Mercurial > repos > artbio > small_read_size_histograms

annotate size_histogram.r @ 0:234b83159ea8 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
author artbio
date Tue, 11 Jul 2017 11:44:36 -0400
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234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
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1 ## Setup R error handling to go to stderr
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
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2 options( show.error.messages=F,
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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3 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
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4 library(RColorBrewer)
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
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5 library(lattice)
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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6 library(latticeExtra)
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
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7 library(grid)
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
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8 library(gridExtra)
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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9 library(optparse)
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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10
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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11 # Parse arguments
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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12 option_list <- list(
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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13 make_option(c("-g", "--global"), type="character", help="Whether distribution is plotted globally or by chromosome"),
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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14 make_option(c("-s", "--size_distribution_tab"), type="character", help="Path to file with tabular size distribution"),
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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15 make_option("--size_distribution_pdf", type="character", help="Path to file with size distribution plot"),
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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16 make_option("--title", type="character", help="Title for readmaps and size distribution"),
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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17 make_option("--ylabel", type="character", help="ylabel for readmaps and size distribution"),
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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18 make_option("--yrange", type="integer", help="Y-axis range"),
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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19 make_option("--rows_per_page", type="integer", help="rows_per_page")
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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20 )
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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22 parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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23 args = parse_args(parser)
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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25 ##cheetahtemplate data frame implementation
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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26 size=read.delim(args$size_distribution_tab, header=T, row.names=NULL)
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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27 n_samples = length(unique (size$sample))
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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28 n_genes = length (unique (levels(size$gene)))
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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30 if (args$yrange != 0) {
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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31 # This is used for specifying the y-axis limits
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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32 ylim=c(-args$yrange, args$yrange)
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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33 } else { ylim="" }
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35 par.settings.size=list(layout.heights=list(top.padding=1, bottom.padding=1),
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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36 strip.background = list(col = c("lightblue", "lightgreen"))
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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37 )
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39 smR.prepanel=function(x,y,...){; yscale=c(-max(abs(y)), max(abs(y)));list(ylim=yscale);} # use if one want y axis in the middle of the plot
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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41 plot_size_distribution = function(df, ...) {
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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42 bc= barchart(count~as.factor(size)|factor(sample, levels=unique(sample))+gene, data = df, origin = 0,
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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43 horizontal=FALSE,
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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44 group=polarity,
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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45 stack=TRUE,
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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46 col=c('red', 'blue'),
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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47 cex=0.75,
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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48 scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.5, alternating=T), x=list(cex=.6 ) ),
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49 xlab = "readsize in nucleotides",
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50 ylab = args$ylabel,
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51 main = args$title,
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52 par.strip.text = list(cex=0.75),
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53 as.table=TRUE,
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54 newpage = T,
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55 ...)
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57 combineLimits(update(useOuterStrips(bc,
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58 strip.left = strip.custom(par.strip.text = list(cex=0.5))
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59 ),
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60 layout=c(n_samples,args$rows_per_page)),
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61 margin.x=F, margin.y=1)
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62 }
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64 # per_gene_size=lapply(genes, function(x) subset(size, gene==x)) # no object in this script
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65
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66 if (args$global == "no") {
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67 width = 8.2677*n_samples/4
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68 } else { width = 8.2677 }
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69
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70 options(warn=-1)
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71 pdf(file=args$size_distribution_pdf, paper="special", height=11.69, width=width)
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73 if (ylim == "" && args$global=="no") {
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74 plot_size_distribution(size, par.settings=par.settings.size)
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75 }
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76 if (ylim != "" && args$global=="no") { plot_size_distribution(size, par.settings=par.settings.size, ylim=ylim)
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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77 }
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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78 if (ylim == "" && args$global=="yes") { bc= barchart(count~as.factor(size)|factor(sample, levels=unique(sample)),
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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79 data = size, origin = 0,
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80 horizontal=FALSE,
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81 group=polarity,
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82 stack=TRUE,
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83 col=c('red', 'blue'),
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84 scales=list(y=list(tick.number=4, rot=90, relation="same"), cex=1),
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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85 xlab = "readsize in nucleotides",
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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86 ylab = args$ylabel,
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87 main = args$title, as.table=TRUE, newpage = T,
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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88 aspect=0.5,
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89 strip = strip.custom(par.strip.text = list(cex = 1), which.given=1, bg="lightblue")
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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90 )
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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91 bc
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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92 }
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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93 if (ylim != "" && args$global=="yes") { bc= barchart(count~as.factor(size)|factor(sample, levels=unique(sample)),
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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94 data = size, origin = 0,
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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95 horizontal=FALSE,
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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96 group=polarity,
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97 stack=TRUE,
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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98 col=c('red', 'blue'),
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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99 scales=list(y=list(tick.number=4, rot=90, relation="same"), cex=1),
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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100 xlab = "readsize in nucleotides",
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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101 ylab = args$ylabel,
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102 ylim = ylim,
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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103 main = args$title, as.table=TRUE, newpage = T,
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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104 aspect=0.5,
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105 strip = strip.custom(par.strip.text = list(cex = 1), which.given=1, bg="lightblue")
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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106 )
234b83159ea8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
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107 bc
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108 }
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109
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110 devname=dev.off()