[Patchwork-commits] r185 - .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
Fri Jun 28 15:55:13 CEST 2013
Author: sebastian_d
Date: 2013-06-28 15:55:12 +0200 (Fri, 28 Jun 2013)
New Revision: 185
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 250kb buggfix by markus
Modified: .git/index
===================================================================
(Binary files differ)
Modified: .git/logs/HEAD
===================================================================
--- .git/logs/HEAD 2013-06-27 15:43:17 UTC (rev 184)
+++ .git/logs/HEAD 2013-06-28 13:55:12 UTC (rev 185)
@@ -57,3 +57,4 @@
c8a8af10a9f5c2312766cbebef91ffa9126061e5 5a2afd158f70d21ed8bf6a45f61a19dbbb6b79c2 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372169352 +0200 commit: deleting pysam to upgrade and test newer version
5a2afd158f70d21ed8bf6a45f61a19dbbb6b79c2 c08551d489e8bc28692c600dfffa7e7d4cb37ca5 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372256038 +0200 commit: Move pysam out of package
c08551d489e8bc28692c600dfffa7e7d4cb37ca5 b617a63c7595a2cb1b2a85e2ed73a67eccac8b32 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372346578 +0200 commit: homepage info update pysam
+b617a63c7595a2cb1b2a85e2ed73a67eccac8b32 f626f1a4b4965df8008d349712318cedf6dde9eb Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372427760 +0200 pull : Fast-forward
Modified: .git/logs/refs/heads/master
===================================================================
--- .git/logs/refs/heads/master 2013-06-27 15:43:17 UTC (rev 184)
+++ .git/logs/refs/heads/master 2013-06-28 13:55:12 UTC (rev 185)
@@ -57,3 +57,4 @@
c8a8af10a9f5c2312766cbebef91ffa9126061e5 5a2afd158f70d21ed8bf6a45f61a19dbbb6b79c2 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372169352 +0200 commit: deleting pysam to upgrade and test newer version
5a2afd158f70d21ed8bf6a45f61a19dbbb6b79c2 c08551d489e8bc28692c600dfffa7e7d4cb37ca5 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372256038 +0200 commit: Move pysam out of package
c08551d489e8bc28692c600dfffa7e7d4cb37ca5 b617a63c7595a2cb1b2a85e2ed73a67eccac8b32 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372346578 +0200 commit: homepage info update pysam
+b617a63c7595a2cb1b2a85e2ed73a67eccac8b32 f626f1a4b4965df8008d349712318cedf6dde9eb Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372427760 +0200 pull : Fast-forward
Modified: .git/logs/refs/remotes/origin/master
===================================================================
--- .git/logs/refs/remotes/origin/master 2013-06-27 15:43:17 UTC (rev 184)
+++ .git/logs/refs/remotes/origin/master 2013-06-28 13:55:12 UTC (rev 185)
@@ -55,3 +55,4 @@
c8a8af10a9f5c2312766cbebef91ffa9126061e5 5a2afd158f70d21ed8bf6a45f61a19dbbb6b79c2 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372169371 +0200 update by push
5a2afd158f70d21ed8bf6a45f61a19dbbb6b79c2 c08551d489e8bc28692c600dfffa7e7d4cb37ca5 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372256058 +0200 update by push
c08551d489e8bc28692c600dfffa7e7d4cb37ca5 b617a63c7595a2cb1b2a85e2ed73a67eccac8b32 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372346594 +0200 update by push
+b617a63c7595a2cb1b2a85e2ed73a67eccac8b32 f626f1a4b4965df8008d349712318cedf6dde9eb Sebastian DiLorenzo <S_D at imv096.medsci.uu.se> 1372427760 +0200 pull : fast-forward
Modified: .git/refs/heads/master
===================================================================
--- .git/refs/heads/master 2013-06-27 15:43:17 UTC (rev 184)
+++ .git/refs/heads/master 2013-06-28 13:55:12 UTC (rev 185)
@@ -1 +1 @@
-b617a63c7595a2cb1b2a85e2ed73a67eccac8b32
+f626f1a4b4965df8008d349712318cedf6dde9eb
Modified: .git/refs/remotes/origin/master
===================================================================
--- .git/refs/remotes/origin/master 2013-06-27 15:43:17 UTC (rev 184)
+++ .git/refs/remotes/origin/master 2013-06-28 13:55:12 UTC (rev 185)
@@ -1 +1 @@
-b617a63c7595a2cb1b2a85e2ed73a67eccac8b32
+f626f1a4b4965df8008d349712318cedf6dde9eb
Modified: pkg/TAPS/R/TAPS.r
===================================================================
--- pkg/TAPS/R/TAPS.r 2013-06-27 15:43:17 UTC (rev 184)
+++ pkg/TAPS/R/TAPS.r 2013-06-28 13:55:12 UTC (rev 185)
@@ -1644,13 +1644,14 @@
#Top part of the plot
#------------------------------------------------------------
+ #nchr=24; if (sum(chr=='chrY')==0) nchr=23
#Loop over and plot the 24 chromosomes
for (c in 1:24)
{
#Pick a chromosome
this <- ideogram[ideogram$c==c,]
#Extract that chromosomes information
- ix <- chr==this$chr
+ ix <- chr==as.character(this$chr)
#Add color depending on the length of this chromosome
col <- rep('#B0B0B030',length(chr))
col[ix & (pos < this$mid)] <- paste(colors_p(sum(ix & (pos < this$mid))), '70', sep='')
@@ -1742,9 +1743,9 @@
for (c in 1:24)
{
this <- ideogram[ideogram$c==c,]
- ix <- chr==this$chr
- mix <- mchr==this$chr #& mval>=(-2)
- six <- schr==this$chr
+ ix <- chr==as.character(this$chr)
+ mix <- mchr==as.character(this$chr) #& mval>=(-2)
+ six <- schr==as.character(this$chr)
#Predefine ymin ymax and sequence between them
ymin=floor(2*min(int,na.rm=T))/2
@@ -1819,7 +1820,7 @@
for(c in 1:24)
{
this <- ideogram[ideogram$c==c,]
- ix <- chr==this$chr
+ ix <- chr==as.character(this$chr)
col <- rep('#B0B0B030',length(chr))
col[ix & (pos < this$mid)] <- paste(colors_p(sum(ix & (pos < this$mid))), '70', sep='')
col[ix & (pos > this$mid)] <- paste(colors_q(sum(ix & (pos > this$mid))), '70', sep='')
@@ -2010,7 +2011,7 @@
#------------------------------------------------------------
#index of the selected chromsome to the chr object
- ix <- chr==this$chr
+ ix <- chr==as.character(this$chr)
notix1 = chr=="chrX"
notix = !ix + notix1
@@ -2090,7 +2091,7 @@
par(mgp =c(0.5,0.25,0))
#Select the correct chromosome and remove stuff lower than -1
- mix <- mchr==this$chr #& mval>(-1)
+ mix <- mchr==as.character(this$chr) #& mval>(-1)
#Predefine ymin ymax and sequence between them
ymin=floor(2*min(int,na.rm=T))/2
@@ -2178,7 +2179,7 @@
mtext(text=this$chr,side=2,las=1,line=-1.2)
#index of the chromData for this chromosome
- dix = chromData$chr == this$chr
+ dix = chromData$chr == as.character(this$chr)
#Add cytoband information as differently colored rectangles
rect(xleft=chromData$chromStart[dix],xright=chromData$chromEnd[dix],
@@ -2213,7 +2214,7 @@
par(mgp =c(0.5,0.25,0))
#Index of correct chromsome and allele frequency not in either 0 or 1
- six <- schr==this$chr & !(sval %in% c(0,1))
+ six <- schr==as.character(this$chr) & !(sval %in% c(0,1))
#plot allele frequency over position
plot(spos[six],sval[six],
@@ -2342,7 +2343,7 @@
#Left side of the plot (Whole genome)
#------------------------------------------------------------
#index of the selected chromsome to the chr object
- ix <- chr==this$chr
+ ix <- chr==as.character(this$chr)
notix1 = chr=="chrX"
notix = !ix + notix1
@@ -2480,7 +2481,7 @@
par(mgp =c(0.5,0.25,0))
#Select the correct chromosome and remove stuff lower than -1
- mix <- mchr==this$chr #& mval>(-1)
+ mix <- mchr==as.character(this$chr) #& mval>(-1)
#Predefine ymin ymax and sequence between them
ymin=floor(min(int[ix]))-0.5
@@ -2548,7 +2549,7 @@
mtext(text="Cytoband",side=2,las=1,line=-1,cex=0.8)
#index of the chromData for this chromosome
- dix = chromData$chr == this$chr
+ dix = chromData$chr == as.character(this$chr)
#Add cytoband information as differently colored rectangles
rect(xleft=chromData$chromStart[dix],xright=chromData$chromEnd[dix],
@@ -2584,7 +2585,7 @@
par(mgp =c(0.5,0.25,0))
#Index of correct chromsome and allele frequency not in either 0 or 1
- six <- schr==this$chr & !(sval %in% c(0,1))
+ six <- schr==as.character(this$chr) & !(sval %in% c(0,1))
#plot allele frequency over position
plot(spos[six],sval[six],
@@ -2807,8 +2808,8 @@
#------------------------------------------------------------
#index of overlapping the selected chromosome region to the chr object
- wix <- chr==this$chr & (((Rstart <= start) & (Rend >= end)) | ((Rstart >= start) & (Rstart <= end)) | ((Rend <= end) & (Rend >= start)))
- ix <- chr==this$chr
+ wix <- chr==as.character(this$chr) & (((Rstart <= start) & (Rend >= end)) | ((Rstart >= start) & (Rstart <= end)) | ((Rend <= end) & (Rend >= start)))
+ ix <- chr==as.character(this$chr)
#Create an index of colors relating to the positions and lengths on this chromosome
col <- rep('#B0B0B030',length(chr))
@@ -2859,7 +2860,7 @@
par(xpd=T)
#Select the correct chromosome and remove stuff lower than -1
- mix <- mchr==this$chr #& mval>(-1)
+ mix <- mchr==as.character(this$chr) #& mval>(-1)
#Create an index of colors relating to the positions and lengths on this chromosome
col=rep('#000000',sum(ix))
@@ -2943,7 +2944,7 @@
mtext(text="Cytoband",side=2,las=1,line=-1,cex=0.8)
#index of the chromData for this chromosome
- dix = chromData$chr == this$chr
+ dix = chromData$chr == as.character(this$chr)
#Add cytoband information as differently colored rectangles
rect(xleft=chromData$chromStart[dix],xright=chromData$chromEnd[dix],
@@ -2982,7 +2983,7 @@
#Index of correct chromsome and allele frequency not in either 0 or 1
- six <- schr==this$chr & !(sval %in% c(0,1))
+ six <- schr==as.character(this$chr) & !(sval %in% c(0,1))
#plot allele frequency over position
plot(spos[six],sval[six],
@@ -3024,9 +3025,9 @@
#Select the correct chromosome and region and remove stuff lower than -1
- mix <- mchr==this$chr & (mpos >= Rstart) & (mpos <= Rend) #& mval>(-1)
+ mix <- mchr==as.character(this$chr) & (mpos >= Rstart) & (mpos <= Rend) #& mval>(-1)
- wix <- chr==this$chr & (((Rstart <= start) & (Rend >= end)) | ((Rstart >= start) & (Rstart <= end)) | ((Rend <= end) & (Rend >= start)))
+ wix <- chr==as.character(this$chr) & (((Rstart <= start) & (Rend >= end)) | ((Rstart >= start) & (Rstart <= end)) | ((Rend <= end) & (Rend >= start)))
cix = ((Rstart >= start) & (Rstart <= end))
start[cix] = Rstart
@@ -3107,7 +3108,7 @@
#Create and index of the genes within region (rstart to rend)
#gix <- kg$chr==this$chr & (((Rstart <= kg$gtxStart) & (Rend >= kg$gtxEnd)) | ((Rstart >= kg$gtxStart) & (Rstart <= kg$gtxEnd)) | ((Rend <= kg$gtxEnd) & (Rend >= kg$gtxStart)))
- gix <- kg$chr==this$chr & ((Rstart <= kg$gtxEnd) & (Rend >= kg$gtxStart))
+ gix <- kg$chr==as.character(this$chr) & ((Rstart <= kg$gtxEnd) & (Rend >= kg$gtxStart))
#If they are only partial overlapping, remove the parts outside of the selected region
cix = ((Rstart >= kg$gtxStart) & (Rstart <= kg$gtxEnd))
@@ -3182,7 +3183,7 @@
#Index of correct chromsome and allele frequency not in either 0 or 1
- six <- schr==this$chr & !(sval %in% c(0,1)) & (spos >= Rstart) & (spos <= Rend)
+ six <- schr==as.character(this$chr) & !(sval %in% c(0,1)) & (spos >= Rstart) & (spos <= Rend)
#plot allele frequency over position
plot(spos[six],sval[six],
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