723463462 015562 5 ustar ligges users yulab.utils/inst/prototype/sra.r 0000644 0001762 0000144 00000000364 14712366206 016531 0 ustar ligges users get_runinfo <- function(sra_id) {
x <- rentrez::entrez_fetch(db='sra', rettype='runinfo', id = sra_id)
read.csv(textConnection(x))
}
id <- "SRX5137765"
d <- get_runinfo(id)
head(d,2)
sprintf("fastq-dump %s", d$Run[1:3])
yulab.utils/inst/prototype/GEO.r 0000644 0001762 0000144 00000001420 14712361503 016343 0 ustar ligges users
get_gse <- function(gseID) {
gsecat <- sub("\\d{3}$", "nnn", gseID)
gsesoft <- sprintf("%s_family.soft.gz", gseID)
url <- sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/soft/%s", gsecat, gseID, gsesoft)
yulab.utils:::mydownload(url, destfile = gsesoft)
GEOquery::getGEO(filename = gsesoft)
}
get_gsm <- function(gse, item = "supplementary_file_1") {
lapply(GEOquery::GSMList(gse), function(x) x@header[item])
}
download_gsm <- function(gsm) {
for (x in gsm) {
destfile <- sub(".*/([^/]+)$", "\\1", x)
yulab.utils:::mydownload(x, destfile = destfile)
}
}
gseID <- "GSE123904"
gse <- get_gse(gseID)
gsm <- get_gsm(gse)
get_gsm(gse, 'extract_protocol_ch1') |> head(2)
download_gsm(gsm)
yulab.utils/man/ 0000755 0001762 0000144 00000000000 14723464027 013311 5 ustar ligges users yulab.utils/man/regexpr-style.Rd 0000644 0001762 0000144 00000002443 14536214433 016411 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/regexpr.R
\name{set_PCRE}
\alias{set_PCRE}
\alias{set_TRE}
\alias{use_perl}
\alias{set_regexpr_style}
\alias{auto_set_regexpr_style}
\title{switch regular expression style (PCRE vs TRE)}
\usage{
set_PCRE()
set_TRE()
use_perl()
set_regexpr_style(style)
auto_set_regexpr_style()
}
\arguments{
\item{style}{one of 'PCRE' or 'TRE'}
}
\value{
logical value of whether use perl
}
\description{
The \code{set_regexpr_style()} allows user to specify which style to be used,
while the \code{auto_set_regexpr_style()} automatically set the style depdending on
the operating system (TRE for Windows and PCRE for other OSs (Linux and Mac)).
}
\details{
\code{set_PCRE()} force to use PCRE style while \code{set_TRE()} force to use TRE.
Note that all these functions are not change the behavior of \code{gsub()} and \code{regexpr()}.
The functions are just set a global option to store the user's choice of whether using \code{perl = TRUE}.
Users can access the option via \code{use_perl()} and pass the return value to \code{gusb()} or \code{regexpr()} to specify the style in use.
}
\references{
\url{https://stackoverflow.com/questions/47240375/regular-expressions-in-base-r-perl-true-vs-the-default-pcre-vs-tre}
}
\author{
Guangchuang Yu
}
yulab.utils/man/install_zip_gh.Rd 0000644 0001762 0000144 00000001212 14506453666 016610 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/install_zip.R
\name{install_zip_gh}
\alias{install_zip_gh}
\title{install_zip_gh}
\usage{
install_zip_gh(repo, ref = "HEAD", args = "--no-build-vignettes")
}
\arguments{
\item{repo}{github repo}
\item{ref}{github branch, default is HEAD, which means the default branch of the GitHub repo}
\item{args}{argument to build package}
}
\value{
No return value, called for installing github package
}
\description{
install github package
}
\details{
it download the zip file first and use \code{install_zip} to install it
}
\author{
Guangchuang Yu
}
yulab.utils/man/yulab_msg.Rd 0000644 0001762 0000144 00000000572 14650622152 015560 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/yulab-msg.R
\name{yulab_msg}
\alias{yulab_msg}
\title{yulab_msg}
\usage{
yulab_msg(pkgname = NULL, n = 1)
}
\arguments{
\item{pkgname}{package name}
\item{n}{number of citation messages}
}
\value{
package message
}
\description{
Messages for R package developed by YuLab
}
\author{
Guangchuang Yu
}
yulab.utils/man/str_wrap.Rd 0000644 0001762 0000144 00000000733 14660652103 015436 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/str-utils.R
\name{str_wrap}
\alias{str_wrap}
\title{str_wrap}
\usage{
str_wrap(string, width = getOption("width"))
}
\arguments{
\item{string}{input string}
\item{width}{the maximum number of characters before wrapping to a new line}
}
\value{
update strings with new line character inserted
}
\description{
wraping long string to multiple lines
}
\author{
Guangchuang Yu
}
yulab.utils/man/yulab-cache.Rd 0000644 0001762 0000144 00000002540 14543172523 015753 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/cache.R
\name{initial_cache}
\alias{initial_cache}
\alias{get_cache}
\alias{rm_cache}
\alias{initial_cache_item}
\alias{get_cache_item}
\alias{rm_cache_item}
\alias{update_cache_item}
\alias{get_cache_element}
\title{cache intermediate data}
\usage{
initial_cache()
get_cache()
rm_cache()
initial_cache_item(item)
get_cache_item(item)
rm_cache_item(item)
update_cache_item(item, elements)
get_cache_element(item, elements)
}
\arguments{
\item{item}{the name of the cached item}
\item{elements}{elements to be cached in the item}
}
\value{
return the cache environment, item or selected elements, depends on the functions.
}
\description{
Yulab provides a set of utilities to cache intermediate data,
including initialize the cached item, update cached item and rmove the cached item, etc.
}
\examples{
\dontrun{
slow_fib <- function(x) {
if (x < 2) return(1)
slow_fib(x-2) + slow_fib(x-1)
}
fast_fib <- function(x) {
if (x < 2) return(1)
res <- get_cache_element('fibonacci', as.character(x))
if (!is.null(res)) {
return(res)
}
res <- fast_fib(x-2) + fast_fib(x-1)
e <- list()
e[[as.character(x)]] <- res
update_cache_item('fibonacci', e)
return(res)
}
system.time(slow_fib(30))
system.time(fast_fib(30))
}
}
yulab.utils/man/str-detect.Rd 0000644 0001762 0000144 00000000677 14660652103 015662 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/str-utils.R
\name{str_detect}
\alias{str_detect}
\title{str_detect}
\usage{
str_detect(string, pattern, negate = FALSE)
}
\arguments{
\item{string}{input string}
\item{pattern}{pattern to look for}
\item{negate}{if TRUE, inverts the resulting boolen vector}
}
\value{
logical vector
}
\description{
Detect the presentce/absence of a match
}
\author{
Guangchuang Yu
}
yulab.utils/man/scihub-dl.Rd 0000644 0001762 0000144 00000000726 14404503310 015440 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/scihub-dl.R
\name{scihub_dl}
\alias{scihub_dl}
\title{download publication via scihub}
\usage{
scihub_dl(doi, scihub = "sci-hub.tw", download = TRUE)
}
\arguments{
\item{doi}{doi}
\item{scihub}{scihub website}
\item{download}{whether download the pdf file}
}
\value{
pdf url
}
\description{
using scihub to download publication using doi
}
\author{
Guangchuang Yu
}
yulab.utils/man/read.cb.Rd 0000644 0001762 0000144 00000000657 14462474155 015111 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/file.R
\name{read.cb}
\alias{read.cb}
\title{read.cb}
\usage{
read.cb(reader = read.table, ...)
}
\arguments{
\item{reader}{function to read the clipboard}
\item{...}{parameters for the reader}
}
\value{
clipboard content, output type depends on the output of the reader
}
\description{
read clipboard
}
\author{
Guangchuang Yu
}
yulab.utils/man/install_zip.Rd 0000644 0001762 0000144 00000000744 14404503310 016116 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/install_zip.R
\name{install_zip}
\alias{install_zip}
\title{install_zip}
\usage{
install_zip(file, args = "--no-build-vignettes")
}
\arguments{
\item{file}{zip file}
\item{args}{argument to build package}
}
\value{
No return value, called for install R package from zip file of source codes
}
\description{
install R package from zip file of source codes
}
\author{
Guangchuang Yu
}
yulab.utils/man/o.Rd 0000644 0001762 0000144 00000000702 14510021774 014025 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/file.R
\name{o}
\alias{o}
\title{o}
\usage{
o(file = ".")
}
\arguments{
\item{file}{to be open; open working directory by default}
}
\value{
No return value, called for opening specific directory or file
}
\description{
open selected directory or file
}
\examples{
\dontrun{
## to open current working directory
o()
}
}
\author{
Guangchuang Yu
}
yulab.utils/man/combinations.Rd 0000644 0001762 0000144 00000000465 14471060707 016267 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/combinations.R
\name{combinations}
\alias{combinations}
\title{combinations}
\usage{
combinations(n)
}
\arguments{
\item{n}{number of sets}
}
\value{
a list of all combinations
}
\description{
all possible combinations of n sets
}
yulab.utils/man/yread.Rd 0000644 0001762 0000144 00000001471 14651201530 014673 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/file.R
\name{yread_tsv}
\alias{yread_tsv}
\alias{yread}
\title{yread}
\usage{
yread_tsv(
file,
reader = utils::read.delim,
params = list(),
cache_dir = tempdir()
)
yread(file, reader = readLines, params = list(), cache_dir = NULL)
}
\arguments{
\item{file}{a file or url}
\item{reader}{a function to read the 'file_url'}
\item{params}{a list of parameters that passed to the 'reader'}
\item{cache_dir}{a folder to store cache files. If set to NULL will disable cache.}
}
\value{
the output of using the 'reader' to read the 'file_url' with parameters specified by the 'params'
}
\description{
read file with caching
}
\details{
This function read a file (local or url) and cache the content.
}
\author{
Yonghe Xia and Guangchuang Yu
}
yulab.utils/man/mat2df.Rd 0000644 0001762 0000144 00000001100 14474263201 014737 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/matrix-utils.R
\name{mat2df}
\alias{mat2df}
\title{mat2df}
\usage{
mat2df(x)
}
\arguments{
\item{x}{the input matrix}
}
\value{
a data.frame in long format with the 'value' column stores the original values
and 'row' and 'col' columns stored in row and column index as in x
}
\description{
convert a matrix to a tidy data frame
(from wide to long format as described in the tidyverse concept)
}
\examples{
x <- matrix(1:15, nrow = 3)
mat2df(x)
}
\author{
Guangchuang Yu
}
yulab.utils/man/packageTitle.Rd 0000644 0001762 0000144 00000000554 14477505127 016204 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/pkg-utils.R
\name{packageTitle}
\alias{packageTitle}
\title{packageTitle}
\usage{
packageTitle(pkg, repo = "CRAN")
}
\arguments{
\item{pkg}{package name}
\item{repo}{'CRAN' and/or 'BioC'}
}
\value{
reverse dependencies
}
\description{
Extract package title
}
\author{
Guangchuang Yu
}
yulab.utils/man/has_internet.Rd 0000644 0001762 0000144 00000000570 14663004013 016251 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/os.R
\name{has_internet}
\alias{has_internet}
\title{has_internet}
\usage{
has_internet(site = "https://www.baidu.com/")
}
\arguments{
\item{site}{URL to test connection}
}
\value{
logical value
}
\description{
test for internect connection via reading lines from a URL
}
\author{
Guangchuang Yu
}
yulab.utils/man/c2.Rd 0000644 0001762 0000144 00000000617 14723464027 014110 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/concat.r
\name{c2}
\alias{c2}
\title{c2}
\usage{
c2(x, y)
}
\arguments{
\item{x}{a vector or chunked_array object}
\item{y}{a vector or chunked_array object}
}
\value{
chunked_array object
}
\description{
chunked array
}
\details{
concate two vector/chunked_array into a chunked_array object
}
\author{
Guangchuang Yu
}
yulab.utils/man/pload.Rd 0000644 0001762 0000144 00000001151 14501256665 014676 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/pkg-utils.R
\name{pload}
\alias{pload}
\title{pload}
\usage{
pload(package, action = "auto")
}
\arguments{
\item{package}{package name}
\item{action}{function used to install package.
If 'action = "auto"', it will try to use 'BiocManager::install()' if it is available.}
}
\value{
the selected package loaded to the R session
}
\description{
loading a package
}
\details{
The function use 'library()' to load the package.
If the package is not installed, the function will try to install it before loading it.
}
\author{
Guangchuang Yu
}
yulab.utils/man/cran-bioc-pkg.Rd 0000644 0001762 0000144 00000000703 14404503310 016175 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/pkg-utils.R
\name{CRANpkg}
\alias{CRANpkg}
\alias{Biocpkg}
\title{print md text of package with link to homepage (CRAN or Bioconductor)}
\usage{
CRANpkg(pkg)
Biocpkg(pkg)
}
\arguments{
\item{pkg}{package name}
}
\value{
md text string
}
\description{
print md text of package with link to homepage (CRAN or Bioconductor)
}
\author{
Guangchuang Yu
}
yulab.utils/man/check_pkg.Rd 0000644 0001762 0000144 00000001272 14462656667 015535 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/pkg-utils.R
\name{check_pkg}
\alias{check_pkg}
\title{check_pkg}
\usage{
check_pkg(pkg, reason = NULL, ...)
}
\arguments{
\item{pkg}{package names}
\item{reason}{the reason to check the pkg. If NULL, it will set the reason to the parent call.}
\item{...}{additional parameters that passed to \code{rlang::check_installed()}}
}
\value{
see also \link[rlang:is_installed]{check_installed}
}
\description{
Check whether the input packages are installed
}
\details{
This function check whether the input packages are installed. If not, it asks the user whether to install the missing packages.
}
\author{
Guangchuang Yu
}
yulab.utils/man/show_in_excel.Rd 0000644 0001762 0000144 00000000562 14404503310 016412 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/file.R
\name{show_in_excel}
\alias{show_in_excel}
\title{show_in_excel}
\usage{
show_in_excel(.data)
}
\arguments{
\item{.data}{a data frame to be open}
}
\value{
original .data
}
\description{
Open data frame in Excel. It can be used in pipe.
}
\author{
Guangchuang Yu
}
yulab.utils/man/exec.Rd 0000644 0001762 0000144 00000000507 14660063734 014526 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/os.R
\name{exec}
\alias{exec}
\title{exec}
\usage{
exec(command)
}
\arguments{
\item{command}{system command to run}
}
\value{
An \code{exec} instance that stores system command outputs
}
\description{
run system command
}
\author{
Guangchuang Yu
}
yulab.utils/man/rbindlist.Rd 0000644 0001762 0000144 00000000511 14474316464 015573 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/list.R
\name{rbindlist}
\alias{rbindlist}
\title{rbindlist}
\usage{
rbindlist(x)
}
\arguments{
\item{x}{a list that have similar elements that can be rbind to a data.frame}
}
\value{
data.frame
}
\description{
rbind a list
}
\author{
Guangchuang Yu
}
yulab.utils/man/get_dependencies.Rd 0000644 0001762 0000144 00000000612 14477505127 017067 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/pkg-utils.R
\name{get_dependencies}
\alias{get_dependencies}
\title{get_dependencies}
\usage{
get_dependencies(pkg, repo = c("CRAN", "BioC"))
}
\arguments{
\item{pkg}{package name}
\item{repo}{'CRAN' and/or 'BioC'}
}
\value{
reverse dependencies
}
\description{
get reverse dependencies
}
\author{
Guangchuang Yu
}
yulab.utils/man/get_fun_from_pkg.Rd 0000644 0001762 0000144 00000000640 14404503310 017074 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/pkg-utils.R
\name{get_fun_from_pkg}
\alias{get_fun_from_pkg}
\title{get_fun_from_pkg}
\usage{
get_fun_from_pkg(pkg, fun)
}
\arguments{
\item{pkg}{package}
\item{fun}{function}
}
\value{
function
}
\description{
load function from package
}
\examples{
get_fun_from_pkg('utils', 'zip')
}
\author{
Guangchuang Yu
}
yulab.utils/man/str-starts-ends.Rd 0000644 0001762 0000144 00000001144 14474263201 016647 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/str-utils.R
\name{str_starts}
\alias{str_starts}
\alias{str_ends}
\title{str_starts}
\usage{
str_starts(string, pattern, negate = FALSE)
str_ends(string, pattern, negate = FALSE)
}
\arguments{
\item{string}{input string}
\item{pattern}{pattern with which the string starts or ends}
\item{negate}{if TRUE, return non-matching elements}
}
\value{
a logical vector
}
\description{
Detect the presence or absence of a pattern at the beginning or end of a string or string vector.
}
\author{
Guangchuang Yu
}
yulab.utils/man/yulab.utils-package.Rd 0000644 0001762 0000144 00000001212 14660773203 017437 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/yulab-utils-package.R
\docType{package}
\name{yulab.utils-package}
\alias{yulab.utils}
\alias{yulab.utils-package}
\title{yulab.utils: Supporting Functions for Packages Maintained by 'YuLab-SMU'}
\description{
Miscellaneous functions commonly used by 'YuLab-SMU'.
}
\seealso{
Useful links:
\itemize{
\item \url{https://yulab-smu.top/}
\item Report bugs at \url{https://github.com/YuLab-SMU/yulab.utils/issues}
}
}
\author{
\strong{Maintainer}: Guangchuang Yu \email{guangchuangyu@gmail.com} (\href{https://orcid.org/0000-0002-6485-8781}{ORCID})
}
\keyword{internal}
yulab.utils/man/mypkg.Rd 0000644 0001762 0000144 00000000531 14404503310 014707 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/pkg-utils.R
\name{mypkg}
\alias{mypkg}
\title{mypkg}
\usage{
mypkg(pkg, url)
}
\arguments{
\item{pkg}{package name}
\item{url}{package url}
}
\value{
md text string
}
\description{
print md text of link to a pakcage
}
\author{
Guangchuang Yu
}
yulab.utils/man/scale_range.Rd 0000644 0001762 0000144 00000000465 14443622064 016044 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/scale.R
\name{scale_range}
\alias{scale_range}
\title{scale-range}
\usage{
scale_range(data)
}
\arguments{
\item{data}{the input data.}
}
\value{
normalized data
}
\description{
normalized data by range
}
\author{
Guangchuang Yu
}
yulab.utils/man/str-extract.Rd 0000644 0001762 0000144 00000000645 14554357677 016103 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/str-utils.R
\name{str_extract}
\alias{str_extract}
\title{str_extract}
\usage{
str_extract(string, pattern)
}
\arguments{
\item{string}{input string}
\item{pattern}{a regular expression to describe the pattern to extracted from the 'string'}
}
\value{
substring
}
\description{
Extract a substring using a pattern
}
\author{
Guangchuang Yu
}
yulab.utils/man/ls2df.Rd 0000644 0001762 0000144 00000000544 14474316464 014621 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/list.R
\name{ls2df}
\alias{ls2df}
\title{Convert a list of vector (e.g, gene IDs) to a data.frame object}
\usage{
ls2df(inputList)
}
\arguments{
\item{inputList}{A list of vector}
}
\value{
a data.frame object.
}
\description{
Convert a list of vector to a data.frame object.
}
yulab.utils/man/mat2list.Rd 0000644 0001762 0000144 00000000554 14474263201 015335 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/matrix-utils.R
\name{mat2list}
\alias{mat2list}
\title{mat2list}
\usage{
mat2list(x)
}
\arguments{
\item{x}{the input matrix}
}
\value{
a list that contains matrix columns as its elements
}
\description{
convert a matrix to a list
}
\examples{
x <- matrix(1:15, nrow = 3)
mat2list(x)
}
yulab.utils/man/github-pkg.Rd 0000644 0001762 0000144 00000000614 14535556535 015651 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/pkg-utils.R
\name{Githubpkg}
\alias{Githubpkg}
\title{print md text of package with link to github repo}
\usage{
Githubpkg(user, pkg)
}
\arguments{
\item{user}{github user}
\item{pkg}{package name}
}
\value{
md text string
}
\description{
print md text of package with link to github repo
}
\author{
Guangchuang Yu
}
yulab.utils/man/is.installed.Rd 0000644 0001762 0000144 00000000754 14404503310 016160 0 ustar ligges users % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/pkg-utils.R
\name{is.installed}
\alias{is.installed}
\title{is.installed}
\usage{
is.installed(packages)
}
\arguments{
\item{packages}{package names}
}
\value{
logical vector
}
\description{
Check whether the input packages are installed
}
\details{
This function check whether the input packages are installed
}
\examples{
is.installed(c("dplyr", "ggplot2"))
}
\author{
Guangchuang Yu
}
yulab.utils/DESCRIPTION 0000644 0001762 0000144 00000001512 14746344222 014242 0 ustar ligges users Package: yulab.utils
Title: Supporting Functions for Packages Maintained by 'YuLab-SMU'
Version: 0.2.0
Authors@R: c(person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6485-8781")))
Description: Miscellaneous functions commonly used by 'YuLab-SMU'.
Depends: R (>= 4.2.0)
Imports: cli, digest, fs, rlang, tools, utils
Suggests: httr2, jsonlite, openssl, rappdirs
ByteCompile: true
License: Artistic-2.0
URL: https://yulab-smu.top/
BugReports: https://github.com/YuLab-SMU/yulab.utils/issues
Encoding: UTF-8
RoxygenNote: 7.3.2
NeedsCompilation: no
Packaged: 2025-01-29 05:58:33 UTC; HUAWEI
Author: Guangchuang Yu [aut, cre] ()
Maintainer: Guangchuang Yu
Repository: CRAN
Date/Publication: 2025-01-29 06:20:02 UTC