diff plot_size_readmap.r @ 8:be0c6b6466cc draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plot_size_readmap.r	Mon Sep 19 06:16:21 2016 -0400
@@ -0,0 +1,145 @@
+## Setup R error handling to go to stderr
+options( show.error.messages=F,
+       error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+library(RColorBrewer)
+library(lattice)
+library(latticeExtra)
+library(grid)
+library(gridExtra)
+library(optparse)
+
+# Parse arguments
+option_list <- list(
+    make_option(c("-r", "--readmap_tab"), type="character", help="Path to file with tabular readmap"),
+    make_option(c("-s", "--size_distribution_tab"), type="character", help="Path to file with tabular size distribution"),
+    make_option("--readmap_pdf", type="character", help="Path to file with readmap plot"),
+    make_option("--size_distribution_pdf", type="character", help="Path to file with size distribution plot"),
+    make_option("--combi_pdf", type="character", help="Path to file with size distribution and readmap plot"),
+    make_option("--title", type="character", help="Title for readmaps and size distribution"),
+    make_option("--xlabel", type="character", help="xlabel for readmaps and size distribution"),
+    make_option("--ylabel", type="character", help="ylabel for readmaps and size distribution"),
+    make_option("--yrange", type="integer", help="Y-axis range"),
+    make_option("--rows_per_page", type="integer", help="rows_per_page")
+    )
+
+parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
+args = parse_args(parser)
+
+## data frames implementation
+
+rm=read.delim(args$readmap_tab, header=T, row.names=NULL)
+n_samples=length(unique(rm$sample))
+genes=unique(levels(rm$gene))
+per_gene_readmap=lapply(genes, function(x) subset(rm, gene==x))
+n_genes=length(per_gene_readmap)
+
+size=read.delim(args$size_distribution_tab, header=T, row.names=NULL)
+per_gene_size=lapply(genes, function(x) subset(size, gene==x))
+
+## end of data frames implementation
+
+## functions
+
+plot_readmap=function(df, ...) {
+combineLimits(xyplot(count~coord|factor(sample, levels=unique(sample))+reorder(gene, count, function(x) -sum(abs(x))),
+data=df,
+type='h',
+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)),
+xlab=NULL, main=NULL, ylab=NULL,
+as.table=T,
+origin = 0,
+horizontal=FALSE,
+group=polarity,
+col=c("red","blue"),
+par.strip.text = list(cex=0.7),
+...))
+}
+
+plot_size_distribution= function(df, ...) {
+  smR.prepanel=function(x,y,...){; yscale=c(-max(abs(y)), max(abs(y)));list(ylim=yscale);}
+  bc= barchart(count~as.factor(size)|factor(sample, levels=unique(sample))+gene, data = df, origin = 0,
+    horizontal=FALSE,
+group=polarity,
+stack=TRUE,
+    col=c('red', 'blue'),
+    cex=0.75,
+    scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.7), x=list(cex=0.7) ),
+    prepanel=smR.prepanel,
+    xlab = NULL,
+    ylab = NULL,
+    main = NULL,
+    as.table=TRUE,
+    newpage = T,
+    par.strip.text = list(cex=0.7),
+    ...)
+  combineLimits(bc)
+  }
+
+## end of functions
+
+## function parameters'
+
+par.settings.readmap=list(layout.heights=list(top.padding=0, bottom.padding=-2.5), strip.background = list(col=c("lightblue","lightgreen")) )
+par.settings.size=list(layout.heights=list(top.padding=-1, bottom.padding=-2.5), strip.background = list(col=c("lightblue","lightgreen")) )
+par.settings.combination.readmap=list(layout.heights=list(top.padding=0, bottom.padding=-3), strip.background=list(col=c("lightblue","lightgreen")) )
+par.settings.combination.size=list(layout.heights=list(top.padding=-2, bottom.padding=-0.5), strip.background=list(col=c("lightblue", "lightgreen")) )
+
+## end of function parameters'
+
+## GRAPHS
+
+if (n_genes > 7) {page_height_simple = 11.69; page_height_combi=11.69; rows_per_page=args$rows_per_page} else {
+                 rows_per_page= n_genes; page_height_simple = 2.5*n_genes; page_height_combi=page_height_simple*2 }
+if (n_samples > 4) {page_width = 8.2677*n_samples/4} else {page_width = 8.2677*n_samples/3} # to test
+
+
+pdf(file=args$readmap_pdf, paper="special", height=page_height_simple, width=page_width)
+for (i in seq(1,n_genes,rows_per_page)) {
+start=i
+end=i+rows_per_page-1
+if (end>n_genes) {end=n_genes}
+if (args$yrange == 0) { readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else {
+readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-args.yrange, args.yrange) , par.settings=par.settings.readmap)) }
+args_list=c(readmap_plot.list, list(nrow=rows_per_page, ncol=1,
+                                    top=textGrob("Read Maps (nucleotide coordinates)", gp=gpar(cex=1), just="top"),
+                                    left=textGrob(args$ylabel, gp=gpar(cex=1), vjust=1, rot=90)
+                                    )
+           )
+do.call(grid.arrange, args_list)
+}
+devname=dev.off()
+
+pdf(file=args$size_distribution_pdf, paper="special", height=page_height_simple, width=page_width)
+for (i in seq(1,n_genes,rows_per_page)) {
+start=i
+end=i+rows_per_page-1
+if (end>n_genes) {end=n_genes}
+plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, par.settings=par.settings.size) )
+args_list=c(plot.list, list(nrow=rows_per_page, ncol=1,
+                            top=textGrob("Size distributions (in nucleotides)", gp=gpar(cex=1), just="top"),
+                            left=textGrob(args$ylabel, gp=gpar(cex=1), vjust=1, rot=90)
+                            )
+            )
+do.call(grid.arrange, args_list)
+}
+devname=dev.off()
+
+pdf(file=args$combi_pdf, paper="special", height=page_height_combi, width=page_width)
+if (rows_per_page %% 2 != 0) { rows_per_page = rows_per_page + 1}
+for (i in seq(1,n_genes,rows_per_page/2)) {
+start=i
+end=i+rows_per_page/2-1
+if (end>n_genes) {end=n_genes}
+if (args$yrange == 0) {readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else {
+readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-args.yrange, args.yrange), par.settings=par.settings.readmap)) }
+size_plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, strip=FALSE, par.settings=par.settings.combination.size))
+plot.list=rbind(readmap_plot.list, size_plot.list )
+args_list=c(plot.list, list(nrow=rows_per_page+1, ncol=1,
+                            top=textGrob(args$title, gp=gpar(cex=1), just="top"),
+                            left=textGrob(args$ylabel, gp=gpar(cex=1), vjust=1, rot=90),
+                            sub=textGrob(args$xlabel, gp=gpar(cex=1), just="bottom")
+                            )
+            )
+do.call(grid.arrange, args_list)
+}
+devname=dev.off()
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