Can run R scripts on the command line

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3750 348d0f76-0448-11de-a6fe-93d51630548a

R/plot_Annotations_BinnedTruthMetrics.R

@@ -1,4 +1,4 @@
-#!/broad/tools/apps/R-2.6.0/bin/Rscript
+#!/bin/env Rscript
 
 args <- commandArgs(TRUE)
 verbose = TRUE
@@ -187,4 +187,4 @@ pdf(outfile, height=7, width=7)
 par(cex=1.1)
 plot(all$value,all$numVariants,xlab=annotationName,log="x",ylab="Num variants in bin",type="h",xaxt="n",ps=14,lwd=4);
 axis(1,axTicks(1), format(axTicks(1), scientific=F))
-dev.off()
+dev.off()

R/plot_ClusterReport.R

@@ -1,4 +1,4 @@
-#!/broad/tools/apps/R-2.6.0/bin/Rscript
+#!/bin/env Rscript
 
 args <- commandArgs(TRUE)
 verbose = TRUE
@@ -16,4 +16,4 @@ maxP = max(data$knownDist, data$novelDist)
 plot(data$annotationValue, data$knownDist, ylim=c(0,maxP),type="b",col="orange",lwd=2,xlab=annotationName,ylab="fraction of SNPs")
 points(data$annotationValue, data$novelDist, type="b",col="blue",lwd=2)
 legend('topright', c('knowns','novels'),lwd=2,col=c("orange","blue"))
-dev.off()
+dev.off()

R/plot_OptimizationCurve.R

@@ -1,4 +1,4 @@
-#!/broad/tools/apps/R-2.6.0/bin/Rscript
+#!/bin/env Rscript
 
 args <- commandArgs(TRUE)
 verbose = TRUE

R/plot_residualError_OtherCovariate.R

@@ -1,4 +1,4 @@
-#!/broad/tools/apps/R-2.6.0/bin/Rscript
+#!/bin/env Rscript
 
 args <- commandArgs(TRUE)
 verbose = TRUE
@@ -105,4 +105,4 @@ if( is.numeric(c$Covariate) ) {
 	}
 	axis(2,axTicks(2), format(axTicks(2), scientific=F))
 }
-dev.off()
+dev.off()

R/plot_residualError_QualityScoreCovariate.R

@@ -1,4 +1,4 @@
-#!/broad/tools/apps/R-2.6.0/bin/Rscript
+#!/bin/env Rscript
 
 args <- commandArgs(TRUE)
 

R/plot_variantROCCurve.R

@@ -1,4 +1,4 @@
-#!/broad/tools/apps/R-2.6.0/bin/Rscript
+#!/bin/env Rscript
 
 args <- commandArgs(TRUE)
 verbose = TRUE
@@ -18,4 +18,4 @@ for(iii in 1:numCurves) {
 	points(data[,iii*3],data[,(iii-1)*3+2],lwd=3,type="l",col=iii)
 }
 legend("bottomright", names(data)[(0:(numCurves-1))*3+1], col=1:numCurves,lwd=3)
-dev.off()
+dev.off()

R/plotting_library.R

@@ -1,4 +1,4 @@
-#!/broad/tools/apps/R-2.6.0/bin/Rscript
+#!/bin/env Rscript
 
 args <- commandArgs(TRUE)
 fileToRead <- args[1]
@@ -94,4 +94,4 @@ PlotHeatmap <- function(inFile,args) {
 
 PlotHeatmap(fileToRead,functionSpecificArgs)
 
-}
+}

R/titvFPEst.R

@@ -41,3 +41,7 @@ cumhist <- function(d) {
     h <- hist(d)
     #plot(h$mids, cumsum(h$count), type="b", col="orange", lwd=2)
 }
+
+revcumsum <- function(x) {
+   return(rev(cumsum(rev(x))))
+}