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R script for Circos plot !
By Abhi 343 days ago
#!/usr/bin/env Rscript
library(RCircos)
# usage: Rscript make_circos.r <sv table> <sample name> <gene label table> <cnv data> <out>
# parse args
args = commandArgs(trailingOnly=TRUE)
sv.file <- args[1]
sample.name <- args[2]
gene.label.file <- args[3]
cnv.file <- args[4]
out.file <- args[5]
# TMP <- Sys.getenv("TMP_DIR")
# tmp.bed = paste0(TMP ,"/" , sample.name, "_bkpts.bed")
tmp.bed = paste0(sample.name, "_bkpts.bed")
# load prereq data
data(UCSC.HG19.Human.CytoBandIdeogram)
# set core parameters
chr.exclude <- NULL;
cyto.info <- UCSC.HG19.Human.CytoBandIdeogram;
tracks.inside <- 10;
tracks.outside <- 5;
RCircos.Set.Core.Components(cyto.info, chr.exclude, tracks.inside, tracks.outside);
rcircos.params <- RCircos.Get.Plot.Parameters();
rcircos.params$text.size <- 1
RCircos.Reset.Plot.Parameters(rcircos.params)
rcircos.cyto <- RCircos.Get.Plot.Ideogram();
rcircos.position <- RCircos.Get.Plot.Positions();
RCircos.List.Plot.Parameters()
link.data <- tryCatch(read.table(sv.file, sep = ',', stringsAsFactors = F, header = T), error=function(e) data.frame())
if (nrow(link.data) != 0) {
link.data <- transform(link.data,
chromStart = as.numeric(chromStart),
chromEnd = as.numeric(chromEnd),
chromStart.1 = as.numeric(chromStart.1),
chromEnd.1 = as.numeric(chromEnd.1))
# write a bed file of all breakpoints to intersect with gene label table
bkpts.1 <- link.data[c("Chromosome", "chromStart", "chromEnd")]
bkpts.2 <- link.data[c("Chromosome.1", "chromStart.1", "chromEnd.1")]
colnames(bkpts.2) <- colnames(bkpts.1)
write.table(rbind(bkpts.1, bkpts.2), tmp.bed, sep = '\t', quote = F, col.names = F, row.names = F)
# only keep labels that fall within an event
print(paste0("bedtools intersect -wb -a ", tmp.bed, " -b ", gene.label.file))
gene.labels <- system(paste0("bedtools intersect -wb -a ", tmp.bed, " -b ", gene.label.file), intern = T)
gene.labels <- data.frame(do.call('rbind', strsplit(gene.labels, '\t', fixed=TRUE)), stringsAsFactors = F)
if (nrow(gene.labels) > 0) {
gene.labels <- gene.labels[,4:ncol(gene.labels)]
# deduplicate labels
gene.labels <- gene.labels[!duplicated(gene.labels),]
colnames(gene.labels) <- c("Chromosome", "chromStart", "chromEnd", "gene")
gene.labels <- transform(gene.labels,
chromStart = as.numeric(chromStart),
chromEnd = as.numeric(chromEnd))
}
# make the plot
png(file=out.file, height=3000, width=3000, res = 500)
RCircos.Set.Plot.Area()
RCircos.Chromosome.Ideogram.Plot()
track.num <- 2
RCircos.Link.Plot(link.data, track.num, TRUE)
title(sample.name, line=-1)
# label the genes
if (nrow(gene.labels) > 0) {
name.col <- 4
side <- "out"
track.num <- 1
RCircos.Gene.Connector.Plot(gene.labels, track.num, side);
track.num <- 2
RCircos.Gene.Name.Plot(gene.labels, name.col, track.num, side);
}
# remove intermediate file
system(paste0("rm -f ", tmp.bed))
} else {
# make empty plot
png(file=out.file, height=3000, width=3000, res = 500)
RCircos.Set.Plot.Area()
RCircos.Chromosome.Ideogram.Plot()
title(sample.name, line=-1)
}
# parse cnv data
cnv = tryCatch(read.csv(cnv.file, stringsAsFactors = F), error=function(e) data.frame())
if (nrow(cnv) != 0) {
colnames(cnv) <- c("Chromosome", "chromStart", "chromEnd", "cnv")
cnv$Chromosome <- paste0('chr', cnv$Chromosome)
cnv$GeneName <- "gene"
cnv <- cnv[, c("Chromosome", "chromStart", "chromEnd", "GeneName", "cnv")]
}
# add CNV heatmap track
if (nrow(cnv) != 0) {
RCircos.Heatmap.Plot(cnv, data.col = 5, track.num = 1, side = "in")
}
dev.off()
#-------- DATA FORMAT ------
chr1 11869 14412 DDX11L1
chr1 14363 29806 WASH7P
chr1 29554 31109 MIR1302-10
chr1 34554 36081 FAM138A
chr1 52473 54936 OR4G4P
chr1 62948 63887 OR4G11P
chr1 69091 70008 OR4F5
chr1 131025 134836 CICP27
chr1 134901 139379 AL627309.1
chr1 157784 157887 RNU6-1100P
chr1 227615 267253 AP006222.2
chr1 228292 228775 AP006222.1
chr1 317720 453948 RP4-669L17.10
chr1 326096 328112 RP4-669L17.8
chr1 329431 332236 CICP7
chr1 334126 334305 RP4-669L17.4
chr1 367640 368634 OR4F29
chr1 379105 379467 WBP1LP7
