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gatk-3.8
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5324 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-02-26 15:35:49 +00:00
parent b089d35b21
commit aaecc271e8
2 changed files with 4 additions and 6 deletions
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2
R/GATKRunReport.R
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@ -181,7 +181,7 @@ generateOneReport <- function(d, header, includeByWeek = T) {
#reportCountingPlot(d$working.directory, head("Working directory")) #reportCountingPlot(d$working.directory, head("Working directory"))
} }
RUNME = F RUNME = T
if ( RUNME ) { if ( RUNME ) {
lastWeek = levels(cut(d$end.time, "weeks"))[-1] lastWeek = levels(cut(d$end.time, "weeks"))[-1]
generateOneReport(d, "Overall") generateOneReport(d, "Overall")

8
R/plot_GATK_performance_log.R
View File

@ -1,6 +1,6 @@
args = commandArgs(TRUE); args = commandArgs(TRUE);
RUNME = T RUNME = F
onCMDLine = ! is.na(args[1]) onCMDLine = ! is.na(args[1])
DATA_FILE = args[1] DATA_FILE = args[1]
DESCRIPTION = args[2] DESCRIPTION = args[2]
@ -29,7 +29,6 @@ everyNth <- function(x, n) {
x[keep,] x[keep,]
} }
l = length(d$units.processed) l = length(d$units.processed)
d$units.processed.margin = vec.margin(d$units.processed) d$units.processed.margin = vec.margin(d$units.processed)
#prev = 0 #prev = 0
@ -53,8 +52,8 @@ generateOneReport <- function(d) {
if ( onCMDLine ) png(paste(DATA_FILE, ".marginal.png", sep=""), width=1080, height=1080) if ( onCMDLine ) png(paste(DATA_FILE, ".marginal.png", sep=""), width=1080, height=1080)
running_median_window = 101 running_median_window = 101
rm = runmed(d$units.processed.margin, running_median_window) rm = runmed(d$units.processed.margin, running_median_window)
POINT_COL = "#0000AA33" POINT_COL = "#0000AA99"
plot(dpoints$elapsed.time, dpoints$units.processed.margin, main=DESCRIPTION, xlab="Elapsed time (sec)", ylab="Units processed in last timing interval", type="p", cex = 0.5, col=POINT_COL) plot(dpoints$elapsed.time, dpoints$units.processed.margin, main=DESCRIPTION, xlab="Elapsed time (sec)", ylab="Units processed in last timing interval", type="p", cex = 0.75, col=POINT_COL)
lines(d$elapsed.time, rm, lwd=3, col="red") lines(d$elapsed.time, rm, lwd=3, col="red")
legend("topleft", c("Observations", "101-elt running median"), fill=c(POINT_COL, "red")) legend("topleft", c("Observations", "101-elt running median"), fill=c(POINT_COL, "red"))
if ( onCMDLine ) dev.off() if ( onCMDLine ) dev.off()
@ -66,4 +65,3 @@ if ( RUNME ) {