[Patchwork-commits] r215 - .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 Sep 29 10:35:22 CEST 2014
Author: sebastian_d
Date: 2014-09-29 10:35:21 +0200 (Mon, 29 Sep 2014)
New Revision: 215
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:
TAPS buggfix
Modified: .git/index
===================================================================
(Binary files differ)
Modified: .git/logs/HEAD
===================================================================
--- .git/logs/HEAD 2014-09-04 12:07:32 UTC (rev 214)
+++ .git/logs/HEAD 2014-09-29 08:35:21 UTC (rev 215)
@@ -97,3 +97,4 @@
90e8ee38aac7ead43935bd7034bd4f11f91d19c4 6734fab24795a8c823c6a97e0131fcfe5a235107 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1401270131 +0200 pull: Fast-forward
6734fab24795a8c823c6a97e0131fcfe5a235107 cefeee2662b45c7daf3b8916b967173f68b6ddcf Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1409562736 +0200 pull: Fast-forward
cefeee2662b45c7daf3b8916b967173f68b6ddcf e8cc7370da527f1d46bb81720f663ceed281e07d Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1409832387 +0200 pull: Fast-forward
+e8cc7370da527f1d46bb81720f663ceed281e07d b5798bb1874d9dc8e50fa5083961a8836d79f76c Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1411979666 +0200 pull: Fast-forward
Modified: .git/logs/refs/heads/master
===================================================================
--- .git/logs/refs/heads/master 2014-09-04 12:07:32 UTC (rev 214)
+++ .git/logs/refs/heads/master 2014-09-29 08:35:21 UTC (rev 215)
@@ -97,3 +97,4 @@
90e8ee38aac7ead43935bd7034bd4f11f91d19c4 6734fab24795a8c823c6a97e0131fcfe5a235107 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1401270131 +0200 pull: Fast-forward
6734fab24795a8c823c6a97e0131fcfe5a235107 cefeee2662b45c7daf3b8916b967173f68b6ddcf Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1409562736 +0200 pull: Fast-forward
cefeee2662b45c7daf3b8916b967173f68b6ddcf e8cc7370da527f1d46bb81720f663ceed281e07d Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1409832387 +0200 pull: Fast-forward
+e8cc7370da527f1d46bb81720f663ceed281e07d b5798bb1874d9dc8e50fa5083961a8836d79f76c Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1411979666 +0200 pull: Fast-forward
Modified: .git/logs/refs/remotes/origin/master
===================================================================
--- .git/logs/refs/remotes/origin/master 2014-09-04 12:07:32 UTC (rev 214)
+++ .git/logs/refs/remotes/origin/master 2014-09-29 08:35:21 UTC (rev 215)
@@ -94,3 +94,4 @@
90e8ee38aac7ead43935bd7034bd4f11f91d19c4 6734fab24795a8c823c6a97e0131fcfe5a235107 Sebastian DiLorenzo <S_D at array-47-13.medsci.uu.se> 1401270130 +0200 pull: fast-forward
6734fab24795a8c823c6a97e0131fcfe5a235107 cefeee2662b45c7daf3b8916b967173f68b6ddcf Sebastian DiLorenzo <S_D at Sebastians-iMac.local> 1409562735 +0200 pull: fast-forward
cefeee2662b45c7daf3b8916b967173f68b6ddcf e8cc7370da527f1d46bb81720f663ceed281e07d Sebastian DiLorenzo <S_D at array-47-13.medsci.uu.se> 1409832387 +0200 pull: fast-forward
+e8cc7370da527f1d46bb81720f663ceed281e07d b5798bb1874d9dc8e50fa5083961a8836d79f76c Sebastian DiLorenzo <S_D at array-47-13.medsci.uu.se> 1411979666 +0200 pull: fast-forward
Modified: .git/refs/heads/master
===================================================================
--- .git/refs/heads/master 2014-09-04 12:07:32 UTC (rev 214)
+++ .git/refs/heads/master 2014-09-29 08:35:21 UTC (rev 215)
@@ -1 +1 @@
-e8cc7370da527f1d46bb81720f663ceed281e07d
+b5798bb1874d9dc8e50fa5083961a8836d79f76c
Modified: .git/refs/remotes/origin/master
===================================================================
--- .git/refs/remotes/origin/master 2014-09-04 12:07:32 UTC (rev 214)
+++ .git/refs/remotes/origin/master 2014-09-29 08:35:21 UTC (rev 215)
@@ -1 +1 @@
-e8cc7370da527f1d46bb81720f663ceed281e07d
+b5798bb1874d9dc8e50fa5083961a8836d79f76c
Modified: pkg/TAPS/R/TAPS.r
===================================================================
--- pkg/TAPS/R/TAPS.r 2014-09-04 12:07:32 UTC (rev 214)
+++ pkg/TAPS/R/TAPS.r 2014-09-29 08:35:21 UTC (rev 215)
@@ -2005,12 +2005,10 @@
if(c == 23)
{
mtext("X", side = 3, line = -1, adj = 0.8, cex = 1)
- }
- else if(c == 24)
+ } else if(c == 24)
{
mtext("Y", side = 3, line = -1, adj = 0.8, cex = 1)
- }
- else
+ } else
{
mtext(c, side = 3, line = -1, adj = 0.8, cex = 1)
}
@@ -2062,6 +2060,7 @@
for (c in 1:24)
{
this <- chroms[chroms$c==c,]
+ if(nrow(this) == 0) next
ix <- chr==as.character(this$chr)
mix <- mchr==as.character(this$chr) #& mval>=(-2)
six <- schr==as.character(this$chr)
@@ -2077,13 +2076,12 @@
{
ymax = 1
}
- seqminmax=seq(ymin,ymax,by=0.5)
+ seqminmax=seq(-2,2,by=0.5)
if(c>1)
{
prelength=prelength+chroms$length[chroms$c==(c-1)]
- }
- else
+ } else
{
prelength=0
}
@@ -2210,7 +2208,7 @@
par(oma = c(0,0,0,0))
par(mgp =c(1,0.5,0))
- #Remove chrY,M,XY
+ #Remove M,XY
sval[mchr=='chrXY'|mchr=='chrM']=NA
#Index to avoid spos/sval values that are all the way at 0 or 1.
@@ -2310,6 +2308,7 @@
#Select the chromosome
this <- chroms[chroms$c==c,]
+ if(nrow(this) == 0) next
#Initialize jpeg
jpeg(paste(name,'_karyotype.',this$chr,'.jpg',sep=''),width=11.7,height=8.3,units="in",res=300)
@@ -2446,7 +2445,7 @@
#{
# ymax = 1
#}
- seqminmax=seq(ymin,ymax,by=0.5)
+ seqminmax=seq(-2,2,by=0.5)
#Create an index of colors relating to the positions and lengths on this chromosome
col=rep('#000000',sum(ix))
@@ -2463,7 +2462,7 @@
axes=F,
col = '#00000005',
xlim = c(0,this$length),
- ylim = c(ymin,ymax))
+ ylim = c(-2,2))
#Add colored segments based on the log-ratio data
segments(x0=start[ix],x1=end[ix],
@@ -2481,8 +2480,8 @@
#labels=c("-1","-.5","0",".5","1","1.5"),
cex.axis=0.6,las=1)
# 1: below
- axis(side=1,tck=0.926,col='#80808040',at=seq(5e6,this$length,by=5e6),
- labels=FALSE,cex.axis=0.6,pos=ymin)
+ # axis(side=1,tck=1.041,col='#80808040',at=seq(5e6,this$length,by=5e6),labels=FALSE,cex.axis=0.6,pos=ymin)
+ segments(x0=seq(5e6,this$length,by=5e6),x1=seq(5e6,this$length,by=5e6),y0=-2,y1=2,col='#80808040')
#axis(side=1,tck=0,pos=ymin,
# cex.axis=0.6,las=1)
# 3: top
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