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comparison lib/insert_vis.R @ 0:1437a2df99c0

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author jesse-erdmann
date Fri, 09 Dec 2011 11:56:56 -0500
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-1:000000000000 0:1437a2df99c0
1 args <- commandArgs(trailingOnly = TRUE)
2 libdata <- read.table(args[2], header=TRUE, sep=",", row.names="Library")
3 pdf(args[4])
4 boxplot (libdata[, 2:8], main="Library Sequences", ylab="Raw Count", xlab="Sequence Type", names=c(1:7))
5 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)
6
7 regiondata <- read.table(args[3], header=TRUE, sep=",", row.names="Library")
8 sortedregiondata <- regiondata[order(regiondata[,1], decreasing=TRUE),]
9 sortedregionmatrix <- data.matrix(sortedregiondata)
10 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)
11 legend("topright", c("Mappable sequences", "Sequences with a mapping"), fill=c("blue", "red"), cex=0.7)
12 abline(v=30.5, lty=2)
13 axis(1, lab=F, at=(c(0:19)*3)+2)
14
15 matrixcalcs <- cbind(sortedregionmatrix, sortedregionmatrix[,2]/sortedregionmatrix[,1])
16 sortedregionmatrix <- matrixcalcs[order(matrixcalcs[,7], decreasing=TRUE), ]
17 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"))
18 legend("topright", c("Mappable sequences", "Sequences with a mapping"), fill=c("blue", "red"), cex=0.7)
19 abline(v=30.5, lty=2)
20 axis(1, lab=F, at=(c(0:19)*3)+2)
21
22 matrixcalcs <- cbind(matrixcalcs, matrixcalcs[,6]/matrixcalcs[,1])
23 sortedregionmatrix <- matrixcalcs[order(matrixcalcs[,8], decreasing=TRUE), ]
24 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"))
25 legend("topright", c("Mappable sequences", "Distinct regions mapped"), fill=c("blue", "red"), cex=0.7)
26 abline(v=30.5, lty=2)
27 axis(1, lab=F, at=(c(0:19)*3)+2)
28
29 dev.off()
30
31