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1 #!/bin/bash
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2
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3 #########################################
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4 ### SPECIFY THE NUMBER OF CPU ###
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5 #########################################
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6 cpu=1
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7
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8
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9
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10
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11 html=$1;shift
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12 parameters=$1;shift
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13 source=$1;shift
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14 input=$1
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15
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16 if [[ $source == "html" ]]
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17 then input=${input%%.*}_files/Mutational_Analysis/Figures/Input_NMF/Input_NMF_Count.txt
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18 fi
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19
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20 output_dir=${html%%.*}_files
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21 mkdir $output_dir
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22
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23 Rscript $SCRIPT_PATH/R/somaticSignature_Galaxy.r $parameters --cpu $cpu --input $input --output $output_dir 2>&1
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24
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25
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26 ## Test the existence of the files and graphs produced by NMF
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27 if [[ ! -e "$output_dir/NMF/Files/MatrixW-Normto100.txt" ]]; then
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28 >&2 echo "error"
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29 exit
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30 fi
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31
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32
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33 echo "<html><body>" >> $html
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34 echo "<center> <h2> NMF Mutational signatures analysis </h2> </center>" >> $html
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35
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36
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37 echo "<table>" >> $html
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38 echo "<tr> <br/> <th><h3>Heatmap of the mixture coefficient matrix</h3></th> </tr>" >> $html
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39 echo "<tr> <td> <center> <br/> <a href="NMF/Files/Cluster_MixtureCoeff.txt">Cluster_MixtureCoeff.txt</a> </center> </td> </tr>" >> $html
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40 echo "<tr>" >> $html
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41
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42 if [[ ! -e "$output_dir/NMF/Figures/Heatmap_MixtureCoeff.png" ]]; then
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43 echo "WARNING: NMF package can't plot the heatmap when the samples size is above 300. <br/>" >> $html
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44 else
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45 echo "<td> <center> <a href="NMF/Figures/Heatmap_MixtureCoeff.png">" >> $html
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46 echo "<img src="NMF/Figures/Heatmap_MixtureCoeff.png" /></a> <center> </td>" >> $html
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47 fi
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48 echo "</tr>" >> $html
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49 echo "</table>" >> $html
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50
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51 echo "<br/><br/>" >> $html
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52
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53 echo "<table>" >> $html
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54 echo "<tr>" >> $html
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55 echo "<th><h3>Signature composition</h3></th>" >> $html
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56 echo "</tr>" >> $html
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57 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
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58 echo "<tr>" >> $html
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59 echo "<td><a href="NMF/Figures/CompositionSomaticMutation.png">" >> $html
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60 echo "<img width="1000" src="NMF/Figures/CompositionSomaticMutation.png" /></a></td>" >> $html
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61 echo "</tr> " >> $html
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62 echo "</table>" >> $html
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63 echo "<br/><br/>" >> $html
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64
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65 echo "<table>" >> $html
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66 echo "<tr>" >> $html
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67 echo "<th><h3>Sample contribution to signatures</h3></th>" >> $html
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68 echo "</tr>" >> $html
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69 echo "<tr><td> <center> <a href="NMF/Files/MatrixH-Inputggplot2.txt">Contribution mutation signature matrix</a></center></td></tr>" >> $html
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70 echo "<tr>" >> $html
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71 echo "<td><a href="NMF/Figures/ContributionMutationSignature.png">" >> $html
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72 echo "<img width="700" src="NMF/Figures/ContributionMutationSignature.png" /></a></td>" >> $html
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73 echo "</tr> " >> $html
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74 echo "</table>" >> $html
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75 echo "<br/><br/>" >> $html
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76
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77
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78 echo "<table>" >> $html
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79 echo "<tr>" >> $html
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80 echo "<th><h3>Average contributions of each signatures in each cluster</h3></th>" >> $html
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81 echo "</tr>" >> $html
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82 echo "<tr><td> <center> <a href="NMF/Files/Average_ContriByCluster.txt">Average contributions</a></center></td></tr>" >> $html
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83 echo "<tr>" >> $html
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84 echo "<td><a href="NMF/Figures/Average_ContriByCluster.png">" >> $html
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85 echo "<img width="700" src="NMF/Figures/Average_ContriByCluster.png" /></a></td>" >> $html
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86 echo "</tr> " >> $html
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87 echo "</table>" >> $html
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88 echo "<br/><br/>" >> $html
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89
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90 echo "<br/><br/><br/><br/>" >> $html
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91
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92
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93
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94 exit 0
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