annotate signature.r @ 5:a7fd04208764 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 24d44a9b7ec9db4dce3d839b597eea2b1be34adb

## 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)    
}