annotate probecoverage.r @ 0:dbeb4a0abfc6 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
author artbio
date Sat, 23 Sep 2017 05:11:49 -0400
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dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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1 ## Setup R error handling to go to stderr
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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2 options( show.error.messages=F,
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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3 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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4 warnings()
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5 library(optparse)
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6 library(ggplot2)
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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7 library(reshape2)
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9 option_list <- list(
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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10 make_option(c("-i", "--input"), type="character", help="Path to dataframe"),
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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11 make_option(c("-t", "--title"), type="character", help="Main Title"),
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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12 make_option("--xlab", type = "character", help="X-axis legend"),
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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13 make_option("--ylab", type = "character", help="Y-axis legend"),
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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14 make_option("--sample", type = "character", help="a space separated of sample labels"),
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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15 make_option(c("-o", "--output"), type = "character", help="path to the pdf plot")
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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16 )
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18 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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19 args = parse_args(parser)
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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20 samples = substr(args$sample, 2, nchar(args$sample)-2)
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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21 samples = strsplit(samples, ", ")
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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23 # data frames implementation
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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25 Table <- read.delim(args$input, header=F)
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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26 headers = c("chromosome", "start", "end", "id")
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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27 for (i in seq(1, length(Table)-4)) {
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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28 headers <- c(headers, samples[[1]][i])
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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29 colnames(Table) <- headers
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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30 }
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32 ## function
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34 cumul <- function(x,y) sum(Table[,y]/(Table$end-Table$start) > x)/length(Table$chromosome)
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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36 ## end of function
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37 ## let's do a dataframe before plotting
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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38 maxdepth <- trunc(max(Table[,5:length(Table)]/(Table$end-Table$start))) + 20
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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39 graphpoints <- data.frame(1:maxdepth)
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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40 i <- 5
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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41 for (colonne in colnames(Table)[5:length(colnames(Table))]) {
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42 graphpoints <- cbind(graphpoints, mapply(cumul, 1:maxdepth, rep(i, maxdepth)))
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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43 i <- i + 1
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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44 }
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45 colnames(graphpoints) <- c("Depth", colnames(Table)[5:length(Table)])
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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46 maxfrac = max(graphpoints[,2:length(graphpoints)])
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48 graphpoints <- melt(graphpoints, id.vars="Depth", variable.name="Samples", value.name="sample_value")
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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50 ## GRAPHS
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52 pdf(file=args$output)
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53 ggplot(data=graphpoints, aes(x=Depth, y=sample_value, group=Samples, colour=Samples)) +
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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54 geom_line(size=1) +
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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55 scale_x_continuous(trans='log2', breaks = 2^(seq(0,log(maxdepth, 2)))) +
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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56 scale_y_continuous(breaks = seq(0, maxfrac, by=maxfrac/10)) +
dbeb4a0abfc6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 102edc0c210d94e9d72f913e2d18c19220c4167c
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57 labs(x=args$xlab, y=args$ylab, title=args$title) +
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58 theme(legend.position="top", legend.title=element_blank(), legend.text=element_text(colour="blue", size=7))
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60 devname=dev.off()
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