view small_rna_maps.r @ 0:6d48150495e3 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959

## Setup R error handling to go to stderr
options( show.error.messages=F,
       error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
warnings()
library(RColorBrewer)
library(lattice)
library(latticeExtra)
library(grid)
library(gridExtra)
library(optparse)
 
option_list <- list(
    make_option(c("-r", "--output_tab"), type="character", help="path to tabular file"),
    make_option(c("-s", "--sizes"), type="character", help="path to size dataframe"),
    make_option("--output_pdf", type = "character", help="path to the pdf file with plot"),
    make_option("--extra_plot", type = "character", help="what additional data should be plotted")
    )
 
parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
args = parse_args(parser)
if (length(args$sizes) != 0) { args$extra_plot <- "SizeDistribution"}
 
# dataset manipulation

Table = read.delim(args$output_tab, header=T, row.names=NULL)
Table <- within(Table, Nbr_reads[Polarity=="R"] <- (Nbr_reads[Polarity=="R"]*-1))
n_samples=length(unique(Table$Dataset))
genes=unique(levels(Table$Chromosome))
per_gene_readmap=lapply(genes, function(x) subset(Table, Chromosome==x))
per_gene_limit=lapply(genes, function(x) c(1, unique(subset(Table, Chromosome==x)$Chrom_length)) )
n_genes=length(per_gene_readmap)
if (args$extra_plot == "SizeDistribution") {
    size=read.delim(args$sizes, header=T, row.names=NULL)
    size <- within(size, Nbr_reads[Polarity=="R"] <- (Nbr_reads[Polarity=="R"]*-1))
    per_gene_size=lapply(genes, function(x) subset(size, Chromosome==x))
    }

## end of data frames implementation

## functions

plot_readmap=function(df, ...) {
    combineLimits(xyplot(Nbr_reads~Coordinate|factor(Dataset, levels=unique(Dataset))+factor(Chromosome, levels=unique(Chromosome)),
    data=df,
    type='h',
    lwd=1.5,
    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=function(df, ...) {
    #smR.prepanel=function(x,y,...) {; yscale=c(y*0, max(abs(y)));list(ylim=yscale);}
    sizeplot = xyplot(eval(as.name(args$extra_plot))~Coordinate|factor(Dataset, levels=unique(Dataset))+factor(Chromosome, levels=unique(Chromosome)),
    data=df,
    type='p',
    cex=0.35,
    pch=19,
    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)),
    xlab=NULL, main=NULL, ylab=NULL,
    as.table=T,
    origin = 0,
    horizontal=FALSE,
    group=Polarity,
    col=c("darkred","darkblue"),
    par.strip.text = list(cex=0.7),
    ...)
    combineLimits(sizeplot)
    }

plot_size_distribution= function(df, ...) {
#  smR.prepanel=function(x,y,...){; yscale=c(-max(abs(y)), max(abs(y)));list(ylim=yscale);}
  bc= barchart(Nbr_reads~as.factor(Size)|factor(Dataset, levels=unique(Dataset))+Chromosome, 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=0), strip.background = list(col=c("lightblue","lightgreen")) )
par.settings.size=list(layout.heights=list(top.padding=0, bottom.padding=0))
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")
graph_legend=list(Coverage="Read counts / Coverage", Median="Read counts / Median size", Mean="Read counts / Mean size", SizeDistribution="Read counts")
graph_bottom=list(Coverage="Nucleotide coordinates", Median="Nucleotide coordinates", Mean="Nucleotide coordinates", SizeDistribution="Read sizes / Nucleotide coordinates")
## end of function parameters'

## GRAPHS

if (n_genes > 5) {page_height_simple = 11.69; page_height_combi=11.69; rows_per_page=6} 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/2} # to test


pdf(file=args$output_pdf, paper="special", height=page_height_simple, width=page_width)
if (rows_per_page %% 2 != 0) { rows_per_page = rows_per_page + 1}
for (i in seq(1,n_genes,rows_per_page/2)) {
    start=i
    end=i+rows_per_page/2-1
    if (end>n_genes) {end=n_genes}
    readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, strip=FALSE, par.settings=par.settings.readmap))
    if (args$extra_plot == "SizeDistribution") {
        size_plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, par.settings=par.settings.size))
        }
    else {
        size_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_size(x, par.settings=par.settings.size))
        }
    
        
    plot.list=rbind(size_plot.list, readmap_plot.list)
    args_list=c(plot.list, list(nrow=rows_per_page+1, ncol=1,
                                    top=textGrob(graph_title[[args$extra_plot]], gp=gpar(cex=1), just="top"),
                                    left=textGrob(graph_legend[[args$extra_plot]], gp=gpar(cex=1), vjust=1, rot=90),
                                    sub=textGrob(graph_bottom[[args$extra_plot]], gp=gpar(cex=1), just="bottom")
                                    )
           )
do.call(grid.arrange, args_list)
}
devname=dev.off()