Mercurial > repos > fubar > rglasso_1_9_8

diff test-data/coxlassotest.html @ 4:5f2db639f8eb draft

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author fubar
date Fri, 19 Dec 2014 05:57:55 -0500
parents b539dcdc6168
children 4b62ea84c318
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/coxlassotest.html	Fri Dec 19 05:57:55 2014 -0500
@@ -0,0 +1,140 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> 
+        <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> 
+        <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> 
+        <meta name="generator" content="Galaxy rgToolFactory.py tool output - see http://g2.trac.bx.psu.edu/" /> 
+        <title></title> 
+        <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> 
+        </head> 
+        <body> 
+        <div class="toolFormBody"> 
+        
+<div class="infomessage">Galaxy Tool "rglasso" run at 19/10/2014 13:11:14</div><br/>
+<div class="toolFormTitle">cox images and outputs</div>
+(Click on a thumbnail image to download the corresponding original PDF image)<br/>
+<div><table class="simple" cellpadding="2" cellspacing="2">
+<tr>
+<td><a href="cox_Coxglmnettest_glmnet_cvdeviance.pdf"><img src="cox_Coxglmnettest_glmnet_cvdeviance.png" title="Click to download a PDF of cox_Coxglmnettest_glmnet_cvdeviance.pdf" hspace="5" width="400" 
+                           alt="Image called cox_Coxglmnettest_glmnet_cvdeviance.pdf"/></a></td>
+
+<td><a href="cox_Coxglmnettest_glmnetdev.pdf"><img src="cox_Coxglmnettest_glmnetdev.png" title="Click to download a PDF of cox_Coxglmnettest_glmnetdev.pdf" hspace="5" width="400" 
+                           alt="Image called cox_Coxglmnettest_glmnetdev.pdf"/></a></td>
+</tr>
+
+</table></div>
+
+<div class="toolFormTitle">cox log output</div>
+
+<pre>
+
+[1] "All partial likelihood coefficients from Cox model at minimum lambda of 0.00138091491730048:"
+
+3 x 1 sparse Matrix of class "dgCMatrix"
+
+                    1
+
+rhubarb  1.124517e-03
+
+vegemite 1.444990e-01
+
+apple    3.344565e-06
+
+
+</pre>
+
+<div class="toolFormTitle">rglasso log output</div>
+
+<pre>
+
+Loading required package: Matrix
+
+Loading required package: methods
+
+Loaded glmnet 1.9-8
+
+Loaded lars 1.2
+
+Warning messages:
+
+1: In if (class(larsres) == "try-error") { :
+
+  the condition has length > 1 and only the first element will be used
+
+2: In plot.window(...) : "label" is not a graphical parameter
+
+3: In plot.xy(xy, type, ...) : "label" is not a graphical parameter
+
+4: In axis(side = side, at = at, labels = labels, ...) :
+
+  "label" is not a graphical parameter
+
+5: In axis(side = side, at = at, labels = labels, ...) :
+
+  "label" is not a graphical parameter
+
+6: In box(...) : "label" is not a graphical parameter
+
+7: In title(...) : "label" is not a graphical parameter
+
+
+</pre>
+
+<div class="toolFormTitle">Other log output</div>
+
+<pre>
+
+## Toolfactory generated command line = Rscript - None None
+
+[1] Cox model: Got yvar= time,status cols 1 n preds= 3 forced in= 3
+
+[2] Cox model: Got yvar= time,status cols 2 n preds= 3 forced in= 3
+
+[1] Results preview:
+
+         regulator partial_likelihood forced_in glmnet_model best_lambda
+
+rhubarb    rhubarb        0.001180324      TRUE          cox  0.01508333
+
+vegemite  vegemite        0.093827440     FALSE          cox  0.01508333
+
+[1] SessionInfo for this R session:
+
+R version 3.1.0 (2014-04-10)
+
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+locale:
+
+ [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C               LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
+
+ [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8    LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
+
+ [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       
+
+attached base packages:
+
+[1] methods   stats     graphics  grDevices utils     datasets  base     
+
+other attached packages:
+
+[1] lars_1.2     glmnet_1.9-8 Matrix_1.1-4
+
+loaded via a namespace (and not attached):
+
+[1] grid_3.1.0      lattice_0.20-29
+
+
+</pre>
+
+<div class="toolFormTitle">All output files available for downloading</div>
+
+<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>
+
+<tr><td><a href="cox_Coxglmnettest_glmnet_cvdeviance.pdf">cox_Coxglmnettest_glmnet_cvdeviance.pdf</a></td><td>6.4 KB</td></tr>
+<tr class="odd_row"><td><a href="cox_Coxglmnettest_glmnetdev.pdf">cox_Coxglmnettest_glmnetdev.pdf</a></td><td>5.2 KB</td></tr>
+<tr><td><a href="cox_rglasso.log">cox_rglasso.log</a></td><td>228 B</td></tr>
+<tr class="odd_row"><td><a href="rglasso.Rscript">rglasso.Rscript</a></td><td>9.8 KB</td></tr>
+<tr><td><a href="rglasso_error.log">rglasso_error.log</a></td><td>671 B</td></tr>
+<tr class="odd_row"><td><a href="rglasso_runner.log">rglasso_runner.log</a></td><td>1.1 KB</td></tr>
+</table></div><br/>
+</div></body></html>
+