Mercurial > repos > artbio > small_rna_signatures
view signature.r @ 8:5c4504825d74 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 8c94de4e247f8a4b71b3904dfbf4a1e21bfcf86a
author | artbio |
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date | Sun, 10 Sep 2017 14:07:21 -0400 |
parents | a35e6f9c1d34 |
children | 8d3ca9652a5b |
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## 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("--h_dataframe", type="character", help="path to h-signature dataframe"), make_option("--z_dataframe", type="character", help="path to z-signature dataframe"), make_option("--plot_method", type = "character", help="How data should be plotted (global or lattice)"), make_option("--pdf", type = "character", help="path to the pdf file with plots"), make_option("--title", type = "character", help="Graph Title") ) parser <- OptionParser(usage = "%prog [options] file", option_list = option_list) args = parse_args(parser) # data frames implementation h_dataframe = read.delim(args$h_dataframe, header=F) colnames(h_dataframe) = c("chrom", "overlap", "sig", "z-score") h_dataframe$sig = h_dataframe$sig * 100 # to get probs in % z_dataframe = read.delim(args$z_dataframe, header=F) colnames(z_dataframe) = c("chrom", "overlap", "sig", "z-score") # functions globalgraph = function () { pdf(args$pdf) par(mfrow=c(2,2),oma = c(0, 0, 3, 0)) plot(z_dataframe[z_dataframe$chrom == "all_chromosomes", c(2,3)], type = "h", main="Numbers of pairs", cex.main=1, xlab="overlap (nt)", ylab="Numbers of pairs", col="darkslateblue", lwd=4) plot(z_dataframe[z_dataframe$chrom == "all_chromosomes", c(2,4)], type = "l", main="Number of pairs Z-scores", cex.main=1, xlab="overlap (nt)", ylab="z-score", pch=19, cex=0.2, col="darkslateblue", lwd=2) plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2,3)], type = "l", main="Overlap probabilities", cex.main=1, xlab="overlap (nt)", ylab="Probability [%]", ylim=c(0,50), pch=19, col="darkslateblue", lwd=2) plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2,4)], type = "l", main="Overlap Probability Z-scores", cex.main=1, xlab="overlap (nt)", ylab="z-score", pch=19, cex=0.2, col="darkslateblue", lwd=2) mtext(args$title, outer = TRUE, cex=1) dev.off() } treillisgraph = function (df, ...) { pdf(args$pdf, paper="special", height=11.69, width=6 ) # 8.2677 p = xyplot(sig ~ overlap|factor(method, levels=unique(method))+chrom, data = df, type = "l", col='darkblue', cex=0.5, scales=list(y=list(tick.number=4, relation="free", cex=0.6, rot=0), x=list(cex=0.6, alternating=FALSE)), xlab = "Overlap", ylab = "signature (Nbr of pairs / Overlap prob.)", main = args$title, par.strip.text=list(cex=.5), pch=19, lwd =2, as.table=TRUE, layout=c(2,12), newpage = T, ...) plot(p) dev.off() } # main if (args$plot_method=="global") { globalgraph() } if(args$plot_method=="lattice") { # rearrange dataframes h_sig = h_dataframe[,c(1,2,3)] h_sig = cbind(rep("Overlap Prob (%)", length(h_sig[,1])), h_sig) colnames(h_sig) = c("method", "chrom", "overlap", "sig") z_pairs = z_dataframe[,c(1,2,3)] z_pairs = cbind(rep("Nbr of pairs", length(z_pairs[,1])), z_pairs) colnames(z_pairs) = c("method", "chrom", "overlap", "sig") lattice_df = rbind(z_pairs, h_sig) par.settings.treillis=list(strip.background = list( col = c("lightblue", "lightgreen"))) treillisgraph(lattice_df, par.settings=par.settings.treillis) }