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Better reporting -- figured out how to drop unused levels in subset 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4438 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-10-06 14:31:51 +00:00
parent 00491fcd2e
commit 0508dd0c31
1 changed files with 16 additions and 8 deletions
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24
R/GATKRunReport.R
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@ -14,7 +14,7 @@ reportCountingPlot <- function(values, name, moreMargin = 0, ...) {
par(las=2) # make label text perpendicular to axis par(las=2) # make label text perpendicular to axis
oldMar <- par("mar") oldMar <- par("mar")
par(mar=c(5,8+moreMargin,4,2)) # increase y-axis margin. par(mar=c(5,8+moreMargin,4,2)) # increase y-axis margin.
barplot(sort(table(factor(values))), horiz=TRUE, cex.names = 0.5, main = name, xlab="Counts", ...) barplot(sort(table(factor(values))), horiz=TRUE, cex.names = 0.5, main = name, xlab="Counts", log="x", ...)
par("mar" = oldMar) par("mar" = oldMar)
par("las" = 1) par("las" = 1)
} }
@ -25,7 +25,7 @@ reportConditionalCountingPlot <- function(values, conditions, name, moreMargin =
par(mar=c(5,8+moreMargin,4,2)) # increase y-axis margin. par(mar=c(5,8+moreMargin,4,2)) # increase y-axis margin.
t = table(values, conditions) t = table(values, conditions)
t = t[, order(colSums(t))] t = t[, order(colSums(t))]
print(list(t = t)) #print(list(t = t))
nconds = dim(t)[2] nconds = dim(t)[2]
cols = rainbow(nconds) cols = rainbow(nconds)
barplot(t, legend.text = T, horiz=TRUE, cex.names = 0.5, main = name, xlab="Counts", col=cols, cex=0.5, ...) barplot(t, legend.text = T, horiz=TRUE, cex.names = 0.5, main = name, xlab="Counts", col=cols, cex=0.5, ...)
@ -74,7 +74,9 @@ if ( onCMDLine ) pdf(args[2])
successfulRuns <- function(d) { successfulRuns <- function(d) {
x <- rep("Successful", length(d$exception.msg)) x <- rep("Successful", length(d$exception.msg))
x[! is.na(d$exception.msg)] <- "Failed" x[d$exception.msg != "NA" & d$is.user.exception == "true"] <- "Failed with UserException"
x[d$exception.msg != "NA" & d$is.user.exception == "false"] <- "Failed with StingException"
x[d$exception.msg != "NA" & (d$is.user.exception == "NA" | is.na(d$is.user.exception))] <- "Failed with StingException before UserException code"
return(x) return(x)
} }
@ -84,14 +86,20 @@ addSection <- function(name) {
title(name, cex=2) title(name, cex=2)
} }
dropit <- function (d, columns = names(d), ...)
{
d[columns] = lapply(d[columns], "[", drop=TRUE, ...)
d
}
generateOneReport <- function(d, header, includeByWeek = T) { generateOneReport <- function(d, header, includeByWeek = T) {
head <- function(s) { head <- function(s) {
return(paste("Section:", header, "\n", s)) return(paste("Section:", header, "\n", s))
} }
excepted <- subset(d, exception.msg != "NA") excepted <- dropit(subset(d, exception.msg != "NA"))
UserExceptions <- subset(excepted, is.user.exception == "true") UserExceptions <- dropit(subset(excepted, is.user.exception == "true"))
StingExceptions <- subset(excepted, is.user.exception == "false" | is.user.exception == "NA" | is.na(is.user.exception)) StingExceptions <- dropit(subset(excepted, is.user.exception == "false" | is.user.exception == "NA" | is.na(is.user.exception)))
addSection(paste("GATK run report", name, "for", Sys.Date(), "\nwith", dim(d)[1], "run repository records")) addSection(paste("GATK run report", name, "for", Sys.Date(), "\nwith", dim(d)[1], "run repository records"))
@ -119,8 +127,8 @@ generateOneReport <- function(d, header, includeByWeek = T) {
#print(list(subd = length(subd$end.time), name=subname)) #print(list(subd = length(subd$end.time), name=subname))
reportCountingPlot(subd$walker.name, head(paste("Walkers with", subname)), col=exceptionColor) reportCountingPlot(subd$walker.name, head(paste("Walkers with", subname)), col=exceptionColor)
reportCountingPlot(subd$exception.at, head(paste(subname, "locations")), 12, col=exceptionColor) reportCountingPlot(subd$exception.at, head(paste(subname, "locations")), 12, col=exceptionColor)
reportCountingPlot(subd$exception.msg, head(paste(subname, "messages")), 12, col=exceptionColor) #reportCountingPlot(subd$exception.msg, head(paste(subname, "messages")), 12, col=exceptionColor)
reportConditionalCountingPlot(subd$user.name, subd$exception.at, head("Walker invocations by user"), 12) reportConditionalCountingPlot(subd$user.name, subd$exception.at, head(paste("Walker invocations by user for", subname)), 12)
if ( includeByWeek && length(subd$end.time) > 0 ) { if ( includeByWeek && length(subd$end.time) > 0 ) {
plotTable(myTable(subd$walker.name, cut(subd$end.time, "weeks"), reqRowNonZero = T), head(paste("Walkers with", subname,"by week")), col=exceptionColor) plotTable(myTable(subd$walker.name, cut(subd$end.time, "weeks"), reqRowNonZero = T), head(paste("Walkers with", subname,"by week")), col=exceptionColor)