From 54adbd258187574c121a5fd551f96d9c724740c5 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 3 Jan 2011 13:33:35 +0000
Subject: [PATCH] Added instantaneous rate plotting routine to performance log
 plotter

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4926 348d0f76-0448-11de-a6fe-93d51630548a
---
 R/plot_GATK_performance_log.R | 27 ++++++++++++++++++++++++++-
 1 file changed, 26 insertions(+), 1 deletion(-)

diff --git a/R/plot_GATK_performance_log.R b/R/plot_GATK_performance_log.R
index d71531221..f63768b14 100644
--- a/R/plot_GATK_performance_log.R
+++ b/R/plot_GATK_performance_log.R
@@ -13,10 +13,35 @@ if ( onCMDLine ) {
 
 if ( onCMDLine ) pdf(OUTPUT_PDF)
 
+vec.margin <- function(x) {
+    l = length(x)
+    d = x[-1] - x[1:(l-1)]
+    c(x[1], d[1:(l-1)])
+}
+
+l = length(d$units.processed)
+d$units.processed.margin = vec.margin(d$units.processed)
+#prev = 0
+#for ( i in 1:l ) {
+#    cur = d$units.processed[i]
+#    d[i,]$units.processed.margin = cur - prev
+#    prev = cur
+#}
+
 generateOneReport <- function(d) {
-    qs = quantile(d$processing.speed, probs = c(0.05, 0.5, 0.95))
+    qs = quantile(d$processing.speed, probs = c(0.01, 0.5, 0.99))
+
+    # unit processing time
     plot(d$elapsed.time, d$processing.speed, main=DESCRIPTION, xlab="Elapsed time (sec)", ylab="Processing speed (seconds per 1M units)", ylim=c(qs[1], qs[3]), type="b", col="cornflowerblue", lwd=2)
     abline(h=qs[2], lty=2)
+
+    # instantaneous processing speed
+    running_median_window = 101
+    rm = runmed(d$units.processed.margin, running_median_window)
+    POINT_COL = "#0000AA33"
+    plot(d$elapsed.time, d$units.processed.margin, main=DESCRIPTION, xlab="Elapsed time (sec)", ylab="Units processed in last timing interval", type="p", cex = 0.5, col=POINT_COL)
+    lines(d$elapsed.time, rm, lwd=3, col="red")
+    legend("topleft", c("Observations", "101-elt running median"), fill=c(POINT_COL, "red"))
 }
 
 if ( RUNME ) {