Mercurial > repos > iarc > mutspec
diff mutspecNmf_wrapper.sh @ 0:8c682b3a7c5b draft
Uploaded
| author | iarc |
|---|---|
| date | Tue, 19 Apr 2016 03:07:11 -0400 |
| parents | |
| children | 916846f73e25 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mutspecNmf_wrapper.sh Tue Apr 19 03:07:11 2016 -0400 @@ -0,0 +1,94 @@ +#!/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