Mercurial > repos > md-anderson-bioinformatics > heat_map_creation_advanced
comparison heatmap_advanced.sh @ 0:8893ea2915cc draft
Initial Version of Advanced Heat Map Tool
| author | insilico-bob |
|---|---|
| date | Tue, 08 Aug 2017 14:01:05 -0400 |
| parents | |
| children | 603f99d9e776 |
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| -1:000000000000 | 0:8893ea2915cc |
|---|---|
| 1 echo $1 $2 $3 $4 $5 $6 $7 $8 $9 ${10} ${11} ${12} ${13} ${14} ${15} ${16} ${17} ${18} ${19} | |
| 2 | |
| 3 #run python to validate the input matrix and covariate files (if any) | |
| 4 #output="$(python ${11}/mda_heatmap_gen.py $@)" | |
| 5 output=$(python ${11}/mda_heatmap_gen.py "$@") | |
| 6 rc=$?; | |
| 7 echo $output; | |
| 8 if [ $rc != 0 ] | |
| 9 then | |
| 10 exit $rc; | |
| 11 fi | |
| 12 | |
| 13 #create temp directory for row and col order and dendro files. | |
| 14 tdir=${11}/$(date +%y%m%d%M%S) | |
| 15 echo $tdir | |
| 16 mkdir $tdir | |
| 17 #run R to cluster matrix | |
| 18 output="$(R --slave --vanilla --file=${11}/CHM_Advanced.R --args $3 $4 $5 $6 $7 $8 $9 $tdir/ROfile.txt $tdir/COfile.txt $tdir/RDfile.txt $tdir/CDfile.txt ${12} ${13} ${14} ${15} 2>&1)" | |
| 19 rc=$?; | |
| 20 if [ $rc != 0 ] | |
| 21 then | |
| 22 echo $output; | |
| 23 if [ `echo "$output" | grep -c "Inf in foreign function call"` -gt 0 ] | |
| 24 then | |
| 25 echo ""; | |
| 26 echo "Note: This error can occur when there is no variation in a row or column. Try a different distance measure or remove rows/columns without variation."; | |
| 27 fi | |
| 28 exit $rc; | |
| 29 fi | |
| 30 | |
| 31 #there are a variable number of triplicate parameters for classification bars | |
| 32 count=0 | |
| 33 classifications='' | |
| 34 | |
| 35 #if row cut was done, add that autogenerated classification | |
| 36 if [ ${12} -gt 1 ] | |
| 37 then | |
| 38 classifications="Class $tdir/ROfile.txt.cut row_categorical" | |
| 39 fi | |
| 40 | |
| 41 #if col cut was done, add that autogenerated classification | |
| 42 if [ ${13} -gt 1 ] | |
| 43 then | |
| 44 classifications="$classifications Class $tdir/COfile.txt.cut col_categorical" | |
| 45 fi | |
| 46 | |
| 47 #now add the user provided classification files | |
| 48 for i in "$@"; do | |
| 49 if [ $count -gt 15 ] | |
| 50 then | |
| 51 classifications=$classifications' '$i | |
| 52 fi | |
| 53 count=$((count+1)) | |
| 54 done | |
| 55 #call java program to generate NGCHM viewer files. | |
| 56 java -jar ${11}/GalaxyMapGen.jar "${1}" "${2}" DataLayer1 $3 linear ${14} ${15} $4 $5 $6 $tdir/ROfile.txt $tdir/RDfile.txt $7 $8 $9 $tdir/COfile.txt $tdir/CDfile.txt ${10} "${16}" $classifications | |
| 57 #clean up tempdir | |
| 58 rm -rf $tdir |