Mercurial > repos > bornea > prohits_dotplot_generator
view Dotplot_Release/R_dotPlot.R @ 27:63cc1f29a57b draft
Uploaded
author | bornea |
---|---|
date | Tue, 19 Apr 2016 11:37:44 -0400 |
parents | bc752a05f16d |
children |
line wrap: on
line source
#!/usr/bin/env Rscript args <- commandArgs(trailingOnly = TRUE) library('latticeExtra') library('colorRamps') data.file <- read.table("SC_data.txt", sep="\t", header=TRUE, row.names=1) ### import spectral count data data.file2 <- read.table("FDR_data.txt", sep="\t", header=TRUE, row.names=1) ### import FDR count data data.file3 <- read.table("clustered_matrix.txt", sep="\t", header=TRUE, row.names=1) ### import clustered matrix data.file4 <- scan("singletons.txt", what="", sep="\n", strip.white=T) ### import singleton data #setting parameters Sfirst=as.numeric(args[1]) #first FDR cutoff Ssecond=as.numeric(args[2]) #second FDR cutoff maxp=as.integer(args[3]) #maximum value for a spectral count #calculate column and row lengths #determine bait and prey ordering bait_levels=names(data.file3) prey_levels=c(rownames(data.file3),data.file4) x_ord=factor(row.names(data.file),levels=prey_levels) y_ord=factor(names(data.file),levels=bait_levels) df<-data.frame(y=rep(y_ord,nrow(data.file)) ,x=rep(x_ord, each=ncol(data.file)) ,z1=as.vector(t(data.file)) # Circle color ,z2=as.vector(t(data.file/apply(data.file,1,max))) # Circle size ,z3=as.vector(t(data.file2)) # FDR ) df$z1[df$z1>maxp] <- maxp #maximum value for spectral count df$z2[df$z2==0] <- NA df$z3[df$z3>Ssecond] <- 0.05*maxp df$z3[df$z3<=Ssecond & df$z3>Sfirst] <- 0.5*maxp df$z3[df$z3<=Sfirst] <- 1*maxp df$z4 <- df$z1 df$z4[df$z4==0] <- 0 df$z4[df$z4>0] <- 2.5 # The labeling for the colorkey labelat = c(0, maxp) labeltext = c(0, maxp) # color scheme to use nmb.colors<-maxp z.colors<-grey(rev(seq(0,0.9,0.9/nmb.colors))) #grayscale color scale #plot pl <- levelplot(z1~x*y, data=df ,col.regions =z.colors #terrain.colors(100) ,scales = list(x = list(rot = 90), y=list(cex=0.8), tck=0) # rotates X,Y labels and changes scale ,colorkey = FALSE ,xlab="Prey", ylab="Bait" ,panel=function(x,y,z,...,col.regions){ print(x) z.c<-df$z1[ (df$x %in% as.character(x)) & (df$y %in% y)] z.2<-df$z2[ (df$x %in% as.character(x)) & (df$y %in% y)] z.3<-df$z3 z.4<-df$z4 panel.xyplot(x,y ,as.table=TRUE ,pch=21 # point type to use (circles in this case) ,cex=((z.2-min(z.2,na.rm=TRUE))/(max(z.2,na.rm=TRUE)-min(z.2,na.rm=TRUE)))*3 #circle size ,fill=z.colors[floor((z.c-min(z.c,na.rm=TRUE))*nmb.colors/(max(z.c,na.rm=TRUE)-min(z.c,na.rm=TRUE)))+1] # circle colors ,col=z.colors[1+z.3] # border colors ,lex=z.4 #border thickness ) } #,main="Fold change" # graph main title ) if(ncol(data.file) > 4) ht=3.5+(0.36*((ncol(data.file)-1)-4)) else ht=3.5 if(nrow(data.file) > 20) wd=8.25+(0.29*(nrow(data.file)-20)) else wd=5+(0.28*(nrow(data.file)-10)) pdf("dotplot.pdf", onefile = FALSE, paper = "special", height = ht, width = wd, pointsize = 2) print(pl) dev.off()