Mercurial > repos > iarc > mutspec
diff mutspecNmf_wrapper.sh @ 7:eda59b985b1c draft default tip
Uploaded
| author | iarc |
|---|---|
| date | Mon, 13 Mar 2017 08:21:19 -0400 |
| parents | 46a10309dfe2 |
| children |
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--- a/mutspecNmf_wrapper.sh Tue Jun 28 02:59:32 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,94 +0,0 @@ -#!/bin/bash - -######################################### -### SPECIFY THE NUMBER OF CPU ### -######################################### -cpu=1 - - - - -html=$1;shift -parameters=$1;shift -source=$1;shift -input=$1 - -if [[ $source == "html" ]] -then input=${input%%.*}_files/Mutational_Analysis/Figures/Input_NMF/Input_NMF_Count.txt -fi - -output_dir=${html%%.*}_files -mkdir $output_dir - -Rscript $SCRIPT_PATH/R/somaticSignature_Galaxy.r $parameters --cpu $cpu --input $input --output $output_dir 2>&1 - - -## Test the existence of the files and graphs produced by NMF -if [[ ! -e "$output_dir/NMF/Files/MatrixW-Normto100.txt" ]]; then - >&2 echo "error" - exit -fi - - -echo "<html><body>" >> $html -echo "<center> <h2> NMF Mutational signatures analysis </h2> </center>" >> $html - - -echo "<table>" >> $html -echo "<tr> <br/> <th><h3>Heatmap of the mixture coefficient matrix</h3></th> </tr>" >> $html -echo "<tr> <td> <center> <br/> <a href="NMF/Files/Cluster_MixtureCoeff.txt">Cluster_MixtureCoeff.txt</a> </center> </td> </tr>" >> $html -echo "<tr>" >> $html - -if [[ ! -e "$output_dir/NMF/Figures/Heatmap_MixtureCoeff.png" ]]; then - echo "WARNING: NMF package can't plot the heatmap when the samples size is above 300. <br/>" >> $html -else - echo "<td> <center> <a href="NMF/Figures/Heatmap_MixtureCoeff.png">" >> $html - echo "<img src="NMF/Figures/Heatmap_MixtureCoeff.png" /></a> <center> </td>" >> $html -fi -echo "</tr>" >> $html -echo "</table>" >> $html - -echo "<br/><br/>" >> $html - -echo "<table>" >> $html -echo "<tr>" >> $html -echo "<th><h3>Signature composition</h3></th>" >> $html -echo "</tr>" >> $html -echo "<tr><td> <center> <a href="NMF/Files/MatrixW-Normto100.txt">Composition somatic mutation (input matrix for the tool MutSpec-Compare)</a><center></td></tr>" >> $html -echo "<tr>" >> $html -echo "<td><a href="NMF/Figures/CompositionSomaticMutation.png">" >> $html -echo "<img width="1000" src="NMF/Figures/CompositionSomaticMutation.png" /></a></td>" >> $html -echo "</tr> " >> $html -echo "</table>" >> $html -echo "<br/><br/>" >> $html - -echo "<table>" >> $html -echo "<tr>" >> $html -echo "<th><h3>Sample contribution to signatures</h3></th>" >> $html -echo "</tr>" >> $html -echo "<tr><td> <center> <a href="NMF/Files/MatrixH-Inputggplot2.txt">Contribution mutation signature matrix</a></center></td></tr>" >> $html -echo "<tr>" >> $html -echo "<td><a href="NMF/Figures/ContributionMutationSignature.png">" >> $html -echo "<img width="700" src="NMF/Figures/ContributionMutationSignature.png" /></a></td>" >> $html -echo "</tr> " >> $html -echo "</table>" >> $html -echo "<br/><br/>" >> $html - - -echo "<table>" >> $html -echo "<tr>" >> $html -echo "<th><h3>Average contributions of each signatures in each cluster</h3></th>" >> $html -echo "</tr>" >> $html -echo "<tr><td> <center> <a href="NMF/Files/Average_ContriByCluster.txt">Average contributions</a></center></td></tr>" >> $html -echo "<tr>" >> $html -echo "<td><a href="NMF/Figures/Average_ContriByCluster.png">" >> $html -echo "<img width="700" src="NMF/Figures/Average_ContriByCluster.png" /></a></td>" >> $html -echo "</tr> " >> $html -echo "</table>" >> $html -echo "<br/><br/>" >> $html - -echo "<br/><br/><br/><br/>" >> $html - - - -exit 0