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annotate small_rna_maps.r @ 2:507383cce5a8 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
author artbio
date Mon, 14 Aug 2017 05:52:34 -0400
parents 6d48150495e3
children 12c14642e6ac
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6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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1 ## Setup R error handling to go to stderr
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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2 options( show.error.messages=F,
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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3 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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4 warnings()
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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5 library(RColorBrewer)
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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6 library(lattice)
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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7 library(latticeExtra)
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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8 library(grid)
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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9 library(gridExtra)
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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10 library(optparse)
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12 option_list <- list(
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507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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13 make_option(c("-f", "--first_dataframe"), type="character", help="path to first dataframe"),
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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14 make_option(c("-e", "--extra_dataframe"), type="character", help="path to additional dataframe"),
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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15 make_option("--extra_plot_method", type = "character", help="How additional data should be plotted"),
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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16 make_option("--output_pdf", type = "character", help="path to the pdf file with plots")
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17 )
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19 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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20 args = parse_args(parser)
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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22 # data frames implementation
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24 Table = read.delim(args$first_dataframe, header=T, row.names=NULL)
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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25 Table <- within(Table, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1))
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6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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26 n_samples=length(unique(Table$Dataset))
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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27 genes=unique(levels(Table$Chromosome))
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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28 per_gene_readmap=lapply(genes, function(x) subset(Table, Chromosome==x))
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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29 per_gene_limit=lapply(genes, function(x) c(1, unique(subset(Table, Chromosome==x)$Chrom_length)) )
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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30 n_genes=length(per_gene_readmap)
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507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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32 ExtraTable=read.delim(args$extra_dataframe, header=T, row.names=NULL)
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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33 if (args$extra_plot_method=='Size') {
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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34 ExtraTable <- within(ExtraTable, Count[Polarity=="R"] <- (Count[Polarity=="R"]*-1))
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6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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35 }
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36 per_gene_size=lapply(genes, function(x) subset(ExtraTable, Chromosome==x))
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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37
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6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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38 ## end of data frames implementation
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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40 ## functions
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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42 first_plot = function(df, ...) {
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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43 combineLimits(xyplot(Counts~Coordinate|factor(Dataset, levels=unique(Dataset))+factor(Chromosome, levels=unique(Chromosome)),
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44 data=df,
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45 type='h',
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46 lwd=1.5,
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47 scales= list(relation="free", x=list(rot=0, cex=0.7, axs="i", tck=0.5), y=list(tick.number=4, rot=90, cex=0.7)),
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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48 xlab=NULL, main=NULL, ylab=NULL,
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49 as.table=T,
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50 origin = 0,
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51 horizontal=FALSE,
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52 group=Polarity,
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53 col=c("red","blue"),
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54 par.strip.text = list(cex=0.7),
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55 ...))
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56 }
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57
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59 second_plot = function(df, ...) {
0
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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60 #smR.prepanel=function(x,y,...) {; yscale=c(y*0, max(abs(y)));list(ylim=yscale);}
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61 sizeplot = xyplot(eval(as.name(args$extra_plot_method))~Coordinate|factor(Dataset, levels=unique(Dataset))+factor(Chromosome, levels=unique(Chromosome)),
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62 data=df,
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63 type='p',
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64 cex=0.35,
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65 pch=19,
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66 scales= list(relation="free", x=list(rot=0, cex=0, axs="i", tck=0.5), y=list(tick.number=4, rot=90, cex=0.7)),
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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67 xlab=NULL, main=NULL, ylab=NULL,
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68 as.table=T,
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69 origin = 0,
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70 horizontal=FALSE,
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71 group=Polarity,
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72 col=c("darkred","darkblue"),
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73 par.strip.text = list(cex=0.7),
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74 ...)
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75 combineLimits(sizeplot)
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76 }
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77
2
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78 second_plot_size = function(df, ...) {
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79 # smR.prepanel=function(x,y,...){; yscale=c(-max(abs(y)), max(abs(y)));list(ylim=yscale);}
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80 bc= barchart(Count~as.factor(Size)|factor(Dataset, levels=unique(Dataset))+Chromosome, data = df, origin = 0,
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81 horizontal=FALSE,
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82 group=Polarity,
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83 stack=TRUE,
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84 col=c('red', 'blue'),
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85 cex=0.75,
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86 scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.7), x=list(cex=0.7) ),
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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87 # prepanel=smR.prepanel,
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88 xlab = NULL,
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89 ylab = NULL,
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90 main = NULL,
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91 as.table=TRUE,
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92 newpage = T,
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93 par.strip.text = list(cex=0.7),
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94 ...)
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95 combineLimits(bc)
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96 }
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97
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98
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99 ## end of functions
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100
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101 ## function parameters
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102 par.settings.readmap=list(layout.heights=list(top.padding=0, bottom.padding=0), strip.background = list(col=c("lightblue","lightgreen")) )
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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103 par.settings.size=list(layout.heights=list(top.padding=0, bottom.padding=0))
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104 graph_title=list(Coverage="Read Maps and Coverages", Median="Read Maps and Median sizes", Mean="Read Maps and Mean sizes", SizeDistribution="Read Maps and Size Distributions")
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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105 graph_legend=list(Coverage="Read counts / Coverage", Median="Read counts / Median size", Mean="Read counts / Mean size", SizeDistribution="Read counts")
2
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106 graph_bottom=list(Coverage="Nucleotide coordinates", Median="Nucleotide coordinates", Mean="Nucleotide coordinates", Size="Read sizes / Nucleotide coordinates")
0
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107 ## end of function parameters'
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108
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109 ## GRAPHS
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110
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111 if (n_genes > 5) {page_height_simple = 11.69; page_height_combi=11.69; rows_per_page=6} else {
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112 rows_per_page= n_genes; page_height_simple = 2.5*n_genes; page_height_combi=page_height_simple*2 }
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113 if (n_samples > 4) {page_width = 8.2677*n_samples/4} else {page_width = 8.2677*n_samples/2} # to test
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114
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115
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116 pdf(file=args$output_pdf, paper="special", height=page_height_simple, width=page_width)
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117 if (rows_per_page %% 2 != 0) { rows_per_page = rows_per_page + 1}
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118 for (i in seq(1,n_genes,rows_per_page/2)) {
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119 start=i
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120 end=i+rows_per_page/2-1
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121 if (end>n_genes) {end=n_genes}
2
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122 first_plot.list=lapply(per_gene_readmap[start:end], function(x) first_plot(x, strip=FALSE, par.settings=par.settings.readmap))
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123 if (args$extra_plot_method == "Size") {
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124 second_plot.list=lapply(per_gene_size[start:end], function(x) second_plot_size(x, par.settings=par.settings.size))
0
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125 }
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126 else {
2
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127 second_plot.list=lapply(per_gene_size[start:end], function(x) second_plot(x, par.settings=par.settings.size))
0
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128 }
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129
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130
2
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131 plot.list=rbind(second_plot.list, first_plot.list)
0
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132 args_list=c(plot.list, list(nrow=rows_per_page+1, ncol=1,
2
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133 top=textGrob(graph_title[[args$extra_plot_method]], gp=gpar(cex=1), just="top"),
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134 left=textGrob(graph_legend[[args$extra_plot_method]], gp=gpar(cex=1), vjust=1, rot=90),
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135 sub=textGrob(graph_bottom[[args$extra_plot_method]], gp=gpar(cex=1), just="bottom")
0
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136 )
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137 )
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138 do.call(grid.arrange, args_list)
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139 }
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140 devname=dev.off()
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141