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comparison mutspecNmf_wrapper.sh @ 0:8c682b3a7c5b draft

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author iarc
date Tue, 19 Apr 2016 03:07:11 -0400
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children 916846f73e25
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-1:000000000000 0:8c682b3a7c5b
1 #!/bin/bash
2
3 #########################################
4 ### SPECIFY THE NUMBER OF CPU ###
5 #########################################
6 cpu=1
7
8
9
10
11 html=$1;shift
12 parameters=$1;shift
13 source=$1;shift
14 input=$1
15
16 if [[ $source == "html" ]]
17 then input=${input%%.*}_files/Mutational_Analysis/Figures/Input_NMF/Input_NMF_Count.txt
18 fi
19
20 output_dir=${html%%.*}_files
21 mkdir $output_dir
22
23 Rscript $SCRIPT_PATH/R/somaticSignature_Galaxy.r $parameters --cpu $cpu --input $input --output $output_dir 2>&1
24
25
26 ## Test the existence of the files and graphs produced by NMF
27 if [[ ! -e "$output_dir/NMF/Files/MatrixW-Normto100.txt" ]]; then
28 >&2 echo "error"
29 exit
30 fi
31
32
33 echo "<html><body>" >> $html
34 echo "<center> <h2> NMF Mutational signatures analysis </h2> </center>" >> $html
35
36
37 echo "<table>" >> $html
38 echo "<tr> <br/> <th><h3>Heatmap of the mixture coefficient matrix</h3></th> </tr>" >> $html
39 echo "<tr> <td> <center> <br/> <a href="NMF/Files/Cluster_MixtureCoeff.txt">Cluster_MixtureCoeff.txt</a> </center> </td> </tr>" >> $html
40 echo "<tr>" >> $html
41
42 if [[ ! -e "$output_dir/NMF/Figures/Heatmap_MixtureCoeff.png" ]]; then
43 echo "WARNING: NMF package can't plot the heatmap when the samples size is above 300. <br/>" >> $html
44 else
45 echo "<td> <center> <a href="NMF/Figures/Heatmap_MixtureCoeff.png">" >> $html
46 echo "<img src="NMF/Figures/Heatmap_MixtureCoeff.png" /></a> <center> </td>" >> $html
47 fi
48 echo "</tr>" >> $html
49 echo "</table>" >> $html
50
51 echo "<br/><br/>" >> $html
52
53 echo "<table>" >> $html
54 echo "<tr>" >> $html
55 echo "<th><h3>Signature composition</h3></th>" >> $html
56 echo "</tr>" >> $html
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
58 echo "<tr>" >> $html
59 echo "<td><a href="NMF/Figures/CompositionSomaticMutation.png">" >> $html
60 echo "<img width="1000" src="NMF/Figures/CompositionSomaticMutation.png" /></a></td>" >> $html
61 echo "</tr> " >> $html
62 echo "</table>" >> $html
63 echo "<br/><br/>" >> $html
64
65 echo "<table>" >> $html
66 echo "<tr>" >> $html
67 echo "<th><h3>Sample contribution to signatures</h3></th>" >> $html
68 echo "</tr>" >> $html
69 echo "<tr><td> <center> <a href="NMF/Files/MatrixH-Inputggplot2.txt">Contribution mutation signature matrix</a></center></td></tr>" >> $html
70 echo "<tr>" >> $html
71 echo "<td><a href="NMF/Figures/ContributionMutationSignature.png">" >> $html
72 echo "<img width="700" src="NMF/Figures/ContributionMutationSignature.png" /></a></td>" >> $html
73 echo "</tr> " >> $html
74 echo "</table>" >> $html
75 echo "<br/><br/>" >> $html
76
77
78 echo "<table>" >> $html
79 echo "<tr>" >> $html
80 echo "<th><h3>Average contributions of each signatures in each cluster</h3></th>" >> $html
81 echo "</tr>" >> $html
82 echo "<tr><td> <center> <a href="NMF/Files/Average_ContriByCluster.txt">Average contributions</a></center></td></tr>" >> $html
83 echo "<tr>" >> $html
84 echo "<td><a href="NMF/Figures/Average_ContriByCluster.png">" >> $html
85 echo "<img width="700" src="NMF/Figures/Average_ContriByCluster.png" /></a></td>" >> $html
86 echo "</tr> " >> $html
87 echo "</table>" >> $html
88 echo "<br/><br/>" >> $html
89
90 echo "<br/><br/><br/><br/>" >> $html
91
92
93
94 exit 0