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HG19_reference_TR_intervals_with_more_than_one_TR.pdf (14644KB, MIME type: application/pdf)

d<-read.table("hg19.2.7.7.full.more.than.one.TR.in.interval.stats.txt", sep="\t", header=TRUE) 
pdf(file="HG19 reference TR intervals with more than one TR.pdf", width = 10, height = 8, pointsize = 14, bg = "white")
hist(d$numTRs,breaks=c(1:max(d$numTRs)),xlim=c(0,max(d$numTRs)),ylim=NULL, main="TR intervals with more than one TR\nDistribution of Number of TRs", xlab = "Number of TRs", ylab = "Count ")
hist(d$lowestAvgScore,breaks=seq(0,2,0.01),xlim=c(0,2),ylim=NULL, main="TR intervals with more than one TR\nDistribution of Lowest Average Score", xlab = "Lowest Average Score", ylab = "Count ")
hist(d$highestAvgScore,breaks=seq(0,2,0.01),xlim=c(0,2),ylim=NULL, main="TR intervals with more than one TR\nDistribution of Highest Average Score", xlab = "Highest Average Score", ylab = "Count ")
hist(d$highestAvgScore-d$lowestAvgScore,breaks=seq(0,2,0.01),xlim=c(0,2),ylim=NULL, main="TR intervals with more than one TR\nDistribution of Difference Between\nHighest Average Score and Lowest Average Score", xlab = "Highest Average Score - Lowest Average Score", ylab = "Count ")
plot(d$lowestAvgScore, d$highestAvgScore,col="black",
main = "TR intervals with more than one TR\nScatterplot of Highest Average Score vs Lowest Average Score",xlab = "Lowest Average Score", ylab = "Highest Average Score",font.lab=2,cex.lab=1.2,las=1,pch=".")
hist(d$LongestArray,breaks=seq(0,250000,10),main="TR intervals with more than one TR\nDistribution of Longest Array Length", xlab = "Longest Array Length", ylab = "Count ",xlim=c(0,1000),ylim=NULL)
hist(d$LongestArray-d$shortestArray,breaks=seq(0,max(d$LongestArray)),xlim=c(0,100),ylim=NULL, main="TR intervals with more than one TR\nDistribution of Difference Between\nLongest Array Length and Shortest Array Length", xlab = "Longest Array Length - Shortest Array Length", ylab = "Count ")
plot(d$shortestArray, d$LongestArray,col="black",
main = "TR intervals with more than one TR\nScatterplot of Longest Array Length vs Shortest Array Length",xlab = "Shortest Array Length", ylab = "Longest Array Length",font.lab=2,cex.lab=1.2,las=1,pch=".",xlim=c(0,1000), ylim=c(0,50000))
plot(d$LongestArray,d$LongestArray-d$shortestArray, col="black",
main = "TR intervals with more than one TR\nScatterplot of Longest Array Length vs Difference in Array Lengths",xlab = "Longest Array Length", ylab = "Difference in Array Lengths",font.lab=2,cex.lab=1.2,las=1,pch=".",xlim=c(0,400), ylim=c(0,100))
hist(d$intervalLength-d$LongestArray,breaks=seq(0,max(d$intervalLength-d$LongestArray)),xlim=c(0,80),ylim=NULL, main="TR intervals with more than one TR\nDistribution of Difference Between\nInterval Length and Longest Array Length", xlab = "Interval Length - Longest Array Length", ylab = "Count")
plot(d$intervalLength,d$LongestArray-d$shortestArray, col="black",
main = "TR intervals with more than one TR\nScatterplot of Interval Length vs Difference in Array Lengths",xlab = "Interval Length", ylab = "Difference in Array Lengths",font.lab=2,cex.lab=1.2,las=1,pch=".",xlim=c(0,400), ylim=c(0,100))
hist((d$LongestArray-d$shortestArray)/d$LongestArray,breaks=seq(0,1,0.1), main="TR intervals with more than one TR\nDistribution of Difference Between Array Lengths\nRelative to Longest Array Length", xlab = "Difference as Percent of Longest Array Length", ylab = "Count")
dev.off()

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