[Patchwork-commits] r196 - .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 Oct 21 13:08:15 CEST 2013
Author: sebastian_d
Date: 2013-10-21 13:08:15 +0200 (Mon, 21 Oct 2013)
New Revision: 196
Modified:
.git/COMMIT_EDITMSG
.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:
buggfix in c(seq(1,22),X) part of plotting
Modified: .git/COMMIT_EDITMSG
===================================================================
--- .git/COMMIT_EDITMSG 2013-10-17 09:02:42 UTC (rev 195)
+++ .git/COMMIT_EDITMSG 2013-10-21 11:08:15 UTC (rev 196)
@@ -1 +1 @@
-Update to TAPS call homepage by markus
+small update to TAPS_plot
Modified: .git/index
===================================================================
(Binary files differ)
Modified: .git/logs/HEAD
===================================================================
--- .git/logs/HEAD 2013-10-17 09:02:42 UTC (rev 195)
+++ .git/logs/HEAD 2013-10-21 11:08:15 UTC (rev 196)
@@ -70,3 +70,4 @@
4a0e2921f140974e7c8a12fd8fddb998c0bd3171 2347ca003cf8ce861e1d4ec1dc0f5c96a0ac3071 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1380027327 +0200 commit: update to datasamples.xlsx handling for different drive modes
2347ca003cf8ce861e1d4ec1dc0f5c96a0ac3071 85d1e6948ab98a6bd2c58f5dc820740c198a5444 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1380028151 +0200 pull : Fast-forward
85d1e6948ab98a6bd2c58f5dc820740c198a5444 0044e7bf9b5beb763bd5f47e54c8b778999eede2 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1381839717 +0200 commit: Update to TAPS call homepage by markus
+0044e7bf9b5beb763bd5f47e54c8b778999eede2 64da542e6e940d1ec28e8b99c82be94c86a2e3fd Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1382000849 +0200 commit: small update to TAPS_plot
Modified: .git/logs/refs/heads/master
===================================================================
--- .git/logs/refs/heads/master 2013-10-17 09:02:42 UTC (rev 195)
+++ .git/logs/refs/heads/master 2013-10-21 11:08:15 UTC (rev 196)
@@ -70,3 +70,4 @@
4a0e2921f140974e7c8a12fd8fddb998c0bd3171 2347ca003cf8ce861e1d4ec1dc0f5c96a0ac3071 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1380027327 +0200 commit: update to datasamples.xlsx handling for different drive modes
2347ca003cf8ce861e1d4ec1dc0f5c96a0ac3071 85d1e6948ab98a6bd2c58f5dc820740c198a5444 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1380028151 +0200 pull : Fast-forward
85d1e6948ab98a6bd2c58f5dc820740c198a5444 0044e7bf9b5beb763bd5f47e54c8b778999eede2 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1381839717 +0200 commit: Update to TAPS call homepage by markus
+0044e7bf9b5beb763bd5f47e54c8b778999eede2 64da542e6e940d1ec28e8b99c82be94c86a2e3fd Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1382000849 +0200 commit: small update to TAPS_plot
Modified: .git/logs/refs/remotes/origin/master
===================================================================
--- .git/logs/refs/remotes/origin/master 2013-10-17 09:02:42 UTC (rev 195)
+++ .git/logs/refs/remotes/origin/master 2013-10-21 11:08:15 UTC (rev 196)
@@ -68,3 +68,4 @@
4a0e2921f140974e7c8a12fd8fddb998c0bd3171 2347ca003cf8ce861e1d4ec1dc0f5c96a0ac3071 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1380027338 +0200 update by push
2347ca003cf8ce861e1d4ec1dc0f5c96a0ac3071 85d1e6948ab98a6bd2c58f5dc820740c198a5444 Sebastian DiLorenzo <S_D at imv092.medsci.uu.se> 1380028151 +0200 pull : fast-forward
85d1e6948ab98a6bd2c58f5dc820740c198a5444 0044e7bf9b5beb763bd5f47e54c8b778999eede2 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1381839752 +0200 update by push
+0044e7bf9b5beb763bd5f47e54c8b778999eede2 64da542e6e940d1ec28e8b99c82be94c86a2e3fd Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1382000861 +0200 update by push
Modified: .git/refs/heads/master
===================================================================
--- .git/refs/heads/master 2013-10-17 09:02:42 UTC (rev 195)
+++ .git/refs/heads/master 2013-10-21 11:08:15 UTC (rev 196)
@@ -1 +1 @@
-0044e7bf9b5beb763bd5f47e54c8b778999eede2
+64da542e6e940d1ec28e8b99c82be94c86a2e3fd
Modified: .git/refs/remotes/origin/master
===================================================================
--- .git/refs/remotes/origin/master 2013-10-17 09:02:42 UTC (rev 195)
+++ .git/refs/remotes/origin/master 2013-10-21 11:08:15 UTC (rev 196)
@@ -1 +1 @@
-0044e7bf9b5beb763bd5f47e54c8b778999eede2
+64da542e6e940d1ec28e8b99c82be94c86a2e3fd
Modified: pkg/TAPS/R/TAPS.r
===================================================================
--- pkg/TAPS/R/TAPS.r 2013-10-17 09:02:42 UTC (rev 195)
+++ pkg/TAPS/R/TAPS.r 2013-10-21 11:08:15 UTC (rev 196)
@@ -1924,6 +1924,7 @@
par(mar = c(0, 0, 0, 0))
par(oma = c(0,0,0,0))
par(mgp =c(1,0.5,0))
+ par(lend=1)
#Calculate previous distance of whole genome so the next chromsome is added
#at the correct coordinate
@@ -2099,7 +2100,7 @@
#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"),cex.axis=0.55,lty=0)#,tck=0,col.ticks='#00000000')
+ axis(side=1,at=pre,pos=0,labels=c(seq(from=1,to=22),"X"),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) #
mtext("Allele frequency",side=2,line=0)
mtext("Chromosomes",side=1,line=1.5,adj=0.4)
@@ -2288,6 +2289,7 @@
par(mar = c(0, 0, 0, 0))
par(oma = c(0,0,0,0))
par(mgp =c(0.5,0.25,0))
+ par(lend=1)
#Select the correct chromosome and remove stuff lower than -1
mix <- mchr==as.character(this$chr) #& mval>(-1)
@@ -2644,6 +2646,7 @@
par(mar = c(0, 0, 0, 0))
par(oma = c(0,0,0,0))
par(mgp =c(0.5,0.25,0))
+ par(lend=1)
#Set colors for total and minor copynumber
col=rep('#000000',sum(ix))
@@ -2690,6 +2693,7 @@
par(mar = c(0, 0, 0, 0))
par(oma = c(0,0,0,0))
par(mgp =c(0.5,0.25,0))
+ par(lend=1)
#Select the correct chromosome and remove stuff lower than -1
mix <- mchr==as.character(this$chr) #& mval>(-1)
@@ -3071,6 +3075,7 @@
par(mar = c(0, 0, 0, 0))
par(oma = c(0,0,0,0))
par(mgp =c(0.5,0,0))
+ par(lend=1)
par(xpd=T)
#Select the correct chromosome and remove stuff lower than -1
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