--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/insert_vis.R	Fri Dec 09 11:56:56 2011 -0500
@@ -0,0 +1,31 @@
+args <- commandArgs(trailingOnly = TRUE)
+libdata <- read.table(args[2], header=TRUE, sep=",", row.names="Library")
+pdf(args[4])
+boxplot (libdata[, 2:8], main="Library Sequences", ylab="Raw Count", xlab="Sequence Type", names=c(1:7))
+legend("topright", c("1:Barcoded sequences", "2:Sequences with mutagen", "3:Mappable sequences", "4:Unique, mappable sequences", "5:Sequences mapped to reference", "6:Unique sequences mapped to reference", "7:Non redundant insertions"), cex=0.7)
+
+regiondata <- read.table(args[3], header=TRUE, sep=",", row.names="Library")
+sortedregiondata <- regiondata[order(regiondata[,1], decreasing=TRUE),]
+sortedregionmatrix <- data.matrix(sortedregiondata)
+barplot(height=t(sortedregionmatrix[c(1:10,(nrow(sortedregionmatrix)-9):nrow(sortedregionmatrix)),1:2]), ylab="Raw Count", beside=TRUE, col=c("blue", "red"), main="Mappable Sequences by Library (Top 10 vs. Bottom 10)", las=2, cex.names=0.7)
+legend("topright", c("Mappable sequences", "Sequences with a mapping"), fill=c("blue", "red"), cex=0.7)
+abline(v=30.5, lty=2)
+axis(1, lab=F, at=(c(0:19)*3)+2)
+
+matrixcalcs <- cbind(sortedregionmatrix, sortedregionmatrix[,2]/sortedregionmatrix[,1])
+sortedregionmatrix <- matrixcalcs[order(matrixcalcs[,7], decreasing=TRUE), ]
+barplot(height=t(sortedregionmatrix[c(1:10,(nrow(sortedregionmatrix)-9):nrow(sortedregionmatrix)),1:2]), ylab="Raw Count", beside=TRUE, main="Successful Mappings by Library (Top 10 vs. Bottom 10)", las=2, cex.names=0.7, col=c("blue", "red"))
+legend("topright", c("Mappable sequences", "Sequences with a mapping"), fill=c("blue", "red"), cex=0.7)
+abline(v=30.5, lty=2)
+axis(1, lab=F, at=(c(0:19)*3)+2)
+
+matrixcalcs <- cbind(matrixcalcs, matrixcalcs[,6]/matrixcalcs[,1])
+sortedregionmatrix <- matrixcalcs[order(matrixcalcs[,8], decreasing=TRUE), ]
+barplot(height=t(sortedregionmatrix[c(1:10,(nrow(sortedregionmatrix)-9):nrow(sortedregionmatrix)),c(1,6)]), ylab="Raw Count", beside=TRUE, main="Redundancy of Mapped Regions by Library (Top 10 vs. Bottom 10)", las=2, cex.names=0.7, col=c("blue", "red"))
+legend("topright", c("Mappable sequences", "Distinct regions mapped"), fill=c("blue", "red"), cex=0.7)
+abline(v=30.5, lty=2)
+axis(1, lab=F, at=(c(0:19)*3)+2)
+
+dev.off()
+
+