/
plot_mosdepth_regions.r
executable file
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plot_mosdepth_regions.r
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#!/usr/bin/env Rscript
################################################
################################################
## LOAD LIBRARIES ##
################################################
################################################
library(optparse)
library(ggplot2)
library(scales)
library(ComplexHeatmap)
library(viridis)
library(tidyverse)
################################################
################################################
## VALIDATE COMMAND-LINE PARAMETERS ##
################################################
################################################
option_list <- list(make_option(c("-i", "--input_files"), type="character", default=NULL, help="Comma-separated list of mosdepth regions output file (typically end in *.regions.bed.gz)", metavar="input_files"),
make_option(c("-s", "--input_suffix"), type="character", default='.regions.bed.gz', help="Portion of filename after sample name to trim for plot title e.g. '.regions.bed.gz' if 'SAMPLE1.regions.bed.gz'", metavar="input_suffix"),
make_option(c("-o", "--output_dir"), type="character", default='./', help="Output directory", metavar="path"),
make_option(c("-p", "--output_suffix"), type="character", default='regions', help="Output suffix", metavar="output_suffix"),
make_option(c("-r", "--regions_prefix"), type="character", default=NULL, help="Replace this prefix from region names before plotting", metavar="regions_prefix"))
opt_parser <- OptionParser(option_list=option_list)
opt <- parse_args(opt_parser)
## Check input files
INPUT_FILES <- unique(unlist(strsplit(opt$input_files,",")))
if (length(INPUT_FILES) == 0) {
print_help(opt_parser)
stop("At least one input file must be supplied", call.=FALSE)
}
if (!all(file.exists(INPUT_FILES))) {
stop(paste("The following input files don't exist:",paste(INPUT_FILES[!file.exists(INPUT_FILES)], sep='', collapse=' '), sep=' '), call.=FALSE)
}
## Check the output directory has a trailing slash, if not add one
OUTDIR <- opt$output_dir
if (tail(strsplit(OUTDIR,"")[[1]],1)!="/") {
OUTDIR <- paste(OUTDIR,"/",sep='')
}
## Create the directory if it doesn't already exist.
if (!file.exists(OUTDIR)) {
dir.create(OUTDIR,recursive=TRUE)
}
OUTSUFFIX <- trimws(opt$output_suffix, "both", whitespace = "\\.")
################################################
################################################
## READ IN DATA ##
################################################
################################################
## Read in data
dat <- NULL
for (input_file in INPUT_FILES) {
sample = gsub(opt$input_suffix,'',basename(input_file))
dat <- rbind(dat, cbind(read.delim(input_file, header=FALSE, sep='\t', stringsAsFactors=FALSE, check.names=FALSE)[,-6], sample, stringsAsFactors=F))
}
## Reformat table
if (ncol(dat) == 6) {
colnames(dat) <- c('chrom', 'start','end', 'region', 'coverage', 'sample')
if (!is.null(opt$regions_prefix)) {
dat$region <- as.character(gsub(opt$regions_prefix, '', dat$region))
}
dat$region <- factor(dat$region, levels=unique(dat$region[order(dat$start)]))
} else {
colnames(dat) <- c('chrom', 'start','end', 'coverage', 'sample')
}
dat$sample <- factor(dat$sample, levels=sort(unique(dat$sample)))
## Write merged coverage data for all samples to file
outfile <- paste(OUTDIR,"all_samples.",OUTSUFFIX,".coverage.tsv", sep='')
write.table(dat, file=outfile, col.names=TRUE, row.names=FALSE, sep='\t', quote=FALSE)
################################################
################################################
## PER-SAMPLE COVERAGE PLOTS ##
################################################
################################################
for (sample in unique(dat$sample)) {
sample_dat <- dat[dat$sample == sample,]
outfile <- paste(OUTDIR,sample,".",OUTSUFFIX,".coverage.tsv", sep='')
write.table(sample_dat,file=outfile, col.names=TRUE, row.names=FALSE, sep='\t', quote=FALSE)
sample_dat$coverage <- sample_dat$coverage + 1
if (ncol(sample_dat) == 6) {
plot <- ggplot(sample_dat,aes(x=region,y=coverage)) +
geom_bar(stat="identity", fill="#D55E00", width=0.6) +
theme_bw() +
theme(
plot.title=element_text(size=10),
axis.text.x=element_text(size=10),
axis.text.y=element_text(size=6)) +
coord_flip() +
scale_x_discrete(expand=c(0, 0)) +
scale_y_continuous(
trans=log10_trans(),
breaks=10^c(0:10),
labels=trans_format('log10', math_format(10^.x)),
expand=c(0, 0)) +
expand_limits(y=1) +
ylab(bquote('log'[10]~'(Coverage+1)')) +
xlab('Amplicon') +
ggtitle(paste(sample,'median coverage per amplicon'))
outfile <- paste(OUTDIR,sample,".",OUTSUFFIX,".coverage.pdf", sep='')
ggsave(file=outfile, plot, height=3+(0.2*length(unique(sample_dat$region))), width=16, units="cm", limitsize=FALSE)
} else {
plot <- ggplot(sample_dat,aes(x=end,y=coverage)) +
geom_ribbon(aes(ymin=0, ymax=coverage), fill="#D55E00", data=) +
theme_bw() +
scale_x_continuous(expand=c(0, 0)) +
scale_y_continuous(
trans=log10_trans(),
breaks=10^c(0:10),
labels=trans_format('log10', math_format(10^.x)),
expand=c(0, 0)) +
expand_limits(y=1) +
ylab(bquote('log'[10]~'(Coverage+1)')) +
xlab('Position (bp)') +
ggtitle(paste(sample,'coverage'))
outfile <- paste(OUTDIR,sample,".",OUTSUFFIX,".coverage.pdf", sep='')
ggsave(file=outfile, plot, height=6, width=12, units="in")
}
}
################################################
################################################
## REGION-BASED HEATMAP ACROSS ALL SAMPLES ##
################################################
################################################
if (ncol(dat) == 6 && length(INPUT_FILES) > 1) {
mat <- spread(dat[,c("sample", "region", "coverage")], sample, coverage, fill=NA, convert=FALSE)
rownames(mat) <- mat[,1]
mat <- t(as.matrix(log10(mat[,-1] + 1)))
heatmap <- Heatmap(mat,
column_title = "Heatmap to show median amplicon coverage across samples",
name = "log10(Coverage+1)",
cluster_rows = TRUE,
cluster_columns = FALSE,
show_row_names = TRUE,
show_column_names = TRUE,
column_title_side = "top",
column_names_side = "bottom",
row_names_side = "right",
rect_gp = gpar(col="white", lwd=1),
show_heatmap_legend = TRUE,
heatmap_legend_param = list(title_gp=gpar(fontsize=12, fontface="bold"), labels_gp=gpar(fontsize=10), direction="horizontal"),
column_title_gp = gpar(fontsize=14, fontface="bold"),
row_names_gp = gpar(fontsize=10, fontface="bold"),
column_names_gp = gpar(fontsize=10, fontface="bold"),
height = unit(5, "mm")*nrow(mat),
width = unit(5, "mm")*ncol(mat),
col = viridis(50))
## Size of heatmaps scaled based on matrix dimensions: https://jokergoo.github.io/ComplexHeatmap-reference/book/other-tricks.html#set-the-same-cell-size-for-different-heatmaps-with-different-dimensions
height = 0.1969*nrow(mat) + (2*1.5)
width = 0.1969*ncol(mat) + (2*1.5)
outfile <- paste(OUTDIR,"all_samples.",OUTSUFFIX,".heatmap.pdf", sep='')
pdf(file=outfile, height=height, width=width)
draw(heatmap, heatmap_legend_side="bottom")
dev.off()
## Write heatmap to file
mat <- mat[row_order(heatmap),]
outfile <- paste(OUTDIR,"all_samples.",OUTSUFFIX,".heatmap.tsv", sep='')
write.table(cbind(sample = rownames(mat), mat), file=outfile, row.names=FALSE, col.names=TRUE, sep="\t", quote=FALSE)
}
################################################
################################################
################################################
################################################