--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/region_motif_compare.r	Tue Aug 05 13:56:22 2014 -0400
@@ -0,0 +1,189 @@
+# Name: region_motif_compare.r
+# Description: Reads in two count files and determines enriched and depleted
+# motifs (or any location based feature) based on poisson tests and gc
+# corrections. All enrichment ratios relative to overall count / gc ratios.
+# Author: Jeremy liu
+# Email: jeremy.liu@yale.edu
+# Date: 14/07/03
+# Note: This script is meant to be invoked with the following command
+# R --slave --vanilla -f ./region_motif_compare.r --args <workingdir> <db> <intab1> <intab2> 
+#   <enriched_tab> <depleted_tab> <plots_png>
+# <workingdir> is working directory of galaxy installation
+# <db> types: "t" test, "p" pouya, "j" jaspar jolma, "m" mouse, "c" combined
+# Dependencies: plotting.r
+
+# Auxiliary function to concatenate multiple strings
+concat <- function(...) {
+	input_list <- list(...)
+	return(paste(input_list, sep="", collapse=""))
+}
+
+# Supress all warning messages to prevent Galaxy treating warnings as errors
+options(warn=-1)
+
+# Set common and data directories
+args <- commandArgs()
+workingDir = args[7]
+commonDir = concat(workingDir, "/tools/my_tools")
+dbCode = args[8]
+# dbCode "c" implemented when pwmFile is loaded
+if (dbCode == "t" | dbCode == "p") {
+	pwmFile = concat(commonDir, "/region_motif_db/pwms/pouya.pwms.from.seq.RData")
+} else if (dbCode == "j") {
+	pwmFile = concat(commonDir, "/region_motif_db/pwms/jaspar.jolma.pwms.from.seq.RData")
+} else if (dbCode == "m") {
+	pwmFile = concat(commonDir, "/region_motif_db/pwms/mm9.pwms.from.seq.RData")
+} else if (dbCode == "c") { # rest of dbCode "c" implemeted when pwmFile loaded
+	pwmFile = concat(commonDir, "/region_motif_db/pwms/pouya.pwms.from.seq.RData")
+	pwmFile2 = concat(commonDir, "/region_motif_db/pwms/jaspar.jolma.pwms.from.seq.RData")
+} else {
+	pwmFile = concat(commonDir, "/region_motif_db/pwms/pouya.pwms.from.seq.RData")
+}
+
+# Set input and reference files
+inTab1 = args[9]
+inTab2 = args[10]
+enrichTab = args[11]
+depleteTab = args[12]
+plotsPng = args[13]
+
+# Load dependencies
+source(concat(commonDir, "/region_motif_lib/plotting.r"))
+
+# Auxiliary function to read in tab file and prepare the data
+read_tsv <- function(file) {
+	data = read.table(file, sep="\t", stringsAsFactors=FALSE)
+	names(data)[names(data) == "V1"] = "motif"
+	names(data)[names(data) == "V2"] = "counts"
+	return(data)
+}
+
+startTime = Sys.time()
+cat("Running ... Started at:", format(startTime, "%a %b %d %X %Y"), "...\n")
+
+# Loading motif position weight matrix (pwm) file and input tab file
+#cat("Loading and reading input region motif count files...\n")
+load(pwmFile) # pwms data structure
+if (dbCode == "c") { # Remaining implementation of dbCode "c" combined 
+	temp = pwms
+	load(pwmFile2)
+	pwms = append(temp, pwms)
+}
+region1DF = read_tsv(inTab1)
+region2DF = read_tsv(inTab2)
+region1Counts = region1DF$counts
+region2Counts = region2DF$counts
+names(region1Counts) = region1DF$motif
+names(region2Counts) = region2DF$motif
+
+# Processing count vectors to account for missing 0 count motifs, then sorting
+#cat("Performing 0 count correction and sorting...\n")
+allNames = union(names(region1Counts), names(region2Counts))
+region1Diff = setdiff(allNames, names(region1Counts))
+region2Diff = setdiff(allNames, names(region2Counts))
+addCounts1 = rep(0, length(region1Diff))
+addCounts2 = rep(0, length(region2Diff))
+names(addCounts1) = region1Diff
+names(addCounts2) = region2Diff
+newCounts1 = append(region1Counts, addCounts1)
+newCounts2 = append(region2Counts, addCounts2)
+region1Counts = newCounts1[sort.int(names(newCounts1), index.return=TRUE)$ix]
+region2Counts = newCounts2[sort.int(names(newCounts2), index.return=TRUE)$ix]
+
+# Generate gc content matrix
+gc = sapply(pwms, function(i) mean(i[2:3,3:18]))
+
+# Apply poisson test, calculate p and q values, and filter significant results
+#cat("Applying poisson test...\n")
+rValue = sum(region2Counts) / sum(region1Counts)
+pValue = sapply(seq(along=region1Counts), function(i) {
+	poisson.test(c(region1Counts[i], region2Counts[i]), r=1/rValue)$p.value
+})
+qValue = p.adjust(pValue, "fdr")
+indices = which(qValue<0.1 & abs(log2(region1Counts/region2Counts/rValue))>log2(1.5))
+
+# Setting up output diagnostic plots, 4 in 1 png image
+png(plotsPng, width=800, height=800)
+xlab = "region1_count"
+ylab = "region2_count"
+lim = c(0.5, 5000)
+layout(matrix(1:4, ncol=2))
+par(mar=c(5, 5, 5, 1))
+
+# Plot all motif counts along the linear correlation coefficient
+plot.scatter(region1Counts+0.5, region2Counts+0.5, log="xy", xlab=xlab, ylab=ylab,
+						 cex.lab=2.2, cex.axis=1.8, xlim=lim, ylim=lim*rValue)
+abline(0, rValue, untf=T)
+abline(0, rValue*2, untf=T, lty=2)
+abline(0, rValue/2, untf=T, lty=2)
+	
+# Plot enriched and depleted motifs in red, housed in second plot    
+plot.scatter(region1Counts+0.5, region2Counts+0.5, log="xy", xlab=xlab, ylab=ylab,
+						 cex.lab=2.2, cex.axis=1.8, xlim=lim, ylim=lim*rValue)
+points(region1Counts[indices]+0.5, region2Counts[indices]+0.5, col="red")
+abline(0, rValue, untf=T)
+abline(0, rValue*2, untf=T, lty=2)
+abline(0, rValue/2, untf=T, lty=2)
+
+# Apply and plot gc correction and loess curve
+#cat("Applying gc correction, rerunning poisson test...\n")
+ind = which(region1Counts>5)
+gc = gc[names(region2Counts)] # Reorder the indices of pwms to match input data
+lo = plot.scatter(gc,log2(region2Counts/region1Counts),draw.loess=T, 
+								xlab="gc content of motif",ylab=paste("log2(",ylab,"/",xlab,")"),
+								cex.lab=2.2,cex.axis=1.8,ind=ind) # This function is in plotting.r
+gcCorrection = 2^approx(lo$loess,xout=gc,rule=2)$y
+save(gc, file="gc.RData")
+
+# Recalculate p and q values, and filter for significant entries
+pValueGC = sapply(seq(along=region1Counts),function(i) {
+	poisson.test(c(region1Counts[i],region2Counts[i]),r=1/gcCorrection[i])$p.value
+})
+qValueGC=p.adjust(pValueGC,"fdr")
+indicesGC = which(qValueGC<0.1 & abs(log2(region1Counts/region2Counts*gcCorrection))>log2(1.5))
+
+# Plot gc corrected motif counts 
+plot.scatter(region1Counts+0.5, (region2Counts+0.5)/gcCorrection, log="xy", 
+						 xlab=xlab, ylab=paste(ylab,"(normalized)"), cex.lab=2.2, cex.axis=1.8,
+						 xlim=lim, ylim=lim)
+points(region1Counts[indicesGC]+0.5, 
+			 (region2Counts[indicesGC]+0.5)/gcCorrection[indicesGC], col="red")
+abline(0,1)
+abline(0,1*2,untf=T,lty=2)
+abline(0,1/2,untf=T,lty=2)
+
+# Trim results, compile statistics and output to file
+# Only does so if significant results are computed
+if(length(indicesGC) > 0) {
+	# Calculate expected counts and enrichment ratios
+	#cat("Calculating statistics...\n")
+	nullExpect = region1Counts * gcCorrection
+	enrichment = region2Counts / nullExpect
+
+	# Reorder selected indices in ascending pvalue
+	#cat("Reordering by ascending pvalue...\n")
+	indicesReorder = indicesGC[order(pValueGC[indicesGC])]
+
+	# Combine data into one data frame and output to two files
+	#cat("Splitting and outputting data...\n")
+	outDF = data.frame(motif=names(pValueGC), p=as.numeric(pValueGC), q=qValueGC, 
+										 stringsAsFactors=F, region_1_count=region1Counts, 
+										 null_expectation=round(nullExpect,2), region_2_count=region2Counts,
+										 enrichment=enrichment)[indicesReorder,]
+	names(outDF)[which(names(outDF)=="region_1_count")]=xlab
+	names(outDF)[which(names(outDF)=="region_2_count")]=ylab
+	indicesEnrich = which(outDF$enrichment>1)
+	indicesDeplete = which(outDF$enrichment<1)
+	outDF$enrichment = ifelse(outDF$enrichment>1,
+														round(outDF$enrichment,3),
+														paste("1/",round(1/outDF$enrichment,3)))
+	write.table(outDF[indicesEnrich,], file=enrichTab, quote=FALSE, 
+							sep="\t", append=FALSE, row.names=FALSE, col.names=TRUE)
+	write.table(outDF[indicesDeplete,], file=depleteTab, quote=FALSE, 
+							sep="\t", append=FALSE, row.names=FALSE, col.names=TRUE)
+}
+
+# Catch display messages and output timing information 
+catchMessage = dev.off()
+cat("Done. Job started at:", format(startTime, "%a %b %d %X %Y."),
+		"Job ended at:", format(Sys.time(), "%a %b %d %X %Y."), "\n")