--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/batch-consistency-plot.r	Thu Jan 17 15:45:33 2013 -0500
@@ -0,0 +1,68 @@
+# 1-20-10 Qunhua Li
+#
+# This program first plots correspondence curve and IDR threshold plot
+# (i.e. number of selected peaks vs IDR) for each pair of sample
+#
+# usage: 
+# Rscript batch-consistency-plot-merged.r [npairs] [output.dir] [input.file.prefix 1, 2, 3 ...]
+# [npairs]: integer, number of consistency analyses
+#          (e.g. if 2 replicates, npairs=1, if 3 replicates, npairs=3
+# [output.prefix]: output directory and file name prefix for plot eg. /plots/idrPlot
+# [input.file.prefix 1, 2, 3]: prefix for the output from batch-consistency-analysis2. They are the input files for merged analysis see below for examples (i.e. saved.file.prefix). It can be multiple files
+#
+
+args <- commandArgs(trailingOnly=T)
+npair <- args[1] # number of curves to plot on the same figure
+output.file.prefix <- args[2] # file name for plot, generated from script at the outer level
+df.txt <- 10
+ntemp <- as.numeric(npair)
+saved.file.prefix <- list() # identifier of filenames that contain the em and URI results
+source("/mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC_tools/idr/functions-all-clayton-12-13.r")
+
+uri.list <- list()
+uri.list.match <- list()
+ez.list <- list()
+legend.txt <- c()
+em.output.list <- list()
+uri.output.list <- list()
+
+for(i in 1:npair){
+  saved.file.prefix[i] <- args[2+i]
+ 
+  load(paste(saved.file.prefix[i], "-uri.sav", sep=""))
+  load(paste(saved.file.prefix[i], "-em.sav", sep=""))
+
+  uri.output.list[[i]] <- uri.output
+  em.output.list[[i]] <- em.output
+
+  ez.list[[i]] <- get.ez.tt.all(em.output, uri.output.list[[i]]$data12.enrich$merge1,
+                                uri.output.list[[i]]$data12.enrich$merge2) # reverse =T for error rate
+
+  # URI for all peaks
+  uri.list[[i]] <- uri.output$uri.n
+  # URI for matched peaks
+  uri.match <- get.uri.matched(em.output$data.pruned, df=df.txt)
+  uri.list.match[[i]] <- uri.match$uri.n
+
+  file.name <- unlist(strsplit(as.character(saved.file.prefix[i]), "/"))
+  
+  legend.txt[i] <- paste(i, "=", file.name[length(file.name)])
+
+}
+
+plot.uri.file <- paste(output.file.prefix, "-plot.ps", sep="")
+
+############# plot and report output
+# plot correspondence curve for each pair,
+# plot number of selected peaks vs IDR 
+# plot all into 1 file
+postscript(paste(output.file.prefix, "-plot.ps", sep=""))
+par(mfcol=c(2,3), mar=c(5,6,4,2)+0.1)
+plot.uri.group(uri.list, NULL, file.name=NULL, c(1:npair), title.txt="all peaks")
+plot.uri.group(uri.list.match, NULL, file.name=NULL, c(1:npair), title.txt="matched peaks")
+plot.ez.group(ez.list, plot.dir=NULL, file.name=NULL, legend.txt=c(1:npair), y.lim=c(0, 0.6))
+plot(0, 1, type="n", xlim=c(0,1), ylim=c(0,1), xlab="", ylab="", xaxt="n", yaxt="n") # legends
+legend(0, 1, legend.txt, cex=0.6)
+
+dev.off()
+