[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

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue Oct 15 14:18:00 CEST 2013 

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 <dilorenzo.sebastian at gmail.com> 1378903472 +0200	pull : Fast-forward
 6f560c07eeb2bc5a9c449af56829257933ebcf87 bd3ab614a6966fa50066cad8cf9682e0a728ea4a Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1378904905 +0200	commit: update taps remove header from merge
 bd3ab614a6966fa50066cad8cf9682e0a728ea4a 4a0e2921f140974e7c8a12fd8fddb998c0bd3171 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1379937620 +0200	commit: hg18 detection added to TAPS
+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

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 <dilorenzo.sebastian at gmail.com> 1378903472 +0200	pull : Fast-forward
 6f560c07eeb2bc5a9c449af56829257933ebcf87 bd3ab614a6966fa50066cad8cf9682e0a728ea4a Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1378904905 +0200	commit: update taps remove header from merge
 bd3ab614a6966fa50066cad8cf9682e0a728ea4a 4a0e2921f140974e7c8a12fd8fddb998c0bd3171 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1379937620 +0200	commit: hg18 detection added to TAPS
+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

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 <S_D at imv092.medsci.uu.se> 1378903403 +0200	pull : fast-forward
 6f560c07eeb2bc5a9c449af56829257933ebcf87 bd3ab614a6966fa50066cad8cf9682e0a728ea4a Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1378904932 +0200	update by push
 bd3ab614a6966fa50066cad8cf9682e0a728ea4a 4a0e2921f140974e7c8a12fd8fddb998c0bd3171 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1379937639 +0200	update by push
+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

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. <br /><br />
+simply "SampleData.xlsx" which will be covered shortly. <br /><br />
 
 <hr class="alt1" />
 
@@ -116,18 +116,18 @@
 <br /><br />
 
 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().
 <br /><br />
 
-An example run of TAPS_call(), where "mainsamplefolder" contains SampleData.txt: <br />
+An example run of TAPS_call(), where "mainsamplefolder" contains SampleData.xlsx: <br />
 
 <pre>
 	TAPS_call(directory="path/to/mainsamplefolder")
 </pre>
 
-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.
 <br /><br />
@@ -169,16 +169,22 @@
 and allele-specific information. <br /><br />
 
 
-<img id="fig1taps" src="css/img/TAPS_call_help.png" alt="Input arguments TAPS_call" title="Figure 1 TAPS"
+<img id="fig1taps" src="css/img/TAPS_call_help2.png" alt="Input arguments TAPS_call" title="Figure 1 TAPS"
  style="width:880px"><br /><br />
 
 
-The <b>cn2</b> argument is the position of copy number 2 on average log-ratio axis. In this example cn2 is ~ -0.2.<br />
+<!--The <b>cn2</b> argument is the position of copy number 2 on average log-ratio axis. In this example cn2 is ~ -0.2.<br />
 The <b>delta</b> argument is the difference between two copynumbers on the average log-ratio axis. In this example we
 used copy number 2 and copy number 3, but we could as well have used copy number 2 and the unmarked copy number
 1 to the left of copy number 2. Delta does not take negative argument input. In this example delta is ~ 0.3.<br />
 The <b>loh</b> argument is the position of homozygous copy number 2 (LOH) on the allelic imbalance axis. 
-In this example loh is ~ 0.75
+In this example loh is ~ 0.75-->
+
+The <b>cn1</b>, <b>cn2</b> and <b>cn3</b> 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. <br />
+The <b>loh</b> argument is the position of homozygous copy number 2 (LOH) on the "Allelic imbalance" axis.
+In this example loh is ~ 0.75 
+
 <br /><br />
 
 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

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