R/genomic_utils.R
In 1156054203/circlize-: Circular Visualization
# == title
# Read/parse cytoband data from a data frame/file/UCSC database
#
# == param
# -cytoband Path of the cytoband file or a data frame that already contains cytoband data
# -species Abbreviations of species. e.g. hg19 for human, mm10 for mouse. If this
# value is specified, the function will download ``cytoBand.txt.gz`` from
# UCSC website automatically.
# -chromosome.index subset of chromosomes, also used to reorder chromosomes.
# -sort.chr Whether chromosome names should be sorted (first sort by numbers then by letters).
# If ``chromosome.index`` is set, this argument is enforced to ``FALSE``
#
# == details
# The function read the cytoband data, sort the chromosome names and calculate the length of each chromosome.
# By default, it is human hg19 cytoband data.
#
# You can find the data structure of the cytoband data from http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/cytoBand.txt.gz
#
# == values
# -``df`` Data frame for cytoband data (rows are sorted if ``sort.chr`` is set to ``TRUE``)
# -``chromosome`` Sorted chromosome names
# -``chr.len`` Length of chromosomes. Orders are same as ``chromosome``
#
# == example
# data = read.cytoband(species = "hg19")
# data = read.cytoband(cytoband = system.file(package = "circlize", "extdata", "cytoBand.txt"))
# cytoband = read.table(system.file(package = "circlize", "extdata", "cytoBand.txt"),
# colClasses = c("character", "numeric", "numeric", "character", "character"), sep = "\t")
# data = read.cytoband(cytoband = cytoband)
read.cytoband = function(cytoband = system.file(package = "circlize",
"extdata", "cytoBand.txt"), species = NULL, chromosome.index = NULL, sort.chr = TRUE) {
# this function should also take charge of the order of chromosome
if(!is.null(chromosome.index)) sort.chr = FALSE
# `species` is prior to `cytoband`
if(!is.null(species)) {
url = paste("http://hgdownload.cse.ucsc.edu/goldenPath/", species, "/database/cytoBand.txt.gz", sep = "")
cytoband = paste0(circos.par("__tempdir__"), "/", species, "_cytoBand.txt.gz")
if(!file.exists(cytoband)) {
e = try(suppressWarnings(download.file(url, destfile = cytoband, quiet = TRUE)), silent = TRUE)
if(class(e) == "try-error") {
file.remove(cytoband)
cytoband_list = readRDS(system.file("extdata", "cytoband_list.rds", package = "circlize"))
if(species %in% names(cytoband_list)) {
cytoband = cytoband_list[[species]]
} else {
stop_wrap("It seems your species name is wrong or UCSC does not provide cytoband data for your species or internet connection was interrupted. If possible, download cytoBand file from ", url, " and use `read.cytoband(file)`.")
}
}
}
}
if(is.data.frame(cytoband)) {
d = cytoband
} else {
if(grepl("\\.gz$", cytoband)) {
cytoband = gzfile(cytoband)
}
d = read.table(cytoband, colClasses = c("character", "numeric", "numeric", "character", "character"), sep = "\t", stringsAsFactors = FALSE)
}
# now cytoband data is normalized to `d`
if(!is.null(chromosome.index)) {
chromosome.index = intersect(chromosome.index, unique(as.vector(d[[1]])))
d = d[d[[1]] %in% chromosome.index, , drop = FALSE]
if(is.factor(d[[1]])) {
# re-factor because levels may decrease due to `chromosome.index`
levels(d[[1]]) = intersect(chromosome.index, unique(as.vector(d[[1]]))) # ensures the remaining order is same as in `chromosome.index`
}
}
if(nrow(d) == 0) {
stop_wrap("Cannot find any chromosome. It is probably related to your chromosome names having or not having 'chr' prefix.")
}
if(is.null(chromosome.index)) {
if(is.factor(d[[1]])) {
chromosome = levels(d[[1]])
} else {
chromosome = unique(d[[1]])
}
} else {
chromosome = chromosome.index
}
if(sort.chr) {
chromosome = sort_chr(chromosome)
}
chr.len = NULL
dnew = NULL
for(chr in chromosome) {
d2 = d[d[[1]] == chr, ]
chr.len = c(chr.len, max(d2[, 3]))
dnew = rbind(dnew, d2)
}
names(chr.len) = chromosome
return(list(df = dnew, chromosome = chromosome, chr.len = chr.len))
}
# == title
# Read/parse chromInfo data from a data frame/file/UCSC database
#
# == param
# -chromInfo Path of the chromInfo file or a data frame that already contains chromInfo data
# -species Abbreviations of species. e.g. hg19 for human, mm10 for mouse. If this
# value is specified, the function will download ``chromInfo.txt.gz`` from
# UCSC website automatically.
# -chromosome.index subset of chromosomes, also used to reorder chromosomes.
# -sort.chr Whether chromosome names should be sorted (first sort by numbers then by letters).
# If ``chromosome.index`` is set, this argument is enforced to ``FALSE``
#
# == details
# The function read the chromInfo data, sort the chromosome names and calculate the length of each chromosome.
# By default, it is human hg19 chromInfo data.
#
# You can find the data structure for the chromInfo data from http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt.gz
#
# == values
# -``df`` Data frame for chromInfo data (rows are sorted if ``sort.chr`` is set to ``TRUE``)
# -``chromosome`` Sorted chromosome names
# -``chr.len`` Length of chromosomes. Order are same as ``chromosome``
#
# == example
# data = read.chromInfo(species = "hg19")
# data = read.chromInfo(chromInfo = system.file(package = "circlize", "extdata", "chromInfo.txt"))
# chromInfo = read.table(system.file(package = "circlize", "extdata", "chromInfo.txt"),
# colClasses = c("character", "numeric"), sep = "\t")
# data = read.chromInfo(chromInfo = chromInfo)
read.chromInfo = function(chromInfo = system.file(package = "circlize",
"extdata", "chromInfo.txt"), species = NULL, chromosome.index = NULL, sort.chr = TRUE) {
# this function should also take charge of the order of chromosome
if(!is.null(chromosome.index)) sort.chr = FALSE
if(!is.null(species)) {
url = paste("http://hgdownload.cse.ucsc.edu/goldenPath/", species, "/database/chromInfo.txt.gz", sep = "")
chromInfo = paste0(circos.par("__tempdir__"), "/", species, "_chromInfo.txt.gz")
if(!file.exists(chromInfo)) {
e = try(suppressWarnings(download.file(url, destfile = chromInfo, quiet = TRUE)), silent = TRUE)
if(class(e) == "try-error") {
file.remove(chromInfo)
chrom_info_list = readRDS(system.file("extdata", "chrom_info_list.rds", package = "circlize"))
if(species %in% names(chrom_info_list)) {
chromInfo = chrom_info_list[[species]]
} else {
stop_wrap("It seems your species name is wrong or UCSC does not provide chromInfo data for your species or internet connection was interrupted. If possible, download chromInfo file from ", url, " and use `read.chromInfo(file)`.")
}
}
}
}
if(is.data.frame(chromInfo)) {
d = chromInfo
} else {
if(grepl("\\.gz$", chromInfo)) {
chromInfo = gzfile(chromInfo)
}
d = read.table(chromInfo, colClasses = c("character", "numeric"), sep = "\t", stringsAsFactors = FALSE)[1:2] # only first two columns
}
rownames(d) = d[[1]]
if(!is.null(chromosome.index)) {
chromosome.index = intersect(chromosome.index, unique(as.vector(d[[1]])))
d = d[d[[1]] %in% chromosome.index, , drop = FALSE]
if(is.factor(d[[1]])) {
# re-factor because levels may decrease due to `chromosome.index`
levels(d[[1]]) = intersect(chromosome.index, unique(as.vector(d[[1]]))) # ensures the remaining order is same as in `chromosome.index`
}
}
if(nrow(d) == 0) {
stop_wrap("Cannot find any chromosome. It is probably related to your chromosome names having or not having 'chr' prefix.")
}
# now cytoband data is normalized to `d`
if(!is.null(chromosome.index)) {
chromosome.index = intersect(chromosome.index, unique(as.vector(d[[1]])))
d = d[d[[1]] %in% chromosome.index, , drop = FALSE]
if(is.factor(d[[1]])) {
# re-factor because levels may decrease due to `chromosome.index`
levels(d[[1]]) = intersect(chromosome.index, unique(as.vector(d[[1]]))) # ensures the remaining order is same as in `chromosome.index`
}
}
if(is.null(chromosome.index)) {
if(is.factor(d[[1]])) {
chromosome = levels(d[[1]])
} else {
chromosome = unique(d[[1]])
}
} else {
chromosome = chromosome.index
}
if(sort.chr) {
chromosome = sort_chr(chromosome)
}
dnew = d[chromosome, , drop = FALSE]
chr.len = dnew[[2]]
names(chr.len) = chromosome
dnew = data.frame(chr = chromosome, start = rep(0, nrow(dnew)), end = dnew[[2]], stringsAsFactors = FALSE)
return(list(df = dnew, chromosome = chromosome, chr.len = chr.len))
}
# == title
# Assign colors to cytogenetic band (hg19) according to the Giemsa stain results
#
# == param
# -x A vector containing the Giemsa stain results
#
# == details
# The color theme is from http://circos.ca/tutorials/course/slides/session-2.pdf, page 42.
cytoband.col = function(x) {
x = as.vector(x)
col.panel = c("gpos100" = rgb(0, 0, 0, maxColorValue = 255),
"gpos" = rgb(0, 0, 0, maxColorValue = 255),
"gpos75" = rgb(130, 130, 130, maxColorValue = 255),
"gpos66" = rgb(160, 160, 160, maxColorValue = 255),
"gpos50" = rgb(200, 200, 200, maxColorValue = 255),
"gpos33" = rgb(210, 210, 210, maxColorValue = 255),
"gpos25" = rgb(200, 200, 200, maxColorValue = 255),
"gvar" = rgb(220, 220, 220, maxColorValue = 255),
"gneg" = rgb(255, 255, 255, maxColorValue = 255),
"acen" = rgb(217, 47, 39, maxColorValue = 255),
"stalk" = rgb(100, 127, 164, maxColorValue = 255) )
col = col.panel[x]
col[is.na(col)] = "#FFFFFF"
names(col) = NULL
return(col)
}
# == title
# Generate random genomic data
#
# == param
# -nr Number of rows
# -nc Number of numeric columns / value columns
# -fun Function for generating random values
# -species species, pass to `read.cytoband`
#
# == details
# The function will uniformly sample positions from the genome. Chromosome names start with "chr"
# and positions are sorted. The final number of rows may not be exactly as same as ``nr``.
generateRandomBed = function(nr = 10000, nc = 1, fun = function(k) rnorm(k, 0, 0.5),
species = NULL) {
cyto = read.cytoband(species = species)
chr.len = cyto$chr.len
chromosome = cyto$chromosome
dl = lapply(seq_along(chr.len), function(i) {
k = round(nr*2 * chr.len[i] / sum(chr.len))
k = ifelse(k %% 2, k + 1, k)
breaks = sort(sample(chr.len[i], k))
res = data.frame(chr = rep(chromosome[i], length(breaks)/2),
start = breaks[seq_along(breaks) %% 2 == 1],
end = breaks[seq_along(breaks) %% 2 == 0],
stringsAsFactors = FALSE)
for(k in seq_len(nc)) {
res = cbind(res, value = fun(length(breaks)/2), stringsAsFactors = FALSE)
}
res
})
df = NULL
for(i in seq_along(dl)) {
df = rbind(df, dl[[i]])
}
if(ncol(df) == 3) {
colnames(df) = c("chr", "start", "end")
} else {
colnames(df) = c("chr", "start", "end", paste0("value", seq_len(ncol(df)-3)))
}
return(df)
}
sort_chr = function(chromosome) {
chromosome = sort(chromosome)
chromosome.ind = gsub("chr", "", chromosome)
chromosome.ind = gsub("_.*$", "", chromosome.ind)
l_num = grepl("^\\d+$", chromosome.ind)
l_letter = !l_num
chromosome.num = chromosome[l_num]
chromosome.levels = chromosome[!l_num]
chromosome.num = chromosome.num[order(as.numeric(chromosome.ind[l_num]))]
chromosome.letter = chromosome.levels[order(chromosome.ind[!l_num])]
chromosome = c(chromosome.num, chromosome.letter)
return(chromosome)
}
1156054203/circlize- documentation built on May 22, 2019, 2 p.m.
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# == title
# Read/parse cytoband data from a data frame/file/UCSC database
#
# == param
# -cytoband Path of the cytoband file or a data frame that already contains cytoband data
# -species Abbreviations of species. e.g. hg19 for human, mm10 for mouse. If this
# value is specified, the function will download ``cytoBand.txt.gz`` from
# UCSC website automatically.
# -chromosome.index subset of chromosomes, also used to reorder chromosomes.
# -sort.chr Whether chromosome names should be sorted (first sort by numbers then by letters).
# If ``chromosome.index`` is set, this argument is enforced to ``FALSE``
#
# == details
# The function read the cytoband data, sort the chromosome names and calculate the length of each chromosome.
# By default, it is human hg19 cytoband data.
#
# You can find the data structure of the cytoband data from http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/cytoBand.txt.gz
#
# == values
# -``df`` Data frame for cytoband data (rows are sorted if ``sort.chr`` is set to ``TRUE``)
# -``chromosome`` Sorted chromosome names
# -``chr.len`` Length of chromosomes. Orders are same as ``chromosome``
#
# == example
# data = read.cytoband(species = "hg19")
# data = read.cytoband(cytoband = system.file(package = "circlize", "extdata", "cytoBand.txt"))
# cytoband = read.table(system.file(package = "circlize", "extdata", "cytoBand.txt"),
# colClasses = c("character", "numeric", "numeric", "character", "character"), sep = "\t")
# data = read.cytoband(cytoband = cytoband)
read.cytoband = function(cytoband = system.file(package = "circlize",
"extdata", "cytoBand.txt"), species = NULL, chromosome.index = NULL, sort.chr = TRUE) {
# this function should also take charge of the order of chromosome
if(!is.null(chromosome.index)) sort.chr = FALSE
# `species` is prior to `cytoband`
if(!is.null(species)) {
url = paste("http://hgdownload.cse.ucsc.edu/goldenPath/", species, "/database/cytoBand.txt.gz", sep = "")
cytoband = paste0(circos.par("__tempdir__"), "/", species, "_cytoBand.txt.gz")
if(!file.exists(cytoband)) {
e = try(suppressWarnings(download.file(url, destfile = cytoband, quiet = TRUE)), silent = TRUE)
if(class(e) == "try-error") {
file.remove(cytoband)
cytoband_list = readRDS(system.file("extdata", "cytoband_list.rds", package = "circlize"))
if(species %in% names(cytoband_list)) {
cytoband = cytoband_list[[species]]
} else {
stop_wrap("It seems your species name is wrong or UCSC does not provide cytoband data for your species or internet connection was interrupted. If possible, download cytoBand file from ", url, " and use `read.cytoband(file)`.")
}
}
}
}
if(is.data.frame(cytoband)) {
d = cytoband
} else {
if(grepl("\\.gz$", cytoband)) {
cytoband = gzfile(cytoband)
}
d = read.table(cytoband, colClasses = c("character", "numeric", "numeric", "character", "character"), sep = "\t", stringsAsFactors = FALSE)
}
# now cytoband data is normalized to `d`
if(!is.null(chromosome.index)) {
chromosome.index = intersect(chromosome.index, unique(as.vector(d[[1]])))
d = d[d[[1]] %in% chromosome.index, , drop = FALSE]
if(is.factor(d[[1]])) {
# re-factor because levels may decrease due to `chromosome.index`
levels(d[[1]]) = intersect(chromosome.index, unique(as.vector(d[[1]]))) # ensures the remaining order is same as in `chromosome.index`
}
}
if(nrow(d) == 0) {
stop_wrap("Cannot find any chromosome. It is probably related to your chromosome names having or not having 'chr' prefix.")
}
if(is.null(chromosome.index)) {
if(is.factor(d[[1]])) {
chromosome = levels(d[[1]])
} else {
chromosome = unique(d[[1]])
}
} else {
chromosome = chromosome.index
}
if(sort.chr) {
chromosome = sort_chr(chromosome)
}
chr.len = NULL
dnew = NULL
for(chr in chromosome) {
d2 = d[d[[1]] == chr, ]
chr.len = c(chr.len, max(d2[, 3]))
dnew = rbind(dnew, d2)
}
names(chr.len) = chromosome
return(list(df = dnew, chromosome = chromosome, chr.len = chr.len))
}
# == title
# Read/parse chromInfo data from a data frame/file/UCSC database
#
# == param
# -chromInfo Path of the chromInfo file or a data frame that already contains chromInfo data
# -species Abbreviations of species. e.g. hg19 for human, mm10 for mouse. If this
# value is specified, the function will download ``chromInfo.txt.gz`` from
# UCSC website automatically.
# -chromosome.index subset of chromosomes, also used to reorder chromosomes.
# -sort.chr Whether chromosome names should be sorted (first sort by numbers then by letters).
# If ``chromosome.index`` is set, this argument is enforced to ``FALSE``
#
# == details
# The function read the chromInfo data, sort the chromosome names and calculate the length of each chromosome.
# By default, it is human hg19 chromInfo data.
#
# You can find the data structure for the chromInfo data from http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt.gz
#
# == values
# -``df`` Data frame for chromInfo data (rows are sorted if ``sort.chr`` is set to ``TRUE``)
# -``chromosome`` Sorted chromosome names
# -``chr.len`` Length of chromosomes. Order are same as ``chromosome``
#
# == example
# data = read.chromInfo(species = "hg19")
# data = read.chromInfo(chromInfo = system.file(package = "circlize", "extdata", "chromInfo.txt"))
# chromInfo = read.table(system.file(package = "circlize", "extdata", "chromInfo.txt"),
# colClasses = c("character", "numeric"), sep = "\t")
# data = read.chromInfo(chromInfo = chromInfo)
read.chromInfo = function(chromInfo = system.file(package = "circlize",
"extdata", "chromInfo.txt"), species = NULL, chromosome.index = NULL, sort.chr = TRUE) {
# this function should also take charge of the order of chromosome
if(!is.null(chromosome.index)) sort.chr = FALSE
if(!is.null(species)) {
url = paste("http://hgdownload.cse.ucsc.edu/goldenPath/", species, "/database/chromInfo.txt.gz", sep = "")
chromInfo = paste0(circos.par("__tempdir__"), "/", species, "_chromInfo.txt.gz")
if(!file.exists(chromInfo)) {
e = try(suppressWarnings(download.file(url, destfile = chromInfo, quiet = TRUE)), silent = TRUE)
if(class(e) == "try-error") {
file.remove(chromInfo)
chrom_info_list = readRDS(system.file("extdata", "chrom_info_list.rds", package = "circlize"))
if(species %in% names(chrom_info_list)) {
chromInfo = chrom_info_list[[species]]
} else {
stop_wrap("It seems your species name is wrong or UCSC does not provide chromInfo data for your species or internet connection was interrupted. If possible, download chromInfo file from ", url, " and use `read.chromInfo(file)`.")
}
}
}
}
if(is.data.frame(chromInfo)) {
d = chromInfo
} else {
if(grepl("\\.gz$", chromInfo)) {
chromInfo = gzfile(chromInfo)
}
d = read.table(chromInfo, colClasses = c("character", "numeric"), sep = "\t", stringsAsFactors = FALSE)[1:2] # only first two columns
}
rownames(d) = d[[1]]
if(!is.null(chromosome.index)) {
chromosome.index = intersect(chromosome.index, unique(as.vector(d[[1]])))
d = d[d[[1]] %in% chromosome.index, , drop = FALSE]
if(is.factor(d[[1]])) {
# re-factor because levels may decrease due to `chromosome.index`
levels(d[[1]]) = intersect(chromosome.index, unique(as.vector(d[[1]]))) # ensures the remaining order is same as in `chromosome.index`
}
}
if(nrow(d) == 0) {
stop_wrap("Cannot find any chromosome. It is probably related to your chromosome names having or not having 'chr' prefix.")
}
# now cytoband data is normalized to `d`
if(!is.null(chromosome.index)) {
chromosome.index = intersect(chromosome.index, unique(as.vector(d[[1]])))
d = d[d[[1]] %in% chromosome.index, , drop = FALSE]
if(is.factor(d[[1]])) {
# re-factor because levels may decrease due to `chromosome.index`
levels(d[[1]]) = intersect(chromosome.index, unique(as.vector(d[[1]]))) # ensures the remaining order is same as in `chromosome.index`
}
}
if(is.null(chromosome.index)) {
if(is.factor(d[[1]])) {
chromosome = levels(d[[1]])
} else {
chromosome = unique(d[[1]])
}
} else {
chromosome = chromosome.index
}
if(sort.chr) {
chromosome = sort_chr(chromosome)
}
dnew = d[chromosome, , drop = FALSE]
chr.len = dnew[[2]]
names(chr.len) = chromosome
dnew = data.frame(chr = chromosome, start = rep(0, nrow(dnew)), end = dnew[[2]], stringsAsFactors = FALSE)
return(list(df = dnew, chromosome = chromosome, chr.len = chr.len))
}
# == title
# Assign colors to cytogenetic band (hg19) according to the Giemsa stain results
#
# == param
# -x A vector containing the Giemsa stain results
#
# == details
# The color theme is from http://circos.ca/tutorials/course/slides/session-2.pdf, page 42.
cytoband.col = function(x) {
x = as.vector(x)
col.panel = c("gpos100" = rgb(0, 0, 0, maxColorValue = 255),
"gpos" = rgb(0, 0, 0, maxColorValue = 255),
"gpos75" = rgb(130, 130, 130, maxColorValue = 255),
"gpos66" = rgb(160, 160, 160, maxColorValue = 255),
"gpos50" = rgb(200, 200, 200, maxColorValue = 255),
"gpos33" = rgb(210, 210, 210, maxColorValue = 255),
"gpos25" = rgb(200, 200, 200, maxColorValue = 255),
"gvar" = rgb(220, 220, 220, maxColorValue = 255),
"gneg" = rgb(255, 255, 255, maxColorValue = 255),
"acen" = rgb(217, 47, 39, maxColorValue = 255),
"stalk" = rgb(100, 127, 164, maxColorValue = 255) )
col = col.panel[x]
col[is.na(col)] = "#FFFFFF"
names(col) = NULL
return(col)
}
# == title
# Generate random genomic data
#
# == param
# -nr Number of rows
# -nc Number of numeric columns / value columns
# -fun Function for generating random values
# -species species, pass to `read.cytoband`
#
# == details
# The function will uniformly sample positions from the genome. Chromosome names start with "chr"
# and positions are sorted. The final number of rows may not be exactly as same as ``nr``.
generateRandomBed = function(nr = 10000, nc = 1, fun = function(k) rnorm(k, 0, 0.5),
species = NULL) {
cyto = read.cytoband(species = species)
chr.len = cyto$chr.len
chromosome = cyto$chromosome
dl = lapply(seq_along(chr.len), function(i) {
k = round(nr*2 * chr.len[i] / sum(chr.len))
k = ifelse(k %% 2, k + 1, k)
breaks = sort(sample(chr.len[i], k))
res = data.frame(chr = rep(chromosome[i], length(breaks)/2),
start = breaks[seq_along(breaks) %% 2 == 1],
end = breaks[seq_along(breaks) %% 2 == 0],
stringsAsFactors = FALSE)
for(k in seq_len(nc)) {
res = cbind(res, value = fun(length(breaks)/2), stringsAsFactors = FALSE)
}
res
})
df = NULL
for(i in seq_along(dl)) {
df = rbind(df, dl[[i]])
}
if(ncol(df) == 3) {
colnames(df) = c("chr", "start", "end")
} else {
colnames(df) = c("chr", "start", "end", paste0("value", seq_len(ncol(df)-3)))
}
return(df)
}
sort_chr = function(chromosome) {
chromosome = sort(chromosome)
chromosome.ind = gsub("chr", "", chromosome)
chromosome.ind = gsub("_.*$", "", chromosome.ind)
l_num = grepl("^\\d+$", chromosome.ind)
l_letter = !l_num
chromosome.num = chromosome[l_num]
chromosome.levels = chromosome[!l_num]
chromosome.num = chromosome.num[order(as.numeric(chromosome.ind[l_num]))]
chromosome.letter = chromosome.levels[order(chromosome.ind[!l_num])]
chromosome = c(chromosome.num, chromosome.letter)
return(chromosome)
}
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