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Bugfix for singleton runs. Now with histograms where possible

This commit is contained in:
Mark DePristo 2011-09-06 16:54:01 -04:00
parent 388d377677
commit 9559115ad5
1 changed files with 18 additions and 5 deletions
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23
public/R/queueJobReport.R
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@ -12,7 +12,9 @@ if ( onCMDLine ) {
inputFileName = args[1] inputFileName = args[1]
outputPDF = args[2] outputPDF = args[2]
} else { } else {
inputFileName = "~/Desktop/broadLocal/GATK/unstable/report.txt" #inputFileName = "~/Desktop/broadLocal/GATK/unstable/report.txt"
inputFileName = "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/Q-25718@node1149.jobreport.txt"
#inputFileName = "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/rodPerformanceGoals/history/report.082711.txt"
outputPDF = NA outputPDF = NA
} }
@ -113,11 +115,22 @@ plotGroup <- function(groupTable) {
textplot(as.data.frame(sum), show.rownames=F) textplot(as.data.frame(sum), show.rownames=F)
title(paste("Job summary for", name, "itemizing each iteration"), cex=3) title(paste("Job summary for", name, "itemizing each iteration"), cex=3)
# histogram of job times by groupAnnotations
if ( length(groupAnnotations) == 1 && dim(sub)[1] > 1 ) {
# todo -- how do we group by annotations?
p <- ggplot(data=sub, aes(x=runtime)) + geom_histogram()
p <- p + xlab("runtime in seconds") + ylab("No. of jobs")
p <- p + opts(title=paste("Job runtime histogram for", name))
print(p)
}
# as above, but averaging over all iterations # as above, but averaging over all iterations
groupAnnotationsNoIteration = setdiff(groupAnnotations, "iteration") groupAnnotationsNoIteration = setdiff(groupAnnotations, "iteration")
sum = cast(melt(sub, id.vars=groupAnnotationsNoIteration, measure.vars=c("runtime")), ... ~ ., fun.aggregate=c(mean, sd)) if ( dim(sub)[1] > 1 ) {
textplot(as.data.frame(sum), show.rownames=F) sum = cast(melt(sub, id.vars=groupAnnotationsNoIteration, measure.vars=c("runtime")), ... ~ ., fun.aggregate=c(mean, sd))
title(paste("Job summary for", name, "averaging over all iterations"), cex=3) textplot(as.data.frame(sum), show.rownames=F)
title(paste("Job summary for", name, "averaging over all iterations"), cex=3)
}
} }
# print out some useful basic information # print out some useful basic information
@ -146,7 +159,7 @@ plotJobsGantt(gatkReportData, T)
plotJobsGantt(gatkReportData, F) plotJobsGantt(gatkReportData, F)
plotProgressByTime(gatkReportData) plotProgressByTime(gatkReportData)
for ( group in gatkReportData ) { for ( group in gatkReportData ) {
plotGroup(group) plotGroup(group)
} }
if ( ! is.na(outputPDF) ) { if ( ! is.na(outputPDF) ) {