[Patchwork-commits] r219 - .git .git/logs .git/logs/refs/heads .git/logs/refs/remotes/origin .git/refs/heads .git/refs/remotes/origin pkg/TAPS/R
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Nov 23 10:54:36 CET 2015
Author: sebastian_d
Date: 2015-11-23 10:54:36 +0100 (Mon, 23 Nov 2015)
New Revision: 219
Modified:
.git/index
.git/logs/HEAD
.git/logs/refs/heads/master
.git/logs/refs/remotes/origin/master
.git/refs/heads/master
.git/refs/remotes/origin/master
pkg/TAPS/R/TAPS.r
Log:
Bjorn and Markus buggfixing
Modified: .git/index
===================================================================
(Binary files differ)
Modified: .git/logs/HEAD
===================================================================
--- .git/logs/HEAD 2015-10-19 11:55:17 UTC (rev 218)
+++ .git/logs/HEAD 2015-11-23 09:54:36 UTC (rev 219)
@@ -101,3 +101,4 @@
b5798bb1874d9dc8e50fa5083961a8836d79f76c 52402622419759bc3642b6f49dd0f4abd2003d38 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1434615906 +0200 pull: Fast-forward
52402622419759bc3642b6f49dd0f4abd2003d38 4bbde19cc8582ba3fb6caf01b1b01165c5db15d6 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1435303966 +0200 pull: Fast-forward
4bbde19cc8582ba3fb6caf01b1b01165c5db15d6 0a1de5c432ad323bbac1093425e9a939f351b50b Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1445255649 +0200 pull: Fast-forward
+0a1de5c432ad323bbac1093425e9a939f351b50b 0b2b81a68a67ce90b6f3c8d65b3cbab6636348b7 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1448272403 +0100 pull: Fast-forward
Modified: .git/logs/refs/heads/master
===================================================================
--- .git/logs/refs/heads/master 2015-10-19 11:55:17 UTC (rev 218)
+++ .git/logs/refs/heads/master 2015-11-23 09:54:36 UTC (rev 219)
@@ -101,3 +101,4 @@
b5798bb1874d9dc8e50fa5083961a8836d79f76c 52402622419759bc3642b6f49dd0f4abd2003d38 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1434615906 +0200 pull: Fast-forward
52402622419759bc3642b6f49dd0f4abd2003d38 4bbde19cc8582ba3fb6caf01b1b01165c5db15d6 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1435303966 +0200 pull: Fast-forward
4bbde19cc8582ba3fb6caf01b1b01165c5db15d6 0a1de5c432ad323bbac1093425e9a939f351b50b Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1445255649 +0200 pull: Fast-forward
+0a1de5c432ad323bbac1093425e9a939f351b50b 0b2b81a68a67ce90b6f3c8d65b3cbab6636348b7 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1448272403 +0100 pull: Fast-forward
Modified: .git/logs/refs/remotes/origin/master
===================================================================
--- .git/logs/refs/remotes/origin/master 2015-10-19 11:55:17 UTC (rev 218)
+++ .git/logs/refs/remotes/origin/master 2015-11-23 09:54:36 UTC (rev 219)
@@ -98,3 +98,4 @@
b5798bb1874d9dc8e50fa5083961a8836d79f76c 52402622419759bc3642b6f49dd0f4abd2003d38 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1434615905 +0200 pull: fast-forward
52402622419759bc3642b6f49dd0f4abd2003d38 4bbde19cc8582ba3fb6caf01b1b01165c5db15d6 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1435303966 +0200 pull: fast-forward
4bbde19cc8582ba3fb6caf01b1b01165c5db15d6 0a1de5c432ad323bbac1093425e9a939f351b50b Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1445255649 +0200 pull: fast-forward
+0a1de5c432ad323bbac1093425e9a939f351b50b 0b2b81a68a67ce90b6f3c8d65b3cbab6636348b7 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1448272403 +0100 pull: fast-forward
Modified: .git/refs/heads/master
===================================================================
--- .git/refs/heads/master 2015-10-19 11:55:17 UTC (rev 218)
+++ .git/refs/heads/master 2015-11-23 09:54:36 UTC (rev 219)
@@ -1 +1 @@
-0a1de5c432ad323bbac1093425e9a939f351b50b
+0b2b81a68a67ce90b6f3c8d65b3cbab6636348b7
Modified: .git/refs/remotes/origin/master
===================================================================
--- .git/refs/remotes/origin/master 2015-10-19 11:55:17 UTC (rev 218)
+++ .git/refs/remotes/origin/master 2015-11-23 09:54:36 UTC (rev 219)
@@ -1 +1 @@
-0a1de5c432ad323bbac1093425e9a939f351b50b
+0b2b81a68a67ce90b6f3c8d65b3cbab6636348b7
Modified: pkg/TAPS/R/TAPS.r
===================================================================
--- pkg/TAPS/R/TAPS.r 2015-10-19 11:55:17 UTC (rev 218)
+++ pkg/TAPS/R/TAPS.r 2015-11-23 09:54:36 UTC (rev 219)
@@ -221,7 +221,6 @@
}
# cat('..plotting.\n')
- #browser()
OverviewPlot(regs$chr,regs$start,regs$end,regs$logs,regs$scores,hg18=hg18,
as.character(Log2$Chromosome),Log2$Start,Log2$Value,as.character(alf$Chromosome),alf$Start,alf$Value,
name=name,MAPD=sampleData$MAPD[i],MHOF=sampleData$MHOF[i])
@@ -519,8 +518,8 @@
try(xx <- kmeans(t1, 2),silent=T) ## Attempt k-means (Hartigan-Wong: has proven very stable)
if (!is.null(xx)) if (min(xx$size) > 0.05*max(xx$size)) { ## On some occations data quality is poor, requiring 5%+ heterozygous SNPs avoids most such cases.
xx=xx$centers
- } else xx=NA
- } else xx=NA
+ } else xx=median(t1,na.rm = T)
+ } else xx=median(t1,na.rm = T)
} else xx=NA
#try (if (is.na(xx)) xx=0:1, silent=T)
#try (if (length(xx)==0) xx=0:1, silent=T)
@@ -2218,7 +2217,7 @@
#Add axis to the left & right of signal
axis(side=2,tck=-0.025,at=seqminmax,cex.axis=0.6,pos=0,las=1)
- axis(side=4,tck=-0.025,at=seqminmax,cex.axis=0.6,pos=max(mpos),las=1)
+ axis(side=4,tck=-0.025,at=seqminmax,cex.axis=0.6,pos=sum(chroms$length),las=1)
mtext("Log-ratio",side=2,line=0)
#Add grey segments
@@ -2249,7 +2248,7 @@
#Add a bar between chromosomes to distinguish them
segments(
- x0=c(chroms$before,sum(chroms$length),max(mpos)),x1=c(chroms$before,sum(chroms$length),max(mpos)),
+ x0=c(chroms$before,sum(chroms$length)),x1=c(chroms$before,sum(chroms$length)),
y0=-100,y1=100,
col='#000000',
lwd=1)
@@ -2327,13 +2326,13 @@
#Add axis to the left,right and below of AI. The below axis is the chromosome numbers 1-24.
axis(side=2,tck=-0.04,at=seq(from=0,to=1,by=0.2),cex.axis=0.6,pos=0,las=1)
axis(side=1,at=pre,pos=0,labels=c(seq(from=1,to=22),"X",'Y'),cex.axis=0.55,lty=0)#,tck=0,col.ticks='#00000000')
- axis(side=4,tck=-0.04,at=seq(from=0,to=1,by=0.2),cex.axis=0.6,pos=max(mpos),las=1) #
+ axis(side=4,tck=-0.04,at=seq(from=0,to=1,by=0.2),cex.axis=0.6,pos=sum(chroms$length),las=1) #
mtext("Allele frequency",side=2,line=0)
mtext("Chromosomes",side=1,line=1.5,adj=0.4)
#Add a bar between chromosomes to distinguish them
segments(
- x0=c(chroms$before,sum(chroms$length),max(mpos)),x1=c(chroms$before,sum(chroms$length),max(mpos)),
+ x0=c(chroms$before,sum(chroms$length)),x1=c(chroms$before,sum(chroms$length)),
y0=0,y1=100,
col='#000000',
lwd=1)
@@ -2403,6 +2402,8 @@
#Select the chromosome
this <- chroms[chroms$c==c,]
+ #Skip current chromosome if it doesn't exist.
+ if(!any(as.character(this$chr) == chr)) next()
if(nrow(this) == 0) next
#Initialize jpeg
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