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annotate coverage_plotting.R @ 0:10f0e4c00b13 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
author artbio
date Tue, 18 Jul 2017 06:30:40 -0400
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10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
artbio
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1 #!/usr/bin/env Rscript
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3 # Help to be printed
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artbio
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4 hlp_description = "This script takes a dataframe containing the coverage values for different miRNAs and plots them."
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5 hlp_usage = "Usage : coverage_ploting.R --dataframe [FILE] --type ['relative' or 'absolute'] --output [FILE]"
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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6 hlp_dataframe = "--dataframe\tFILE\tThis is a dataframe containing coverage values obtained from mircounts.py"
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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7 hlp_type = "--type\t\tSTRING\tType of ploting, either relative or absoute coverage values (default='relative')"
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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8 hlp_output = "--output\tFILE\tFile to output the pdf to\n"
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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10 hlp = paste(hlp_description,hlp_usage,hlp_dataframe,hlp_type,hlp_output,sep="\n")
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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11 #print(hlp)
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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13 # Setup R error handling to go to stderr
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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14 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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16 library(optparse)
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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17 library(lattice)
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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19 # Get arguments
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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20 option_list <- list(
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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21 make_option(c("-d", "--dataframe"), type="character",
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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22 help="Dataframe containing coverage values obtained from mircounts.py"),
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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23 make_option(c("-t", "--type"), type="character", default="relative",
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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24 help="Type of plotting, either relative or absoute coverage values (default='relative')"),
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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25 make_option(c("-o", "--output"), type="character", help="File to output the pdf to")
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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26 )
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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27 parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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28 args = parse_args(parser)
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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30 if ( !('dataframe' %in% names(args)) || !('output' %in% names(args))) {
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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31 stop("'--dataframe' and '--output' parametters are not optional. Please retry.")
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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32 }
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34 # Plot
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35 coverage = read.delim(args$dataframe, header=T)
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36 if (args$type =="relative") {
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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37 graph = xyplot(Norm_count~Norm_offset | Mir_hairpin, data=coverage, col=c("darkblue"), type="l", lwd=1.5,
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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38 scales=list(x=list(cex=.5), y=list(cex=.5)), par.strip.text=list(cex=.5),
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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39 strip=strip.custom(which.given=1, bg="lightblue"), layout=c(4,15),
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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40 as.table=T, xlab="Normalized Counts", ylab="Normalized coordinates",
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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41 main="miRNA coverage maps")
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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42 } else {
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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43 graph = xyplot(Count~Offset | Mir_hairpin, data=coverage, col=c("darkblue"), type="l", lwd=1.5,
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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44 scales=list(x=list(cex=.5), y=list(cex=.5)), par.strip.text=list(cex=.5),
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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45 strip=strip.custom(which.given=1, bg="lightblue"), layout=c(4,15),
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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46 as.table=T, xlab="Counts", ylab="Coordinates",
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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47 main="miRNA coverage plots")
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48 }
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49
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50 # PDF output
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51 pdf(file=args$output, paper="special", height=11.69, width=8.2677)
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52 plot(graph, newpage = T)
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53 dev.off()