annotate heatmap.sh @ 3:603d5c39e8dc draft

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author insilico-bob
date Thu, 26 Jan 2017 09:53:30 -0500
parents e2b3920e20c1
children 16593e40c2cd
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insilico-bob
parents:
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1 echo $1 $2 $3 $4 $5 $6 $7 $8 $9 ${10} ${11} ${12} ${13} ${14} ${15} ${16} ${17}
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insilico-bob
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2 #create temp directory for row and col order and dendro files.
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insilico-bob
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3 tdir=${11}/$(date +%y%m%d%M%S)
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insilico-bob
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4 echo $tdir
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insilico-bob
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5 mkdir $tdir
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insilico-bob
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6 #run R to cluster matrix
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7 output="$(R --slave --vanilla --file=${11}/CHM.R --args $3 $4 $5 $6 $7 $8 $9 $tdir/ROfile.txt $tdir/COfile.txt $tdir/RDfile.txt $tdir/CDfile.txt ${12} ${13} ${14} ${15} 2>&1)"
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insilico-bob
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8 rc=$?;
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insilico-bob
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9 if [ $rc != 0 ]
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10 then
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insilico-bob
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11 echo $output;
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insilico-bob
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12 if [ `echo "$output" | grep -c "Inf in foreign function call"` -gt 0 ]
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insilico-bob
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13 then
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insilico-bob
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14 echo "";
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insilico-bob
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15 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.";
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insilico-bob
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16 fi
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insilico-bob
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17 exit $rc;
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insilico-bob
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18 fi
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insilico-bob
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19
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insilico-bob
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20 #there are a variable number of triplicate parameters for classification bars
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insilico-bob
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21 count=0
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insilico-bob
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22 classifications=''
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insilico-bob
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23
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insilico-bob
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24 #if row cut was done, add that autogenerated classification
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insilico-bob
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25 if [ ${12} -gt 1 ]
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insilico-bob
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26 then
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insilico-bob
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27 classifications="Class $tdir/ROfile.txt.cut row_categorical"
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insilico-bob
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28 fi
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insilico-bob
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29
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insilico-bob
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30 #if col cut was done, add that autogenerated classification
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31 if [ ${13} -gt 1 ]
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insilico-bob
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32 then
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33 classifications="$classifications Class $tdir/COfile.txt.cut col_categorical"
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34 fi
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35
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36 #now add the user provided classification files
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37 for i in "$@"; do
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insilico-bob
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38 if [ $count -gt 14 ]
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39 then
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40 classifications=$classifications' '$i
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insilico-bob
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41 fi
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insilico-bob
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42 count=$((count+1))
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insilico-bob
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43 done
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insilico-bob
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44 #call java program to generate NGCHM viewer files.
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insilico-bob
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45 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} $classifications
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insilico-bob
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46 #clean up tempdir
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insilico-bob
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47 rm -rf $tdir