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More plots in report 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4225 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-09-08 02:56:51 +00:00
parent c524a9ec83
commit 594fb4a547
1 changed files with 20 additions and 7 deletions
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27
R/GATKRunReport.R
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@ -1,6 +1,7 @@
args = commandArgs(TRUE); args = commandArgs(TRUE);
onCMDLine = ! is.na(args[1]) onCMDLine = ! is.na(args[1])
if (! is.na(args[3]) ) { name = args[3] } else { name = "" }
if ( onCMDLine ) { if ( onCMDLine ) {
print(paste("Reading data from", args[1])) print(paste("Reading data from", args[1]))
@ -27,7 +28,7 @@ myTable <- function(x, y, reqRowNonZero = F) {
table <- prop.table(table(x, y), 2) table <- prop.table(table(x, y), 2)
ncols = dim(table)[2] ncols = dim(table)[2]
print(table) #print(table)
if ( reqRowNonZero ) if ( reqRowNonZero )
table = table[addmargins(table)[1:dim(table)[1],ncols] > 0,] table = table[addmargins(table)[1:dim(table)[1],ncols] > 0,]
@ -40,7 +41,9 @@ plotTable <- function(table, name) {
ncols = dim(table)[2] ncols = dim(table)[2]
nrows = dim(table)[1] nrows = dim(table)[1]
cols = rainbow(nrows) cols = rainbow(nrows)
plot( as.numeric(table[1,]), type="n", ylim=c(0,1), main = name, ylab="Frequency", xlab="Date", xaxt="n") tableMin = min(apply(table, 2, min))
tableMax = max(apply(table, 2, max))
plot( as.numeric(apply(table, 2, sum)), ylim=c(tableMin, tableMax), type="n", main = name, ylab="Frequency", xlab="Date", xaxt="n")
axis(1, 1:ncols, labels=colnames(table)) axis(1, 1:ncols, labels=colnames(table))
for ( i in 1:nrows ) for ( i in 1:nrows )
points(table[i,], type="b", col=cols[i]) points(table[i,], type="b", col=cols[i])
@ -52,6 +55,12 @@ RUNNING_GATK_RUNTIME <- 60 * 5 # 5 minutes => bad failure
if ( onCMDLine ) pdf(args[2]) if ( onCMDLine ) pdf(args[2])
successfulRuns <- function(d) {
x <- rep("Successful", length(d$exception.msg))
x[! is.na(d$exception.msg)] <- "Failed"
return(x)
}
generateOneReport <- function(d, header, includeByWeek = T) { generateOneReport <- function(d, header, includeByWeek = T) {
head <- function(s) { head <- function(s) {
return(paste("Section:", header, ":", s)) return(paste("Section:", header, ":", s))
@ -62,17 +71,21 @@ generateOneReport <- function(d, header, includeByWeek = T) {
par("mar", c(5, 4, 4, 2)) par("mar", c(5, 4, 4, 2))
frame() frame()
title(paste("Section:", header), cex=2) title(paste("GATK run report", name, "for", Sys.Date(), "\nwith", dim(d)[1], "run repository records"), cex=2)
reportCountingPlot(d$walker.name, head("Walker invocations"))
reportCountingPlot(d$svn.version, head("GATK SVN version"))
# cuts by time # cuts by time
plotTable(myTable(d$svn.version, d$start.time), head("SVN version by day"))
if ( includeByWeek ) { if ( includeByWeek ) {
plotTable(table(rep("GATK Invocations", length(d$start.time)), cut(d$start.time, "weeks")), head("GATK Invocations by week"))
plotTable(myTable(successfulRuns(d), cut(d$start.time, "weeks")), head("Successful and failing GATK invocations per week"))
plotTable(myTable(d$svn.version, cut(d$start.time, "weeks")), head("SVN version by week")) plotTable(myTable(d$svn.version, cut(d$start.time, "weeks")), head("SVN version by week"))
plotTable(myTable(excepted$walker.name, cut(excepted$start.time, "weeks"), reqRowNonZero = T), head("Walkers with exceptions by week")) plotTable(myTable(excepted$walker.name, cut(excepted$start.time, "weeks"), reqRowNonZero = T), head("Walkers with exceptions by week"))
} }
plotTable(table(rep("GATK Invocations", length(d$start.time)), d$start.time), head("GATK Invocations by day"))
plotTable(myTable(d$svn.version, d$start.time), head("SVN version by day"))
reportCountingPlot(d$walker.name, head("Walker invocations"))
reportCountingPlot(d$svn.version, head("GATK SVN version"))
# reportCountingPlot(d$java.tmp.directory, head("Java tmp directory")) # reportCountingPlot(d$java.tmp.directory, head("Java tmp directory"))
reportCountingPlot(d$working.directory, head("Working directory")) reportCountingPlot(d$working.directory, head("Working directory"))