From noreply at r-forge.r-project.org Tue Oct 15 14:18:00 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Tue, 15 Oct 2013 14:18:00 +0200 (CEST) Subject: [Patchwork-commits] r194 - .git .git/logs .git/logs/refs/heads .git/logs/refs/remotes/origin .git/refs/heads .git/refs/remotes/origin www www/css/img Message-ID: <20131015121800.7F25E185AE8@r-forge.r-project.org> Author: sebastian_d Date: 2013-10-15 14:17:59 +0200 (Tue, 15 Oct 2013) New Revision: 194 Added: www/css/img/TAPS_call_help2.png Removed: www/css/img/TAPS_call_help.png 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 www/TAPS_exec.php Log: Update to TAPS call homepage by markus Modified: .git/COMMIT_EDITMSG =================================================================== --- .git/COMMIT_EDITMSG 2013-09-24 15:25:34 UTC (rev 193) +++ .git/COMMIT_EDITMSG 2013-10-15 12:17:59 UTC (rev 194) @@ -1 +1 @@ -hg18 detection added to TAPS +Update to TAPS call homepage by markus Modified: .git/index =================================================================== (Binary files differ) Modified: .git/logs/HEAD =================================================================== --- .git/logs/HEAD 2013-09-24 15:25:34 UTC (rev 193) +++ .git/logs/HEAD 2013-10-15 12:17:59 UTC (rev 194) @@ -67,3 +67,6 @@ 7375bc63263a290cbfb537af8c38af2df6ba0f0c 6f560c07eeb2bc5a9c449af56829257933ebcf87 Sebastian DiLorenzo 1378903472 +0200 pull : Fast-forward 6f560c07eeb2bc5a9c449af56829257933ebcf87 bd3ab614a6966fa50066cad8cf9682e0a728ea4a Sebastian DiLorenzo 1378904905 +0200 commit: update taps remove header from merge bd3ab614a6966fa50066cad8cf9682e0a728ea4a 4a0e2921f140974e7c8a12fd8fddb998c0bd3171 Sebastian DiLorenzo 1379937620 +0200 commit: hg18 detection added to TAPS +4a0e2921f140974e7c8a12fd8fddb998c0bd3171 2347ca003cf8ce861e1d4ec1dc0f5c96a0ac3071 Sebastian DiLorenzo 1380027327 +0200 commit: update to datasamples.xlsx handling for different drive modes +2347ca003cf8ce861e1d4ec1dc0f5c96a0ac3071 85d1e6948ab98a6bd2c58f5dc820740c198a5444 Sebastian DiLorenzo 1380028151 +0200 pull : Fast-forward +85d1e6948ab98a6bd2c58f5dc820740c198a5444 0044e7bf9b5beb763bd5f47e54c8b778999eede2 Sebastian DiLorenzo 1381839717 +0200 commit: Update to TAPS call homepage by markus Modified: .git/logs/refs/heads/master =================================================================== --- .git/logs/refs/heads/master 2013-09-24 15:25:34 UTC (rev 193) +++ .git/logs/refs/heads/master 2013-10-15 12:17:59 UTC (rev 194) @@ -67,3 +67,6 @@ 7375bc63263a290cbfb537af8c38af2df6ba0f0c 6f560c07eeb2bc5a9c449af56829257933ebcf87 Sebastian DiLorenzo 1378903472 +0200 pull : Fast-forward 6f560c07eeb2bc5a9c449af56829257933ebcf87 bd3ab614a6966fa50066cad8cf9682e0a728ea4a Sebastian DiLorenzo 1378904905 +0200 commit: update taps remove header from merge bd3ab614a6966fa50066cad8cf9682e0a728ea4a 4a0e2921f140974e7c8a12fd8fddb998c0bd3171 Sebastian DiLorenzo 1379937620 +0200 commit: hg18 detection added to TAPS +4a0e2921f140974e7c8a12fd8fddb998c0bd3171 2347ca003cf8ce861e1d4ec1dc0f5c96a0ac3071 Sebastian DiLorenzo 1380027327 +0200 commit: update to datasamples.xlsx handling for different drive modes +2347ca003cf8ce861e1d4ec1dc0f5c96a0ac3071 85d1e6948ab98a6bd2c58f5dc820740c198a5444 Sebastian DiLorenzo 1380028151 +0200 pull : Fast-forward +85d1e6948ab98a6bd2c58f5dc820740c198a5444 0044e7bf9b5beb763bd5f47e54c8b778999eede2 Sebastian DiLorenzo 1381839717 +0200 commit: Update to TAPS call homepage by markus Modified: .git/logs/refs/remotes/origin/master =================================================================== --- .git/logs/refs/remotes/origin/master 2013-09-24 15:25:34 UTC (rev 193) +++ .git/logs/refs/remotes/origin/master 2013-10-15 12:17:59 UTC (rev 194) @@ -65,3 +65,5 @@ 7375bc63263a290cbfb537af8c38af2df6ba0f0c 6f560c07eeb2bc5a9c449af56829257933ebcf87 Sebastian DiLorenzo 1378903403 +0200 pull : fast-forward 6f560c07eeb2bc5a9c449af56829257933ebcf87 bd3ab614a6966fa50066cad8cf9682e0a728ea4a Sebastian DiLorenzo 1378904932 +0200 update by push bd3ab614a6966fa50066cad8cf9682e0a728ea4a 4a0e2921f140974e7c8a12fd8fddb998c0bd3171 Sebastian DiLorenzo 1379937639 +0200 update by push +4a0e2921f140974e7c8a12fd8fddb998c0bd3171 2347ca003cf8ce861e1d4ec1dc0f5c96a0ac3071 Sebastian DiLorenzo 1380027338 +0200 update by push +2347ca003cf8ce861e1d4ec1dc0f5c96a0ac3071 85d1e6948ab98a6bd2c58f5dc820740c198a5444 Sebastian DiLorenzo 1380028151 +0200 pull : fast-forward Modified: .git/refs/heads/master =================================================================== --- .git/refs/heads/master 2013-09-24 15:25:34 UTC (rev 193) +++ .git/refs/heads/master 2013-10-15 12:17:59 UTC (rev 194) @@ -1 +1 @@ -4a0e2921f140974e7c8a12fd8fddb998c0bd3171 +0044e7bf9b5beb763bd5f47e54c8b778999eede2 Modified: .git/refs/remotes/origin/master =================================================================== --- .git/refs/remotes/origin/master 2013-09-24 15:25:34 UTC (rev 193) +++ .git/refs/remotes/origin/master 2013-10-15 12:17:59 UTC (rev 194) @@ -1 +1 @@ -4a0e2921f140974e7c8a12fd8fddb998c0bd3171 +85d1e6948ab98a6bd2c58f5dc820740c198a5444 Modified: www/TAPS_exec.php =================================================================== --- www/TAPS_exec.php 2013-09-24 15:25:34 UTC (rev 193) +++ www/TAPS_exec.php 2013-10-15 12:17:59 UTC (rev 194) @@ -100,7 +100,7 @@ This will have generated one "<samplename>_overview.jpeg" in the main directory (should there be one), several plots and .Rdata files in the sample folder and a file named -simply "SampleData.txt" which will be covered shortly.

+simply "SampleData.xlsx" which will be covered shortly.

@@ -116,18 +116,18 @@

TAPS_call() also has "directory" as its main argument, the parameters are read from the file -"SampleData.txt". If you desire to execute TAPS_call() on many samples, add the arguments to the -main directory SampleData.txt. If you want to execute TAPS_call() on just one sample, add the arguments -for that sample to SampleData.txt and specify that sample using the "directory" argument of TAPS_call(). +"SampleData.xlsx". If you desire to execute TAPS_call() on many samples, add the arguments to the +main directory SampleData.xlsx. If you want to execute TAPS_call() on just one sample, add the arguments +for that sample to SampleData.xlsx and specify that sample using the "directory" argument of TAPS_call().

-An example run of TAPS_call(), where "mainsamplefolder" contains SampleData.txt:
+An example run of TAPS_call(), where "mainsamplefolder" contains SampleData.xlsx: 
 	TAPS_call(directory="path/to/mainsamplefolder")
-To infer the arguments for SampleData.txt that TAPS_call() uses you will need to look at one of +To infer the arguments for SampleData.xlsx that TAPS_call() uses you will need to look at one of the chromosomal plots generated using TAPS_plot(). The structure and relationships in the plot can be interpreted to figure out the most probable locations of the allele-specific copynumbers.

@@ -169,16 +169,22 @@ and allele-specific information.

-Input arguments TAPS_call

-The cn2 argument is the position of copy number 2 on average log-ratio axis. In this example cn2 is ~ -0.2.
+ + +The cn1, cn2 and cn3 arguments are the positions of copy number 1, 2 and 3 on +the "Average log-ratio" axis. In this example cn2 is ~ -0.15. You need only provide any two of these values.
+The loh argument is the position of homozygous copy number 2 (LOH) on the "Allelic imbalance" axis. +In this example loh is ~ 0.75 +

After running TAPS_call() you will have an additional set of plots in the sample folders which includes your Deleted: www/css/img/TAPS_call_help.png =================================================================== (Binary files differ) Added: www/css/img/TAPS_call_help2.png =================================================================== (Binary files differ) Property changes on: www/css/img/TAPS_call_help2.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream From noreply at r-forge.r-project.org Thu Oct 17 11:02:42 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 17 Oct 2013 11:02:42 +0200 (CEST) Subject: [Patchwork-commits] r195 - .git/logs/refs/remotes/origin .git/refs/remotes/origin pkg/TAPS/man Message-ID: <20131017090242.6783F185A7B@r-forge.r-project.org> Author: sebastian_d Date: 2013-10-17 11:02:42 +0200 (Thu, 17 Oct 2013) New Revision: 195 Modified: .git/logs/refs/remotes/origin/master .git/refs/remotes/origin/master pkg/TAPS/man/TAPS_plot.Rd Log: small update to TAPS_plot documentation Modified: .git/logs/refs/remotes/origin/master =================================================================== --- .git/logs/refs/remotes/origin/master 2013-10-15 12:17:59 UTC (rev 194) +++ .git/logs/refs/remotes/origin/master 2013-10-17 09:02:42 UTC (rev 195) @@ -67,3 +67,4 @@ bd3ab614a6966fa50066cad8cf9682e0a728ea4a 4a0e2921f140974e7c8a12fd8fddb998c0bd3171 Sebastian DiLorenzo 1379937639 +0200 update by push 4a0e2921f140974e7c8a12fd8fddb998c0bd3171 2347ca003cf8ce861e1d4ec1dc0f5c96a0ac3071 Sebastian DiLorenzo 1380027338 +0200 update by push 2347ca003cf8ce861e1d4ec1dc0f5c96a0ac3071 85d1e6948ab98a6bd2c58f5dc820740c198a5444 Sebastian DiLorenzo 1380028151 +0200 pull : fast-forward +85d1e6948ab98a6bd2c58f5dc820740c198a5444 0044e7bf9b5beb763bd5f47e54c8b778999eede2 Sebastian DiLorenzo 1381839752 +0200 update by push Modified: .git/refs/remotes/origin/master =================================================================== --- .git/refs/remotes/origin/master 2013-10-15 12:17:59 UTC (rev 194) +++ .git/refs/remotes/origin/master 2013-10-17 09:02:42 UTC (rev 195) @@ -1 +1 @@ -85d1e6948ab98a6bd2c58f5dc820740c198a5444 +0044e7bf9b5beb763bd5f47e54c8b778999eede2 Modified: pkg/TAPS/man/TAPS_plot.Rd =================================================================== --- pkg/TAPS/man/TAPS_plot.Rd 2013-10-15 12:17:59 UTC (rev 194) +++ pkg/TAPS/man/TAPS_plot.Rd 2013-10-17 09:02:42 UTC (rev 195) @@ -7,7 +7,7 @@ \title{ -Tumor Abberation Prediction Suite +Tumor Aberration Prediction Suite } \description{ From noreply at r-forge.r-project.org Mon Oct 21 13:08:15 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 21 Oct 2013 13:08:15 +0200 (CEST) Subject: [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 Message-ID: <20131021110815.C9452185B84@r-forge.r-project.org> 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 1380027327 +0200 commit: update to datasamples.xlsx handling for different drive modes 2347ca003cf8ce861e1d4ec1dc0f5c96a0ac3071 85d1e6948ab98a6bd2c58f5dc820740c198a5444 Sebastian DiLorenzo 1380028151 +0200 pull : Fast-forward 85d1e6948ab98a6bd2c58f5dc820740c198a5444 0044e7bf9b5beb763bd5f47e54c8b778999eede2 Sebastian DiLorenzo 1381839717 +0200 commit: Update to TAPS call homepage by markus +0044e7bf9b5beb763bd5f47e54c8b778999eede2 64da542e6e940d1ec28e8b99c82be94c86a2e3fd Sebastian DiLorenzo 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 1380027327 +0200 commit: update to datasamples.xlsx handling for different drive modes 2347ca003cf8ce861e1d4ec1dc0f5c96a0ac3071 85d1e6948ab98a6bd2c58f5dc820740c198a5444 Sebastian DiLorenzo 1380028151 +0200 pull : Fast-forward 85d1e6948ab98a6bd2c58f5dc820740c198a5444 0044e7bf9b5beb763bd5f47e54c8b778999eede2 Sebastian DiLorenzo 1381839717 +0200 commit: Update to TAPS call homepage by markus +0044e7bf9b5beb763bd5f47e54c8b778999eede2 64da542e6e940d1ec28e8b99c82be94c86a2e3fd Sebastian DiLorenzo 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 1380027338 +0200 update by push 2347ca003cf8ce861e1d4ec1dc0f5c96a0ac3071 85d1e6948ab98a6bd2c58f5dc820740c198a5444 Sebastian DiLorenzo 1380028151 +0200 pull : fast-forward 85d1e6948ab98a6bd2c58f5dc820740c198a5444 0044e7bf9b5beb763bd5f47e54c8b778999eede2 Sebastian DiLorenzo 1381839752 +0200 update by push +0044e7bf9b5beb763bd5f47e54c8b778999eede2 64da542e6e940d1ec28e8b99c82be94c86a2e3fd Sebastian DiLorenzo 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