Mercurial > repos > artbio > small_rna_maps

comparison small_rna_maps.r @ 0:6d48150495e3 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
author artbio
date Mon, 24 Jul 2017 06:28:45 -0400
parents
children 507383cce5a8
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-1:000000000000 0:6d48150495e3
1 ## Setup R error handling to go to stderr
2 options( show.error.messages=F,
3 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
4 warnings()
5 library(RColorBrewer)
6 library(lattice)
7 library(latticeExtra)
8 library(grid)
9 library(gridExtra)
10 library(optparse)
11
12 option_list <- list(
13 make_option(c("-r", "--output_tab"), type="character", help="path to tabular file"),
14 make_option(c("-s", "--sizes"), type="character", help="path to size dataframe"),
15 make_option("--output_pdf", type = "character", help="path to the pdf file with plot"),
16 make_option("--extra_plot", type = "character", help="what additional data should be plotted")
17 )
18
19 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
20 args = parse_args(parser)
21 if (length(args$sizes) != 0) { args$extra_plot <- "SizeDistribution"}
22
23 # dataset manipulation
24
25 Table = read.delim(args$output_tab, header=T, row.names=NULL)
26 Table <- within(Table, Nbr_reads[Polarity=="R"] <- (Nbr_reads[Polarity=="R"]*-1))
27 n_samples=length(unique(Table$Dataset))
28 genes=unique(levels(Table$Chromosome))
29 per_gene_readmap=lapply(genes, function(x) subset(Table, Chromosome==x))
30 per_gene_limit=lapply(genes, function(x) c(1, unique(subset(Table, Chromosome==x)$Chrom_length)) )
31 n_genes=length(per_gene_readmap)
32 if (args$extra_plot == "SizeDistribution") {
33 size=read.delim(args$sizes, header=T, row.names=NULL)
34 size <- within(size, Nbr_reads[Polarity=="R"] <- (Nbr_reads[Polarity=="R"]*-1))
35 per_gene_size=lapply(genes, function(x) subset(size, Chromosome==x))
36 }
37
38 ## end of data frames implementation
39
40 ## functions
41
42 plot_readmap=function(df, ...) {
43 combineLimits(xyplot(Nbr_reads~Coordinate|factor(Dataset, levels=unique(Dataset))+factor(Chromosome, levels=unique(Chromosome)),
44 data=df,
45 type='h',
46 lwd=1.5,
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)),
48 xlab=NULL, main=NULL, ylab=NULL,
49 as.table=T,
50 origin = 0,
51 horizontal=FALSE,
52 group=Polarity,
53 col=c("red","blue"),
54 par.strip.text = list(cex=0.7),
55 ...))
56 }
57
58
59 plot_size=function(df, ...) {
60 #smR.prepanel=function(x,y,...) {; yscale=c(y*0, max(abs(y)));list(ylim=yscale);}
61 sizeplot = xyplot(eval(as.name(args$extra_plot))~Coordinate|factor(Dataset, levels=unique(Dataset))+factor(Chromosome, levels=unique(Chromosome)),
62 data=df,
63 type='p',
64 cex=0.35,
65 pch=19,
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)),
67 xlab=NULL, main=NULL, ylab=NULL,
68 as.table=T,
69 origin = 0,
70 horizontal=FALSE,
71 group=Polarity,
72 col=c("darkred","darkblue"),
73 par.strip.text = list(cex=0.7),
74 ...)
75 combineLimits(sizeplot)
76 }
77
78 plot_size_distribution= function(df, ...) {
79 # smR.prepanel=function(x,y,...){; yscale=c(-max(abs(y)), max(abs(y)));list(ylim=yscale);}
80 bc= barchart(Nbr_reads~as.factor(Size)|factor(Dataset, levels=unique(Dataset))+Chromosome, data = df, origin = 0,
81 horizontal=FALSE,
82 group=Polarity,
83 stack=TRUE,
84 col=c('red', 'blue'),
85 cex=0.75,
86 scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.7), x=list(cex=0.7) ),
87 # prepanel=smR.prepanel,
88 xlab = NULL,
89 ylab = NULL,
90 main = NULL,
91 as.table=TRUE,
92 newpage = T,
93 par.strip.text = list(cex=0.7),
94 ...)
95 combineLimits(bc)
96 }
97
98
99 ## end of functions
100
101 ## function parameters
102 par.settings.readmap=list(layout.heights=list(top.padding=0, bottom.padding=0), strip.background = list(col=c("lightblue","lightgreen")) )
103 par.settings.size=list(layout.heights=list(top.padding=0, bottom.padding=0))
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")
105 graph_legend=list(Coverage="Read counts / Coverage", Median="Read counts / Median size", Mean="Read counts / Mean size", SizeDistribution="Read counts")
106 graph_bottom=list(Coverage="Nucleotide coordinates", Median="Nucleotide coordinates", Mean="Nucleotide coordinates", SizeDistribution="Read sizes / Nucleotide coordinates")
107 ## end of function parameters'
108
109 ## GRAPHS
110
111 if (n_genes > 5) {page_height_simple = 11.69; page_height_combi=11.69; rows_per_page=6} else {
112 rows_per_page= n_genes; page_height_simple = 2.5*n_genes; page_height_combi=page_height_simple*2 }
113 if (n_samples > 4) {page_width = 8.2677*n_samples/4} else {page_width = 8.2677*n_samples/2} # to test
114
115
116 pdf(file=args$output_pdf, paper="special", height=page_height_simple, width=page_width)
117 if (rows_per_page %% 2 != 0) { rows_per_page = rows_per_page + 1}
118 for (i in seq(1,n_genes,rows_per_page/2)) {
119 start=i
120 end=i+rows_per_page/2-1
121 if (end>n_genes) {end=n_genes}
122 readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, strip=FALSE, par.settings=par.settings.readmap))
123 if (args$extra_plot == "SizeDistribution") {
124 size_plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, par.settings=par.settings.size))
125 }
126 else {
127 size_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_size(x, par.settings=par.settings.size))
128 }
129
130
131 plot.list=rbind(size_plot.list, readmap_plot.list)
132 args_list=c(plot.list, list(nrow=rows_per_page+1, ncol=1,
133 top=textGrob(graph_title[[args$extra_plot]], gp=gpar(cex=1), just="top"),
134 left=textGrob(graph_legend[[args$extra_plot]], gp=gpar(cex=1), vjust=1, rot=90),
135 sub=textGrob(graph_bottom[[args$extra_plot]], gp=gpar(cex=1), just="bottom")
136 )
137 )
138 do.call(grid.arrange, args_list)
139 }
140 devname=dev.off()
141