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annotate lattice_small_rna_map.r @ 3:2e0dc6032a98 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
author artbio
date Tue, 18 Jul 2017 13:34:36 -0400
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children 6ff925458e05
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2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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1 ## Setup R error handling to go to stderr
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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2 #options( show.error.messages=F,
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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3 # error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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4 warnings()
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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5 library(RColorBrewer)
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6 library(lattice)
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7 library(latticeExtra)
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8 library(grid)
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9 library(gridExtra)
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10 library(optparse)
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11
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12 option_list <- list(
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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13 make_option(c("-r", "--output_tab"), type="character", help="path to tabular file"),
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14 make_option("--output_pdf", type = "character", help="path to the pdf file with plot")
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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15 )
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17 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
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18 args = parse_args(parser)
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20 # dataset manipulation
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21
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22 Table = read.delim(args$output_tab, header=T, row.names=NULL)
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23 Table <- within(Table, Nbr_reads[Polarity=="R"] <- (Nbr_reads[Polarity=="R"]*-1))
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24 n_samples=length(unique(Table$Dataset))
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25 genes=unique(levels(Table$Chromosome))
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26 per_gene_readmap=lapply(genes, function(x) subset(Table, Chromosome==x))
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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27 per_gene_limit=lapply(genes, function(x) c(1, unique(subset(Table, Chromosome==x)$Chrom_length)) )
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28 n_genes=length(per_gene_readmap)
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29 ## end of data frames implementation
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30
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31 ## functions
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32
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33 plot_readmap=function(df, ...) {
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34 combineLimits(xyplot(Nbr_reads~Coordinate|factor(Dataset, levels=unique(Dataset))+factor(Chromosome, levels=unique(Chromosome)),
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35 data=df,
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36 type='h',
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37 scales= list(relation="free", x=list(rot=0, cex=0.7, axs="i", tck=0.1), y=list(tick.number=4, rot=90, cex=0.7)),
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38 xlab=NULL, main=NULL, ylab=NULL,
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39 as.table=T,
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40 origin = 0,
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41 horizontal=FALSE,
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42 group=Polarity,
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43 col=c("red","blue"),
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44 par.strip.text = list(cex=0.7),
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45 ...))
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46 }
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47
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48
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49 plot_size=function(df, ...) {
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50 smR.prepanel=function(x,y,...) {; yscale=c(y*0, max(abs(y)));list(ylim=yscale);}
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51 sizeplot = xyplot(Median~Coordinate|factor(Dataset, levels=unique(Dataset))+factor(Chromosome, levels=unique(Chromosome)),
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52 data=df,
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53 type='p',
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54 cex=0.5,
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55 pch=19,
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56 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)),
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57 xlab=NULL, main=NULL, ylab=NULL,
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58 as.table=T,
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59 origin = 0,
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60 horizontal=FALSE,
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61 group=Polarity,
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62 col=c("darkred","darkblue"),
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63 par.strip.text = list(cex=0.7),
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64 ...)
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65 combineLimits(sizeplot)
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66 }
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67
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68
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69 ## end of functions
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70
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71 ## function parameters
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72 par.settings.readmap=list(layout.heights=list(top.padding=0, bottom.padding=0), strip.background = list(col=c("lightblue","lightgreen")) )
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73 par.settings.size=list(layout.heights=list(top.padding=0, bottom.padding=0))
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74 ## end of function parameters'
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75
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76 ## GRAPHS
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77
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78 if (n_genes > 7) {page_height_simple = 11.69; page_height_combi=11.69; rows_per_page=10} else {
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79 rows_per_page= n_genes; page_height_simple = 2.5*n_genes; page_height_combi=page_height_simple*2 }
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80 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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81
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82
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83 pdf(file=args$output_pdf, paper="special", height=page_height_simple, width=page_width)
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84 if (rows_per_page %% 2 != 0) { rows_per_page = rows_per_page + 1}
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85 for (i in seq(1,n_genes,rows_per_page/2)) {
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86 start=i
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87 end=i+rows_per_page/2-1
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88 if (end>n_genes) {end=n_genes}
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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89 readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, xlim=c(1, x$Chrom_length[1]), strip=FALSE, par.settings=par.settings.readmap))
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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90 size_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_size(x, xlim=c(1, x$Chrom_length[1]), par.settings=par.settings.size))
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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91
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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92 plot.list=rbind(size_plot.list, readmap_plot.list)
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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93 args_list=c(plot.list, list(nrow=rows_per_page+1, ncol=1,
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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94 top=textGrob("Read Maps and Median sizes", gp=gpar(cex=1), just="top"),
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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95 left=textGrob("Read counts / Median size", gp=gpar(cex=1), vjust=1, rot=90),
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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96 sub=textGrob("Nucleotide coordinates", gp=gpar(cex=1), just="bottom")
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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97 )
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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98 )
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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99 do.call(grid.arrange, args_list)
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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100 }
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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101 devname=dev.off()
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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102