annotate probecoverage.r @ 5:2ec6529e555d draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit c249a0b083ab1c53744839e797b4b8856f5516f9

## Setup R error handling to go to stderr
options( show.error.messages=F,
       error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
warnings()
library(optparse)
library(ggplot2)
library(reshape2)

option_list <- list(
    make_option(c("-i", "--input"), type="character", help="Path to dataframe"),
    make_option(c("-t", "--title"), type="character", help="Main Title"),
    make_option("--xlab", type = "character", help="X-axis legend"),
    make_option("--ylab", type = "character", help="Y-axis legend"),
    make_option("--sample", type = "character", help="a space separated of sample labels"),
    make_option("--method", type = "character", help="bedtools or pysam"),
    make_option(c("-o", "--output"), type = "character", help="path to the pdf plot")
    )
 
parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
args = parse_args(parser)
samples = substr(args$sample, 2, nchar(args$sample)-2)
samples = strsplit(samples, ", ")
 
# data frames implementation

Table <- read.delim(args$input, header=F)
headers = c("chromosome", "start", "end", "id")
for (i in seq(1, length(Table)-4)) {
    headers <- c(headers, samples[[1]][i])
colnames(Table) <- headers
}

## function
if (args$method == 'bedtools') {
    cumul <- function(x,y) sum(Table[,y]/(Table$end-Table$start) > x)/length(Table$chromosome)
    } else {
    cumul <- function(x,y) sum(Table[,y] > x)/length(Table$chromosome)
    }
scaleFUN <- function(x) sprintf("%.3f", x)

## end of function
## let's do a dataframe before plotting
if (args$method == 'bedtools') {
    maxdepth <- trunc(max(Table[,5:length(Table)]/(Table$end-Table$start))) + 20
    } else {
    maxdepth <- trunc(max(Table[,5:length(Table)])) + 20
    }

graphpoints <- data.frame(1:maxdepth)
i <- 5
for (colonne in colnames(Table)[5:length(colnames(Table))]) {
    graphpoints <- cbind(graphpoints,  mapply(cumul, 1:maxdepth, rep(i, maxdepth)))
    i <- i + 1
    }
colnames(graphpoints) <- c("Depth", colnames(Table)[5:length(Table)])
maxfrac = max(graphpoints[,2:length(graphpoints)])

graphpoints <- melt(graphpoints, id.vars="Depth", variable.name="Samples", value.name="sample_value")

## GRAPHS

pdf(file=args$output)
ggplot(data=graphpoints, aes(x=Depth, y=sample_value, colour=Samples)) +
      geom_line(size=1) +
      scale_x_continuous(trans='log2', breaks = 2^(seq(0,log(maxdepth, 2)))) +
      scale_y_continuous(breaks = seq(0, maxfrac, by=maxfrac/10), labels=scaleFUN) +
      labs(x=args$xlab, y=args$ylab, title=args$title) +
      theme(legend.position="top", legend.title=element_blank(), legend.text=element_text(colour="blue", size=7))
      
      
##      facet_wrap(~Samples, ncol=2)

devname=dev.off()