Mercurial > repos > md-anderson-bioinformatics > heat_map_creation

comparison heatmap.sh @ 38:605ec840a06b draft

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author insilico-bob
date Thu, 20 Jun 2019 11:30:12 -0400
parents 58437af2d675
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comparison
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37:f2272e907f1b 38:605ec840a06b
1 #echo $1 $2 $3 $4 $5 $6 $7 $8 $9 ${10} ${11} ${12} ${13} ${14} ${15} ${16} ${17} ${18} 1 #echo "1: " $1" 2: " $2" 3: " $3" 4: "$4" 5: "$5 " 6: "$6 "7: "$7" 8: "$8 " 9: "$9" 10: "${10}" 11: "${11} "12: "${12}
2 #echo " 13: "${13}" 14: "${14}" 15: "${15}" 16: "${16} "17: "${17}" 18: "${18}" 19: "${19}" 20: "${20}" 21: "${21} " 22: "${22}" 23:" ${23}
2 3
3 #get tool data and tool install directories 4 #Count total number of parameters and classification parameters
4 tooldir=$(cut -d';' -f1 <<< ${12}) 5 parmSize=0
5 tooldata=$(cut -d';' -f2 <<< ${12}) 6 classSize=0
7 matrixSize=0
8 for i in "$@"; do
9 currParm=$(cut -d'|' -f1 <<< $i)
10 parmSize=$((parmSize+1))
11 if [ $currParm = "classification" ]
12 then
13 classSize=$((classSize+1))
14 fi
15 done
6 16
17 #Get tool data and tool install directories
18 tooldir=$1
19 tooldata=$2
7 #create temp directory for row and col order and dendro files. 20 #create temp directory for row and col order and dendro files.
8 tdir=$tooldata/$(date +%y%m%d%M%S) 21 tdir=$tooldata/$(date +%y%m%d%M%S)
9 echo $tdir
10 mkdir $tdir 22 mkdir $tdir
23 #echo "tdir: "$tdir
24
25 #Extract parameters for row and column order and dendro files
26 rowOrderFile=$tdir/ROfile.txt
27 rowDendroFile=$tdir/RDfile.txt
28 colOrderFile=$tdir/COfile.txt
29 colDendroFile=$tdir/CDfile.txt
30 rowOrderJson='"order_file": "'$rowOrderFile'",'
31 rowDendroJson='"dendro_file": "'$rowDendroFile'",'
32 colOrderJson='"order_file": "'$colOrderFile'",'
33 colDendroJson='"dendro_file": "'$colDendroFile'",'
34
35 #BEGIN: Construct JSON for all non-repeating parameters
36 parmJson='{'
37 rowConfigJson='"row_configuration": {'
38 colConfigJson='"col_configuration": {'
39
40 ctr=0
41 for i in "$@"; do
42 if [ $ctr -gt 1 ]
43 then
44 currParm=$(cut -d'|' -f1 <<< $i)
45 if [ $currParm != "matrix_files" ] && [ $currParm != "row_configuration" ] && [ $currParm != "col_configuration" ] && [ $currParm != "classification" ]
46 then
47 #Parse pipe-delimited parameter parameter
48 parmJson=$parmJson' "'$(cut -d'|' -f1 <<< $i)'":"'$(cut -d'|' -f2 <<< $i)'",'
49 fi
50 if [ $currParm = "row_configuration" ]
51 then
52 rowOrder=$(cut -d'|' -f3 <<< $i)
53 rowDistance=$(cut -d'|' -f5 <<< $i)
54 rowAgglomeration=$(cut -d'|' -f7 <<< $i)
55 rowCuts=$(cut -d'|' -f9 <<< $i)
56 rowLabels=$(cut -d'|' -f11 <<< $i)
57 dataTypeJson='"'$(cut -d'|' -f10 <<< $i)'":["'$rowLabels'"]'
58 if [ $rowOrder = 'Hierarchical' ]
59 then
60 rowConfigJson=$rowConfigJson$rowOrderJson$rowDendroJson
61 fi
62 rowConfigJson=$rowConfigJson'"'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'","'$(cut -d'|' -f6 <<< $i)'":"'$(cut -d'|' -f7 <<< $i)'",'$dataTypeJson'},'
63 fi
64 if [ $currParm = "col_configuration" ]
65 then
66 colOrder=$(cut -d'|' -f3 <<< $i)
67 colDistance=$(cut -d'|' -f5 <<< $i)
68 colAgglomeration=$(cut -d'|' -f7 <<< $i)
69 colCuts=$(cut -d'|' -f9 <<< $i)
70 colLabels=$(cut -d'|' -f11 <<< $i)
71 dataTypeJson='"'$(cut -d'|' -f10 <<< $i)'":["'$colLabels'"]'
72 if [ $colOrder = 'Hierarchical' ]
73 then
74 colConfigJson=$colConfigJson$colOrderJson$colDendroJson
75 fi
76 colConfigJson=$colConfigJson'"'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'","'$(cut -d'|' -f6 <<< $i)'":"'$(cut -d'|' -f7 <<< $i)'",'$dataTypeJson'},'
77 fi
78 fi
79 ctr=$((ctr+1))
80 done
81 #END: Construct JSON for all non-repeating parameters
82 #echo "rowCuts: "$rowCuts
83 #echo "colCuts: "$colCuts
84 #echo "ROW CONFIG JSON: "$rowConfigJson
85 #echo "COL CONFIG JSON: "$colConfigJson
86
87 #BEGIN: Construct JSON for data layers
88 matrixJson='"matrix_files": [ '
89 inputMatrix=''
90 for i in "$@"; do
91 currParm=$(cut -d'|' -f1 <<< $i)
92 if [ $currParm = "matrix_files" ]
93 then
94 #Parse pipe-delimited parameter parameter
95 matrixJson=$matrixJson' {"'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'","'$(cut -d'|' -f6 <<< $i)'":"'$(cut -d'|' -f7 <<< $i)'"}'
96 inputMatrix=$(cut -d'|' -f3 <<< $i)
97 fi
98 done
99 matrixJson=$matrixJson"],"
100 #END: Construct JSON for data layers
101
102 #BEGIN: Construct JSON for classification files
103 classJson='"classification_files": [ '
104 classIter=0
105 for i in "$@"; do
106 currParm=$(cut -d'|' -f1 <<< $i)
107 if [ $currParm = "classification" ]
108 then
109 classIter=$((classIter+1))
110 #Parse pipe-delimited 3-part classification bar parameter
111 classJson=$classJson' {"'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'"'
112 classCat=$(cut -d'|' -f7 <<< $i)
113 classColorType=$(cut -d'_' -f2 <<< $classCat)
114 classJson=$classJson','
115 classJson=$classJson' "position":"'$(cut -d'_' -f1 <<< $classCat)'","color_map": {"type":"'$classColorType'"}}'
116 if [ $classIter -lt $classSize ]
117 then
118 classJson=$classJson','
119 fi
120 fi
121 done
122 classJson=$classJson']'
123 #END: Construct JSON for classification files
124
125 parmJson=$parmJson$matrixJson$rowConfigJson$colConfigJson$classJson
126 parmJson=$parmJson'}'
127 #echo "HEATMAP PARAMETERS JSON: "$parmJson
11 128
12 #run R to cluster matrix 129 #run R to cluster matrix
13 output="$(R --slave --vanilla --file=$tooldir/CHM.R --args $4 $5 $6 $7 $8 $9 ${10} $tdir/ROfile.txt $tdir/COfile.txt $tdir/RDfile.txt $tdir/CDfile.txt ${13} ${14} ${15} ${16} 2>&1)" 130 output="$(R --slave --vanilla --file=$tooldir/CHM.R --args $inputMatrix $rowOrder $rowDistance $rowAgglomeration $colOrder $colDistance $colAgglomeration $rowOrderFile $colOrderFile $rowDendroFile $colDendroFile $rowCuts $colCuts $rowLabels $colLabels 2>&1)"
14 rc=$?; 131 rc=$?;
15 if [ $rc != 0 ] 132 if [ $rc != 0 ]
16 then 133 then
17 echo $output; 134 echo $output;
18 if [ `echo "$output" | grep -c "Inf in foreign function call"` -gt 0 ] 135 if [ `echo "$output" | grep -c "Inf in foreign function call"` -gt 0 ]
22 echo "This error may also be caused when a covariate file has inadvertently been selected as an Input Matrix. Check your Input Matrix entry."; 139 echo "This error may also be caused when a covariate file has inadvertently been selected as an Input Matrix. Check your Input Matrix entry.";
23 fi 140 fi
24 exit $rc; 141 exit $rc;
25 fi 142 fi
26 143
27 #there are a variable number of triplicate parameters for classification bars
28 count=0
29 classifications=''
30
31 #if row cut was done, add that autogenerated classification
32 if [ ${13} -gt 1 ]
33 then
34 classifications="Class $tdir/ROfile.txt.cut row_categorical"
35 fi
36
37 #if col cut was done, add that autogenerated classification
38 if [ ${14} -gt 1 ]
39 then
40 classifications="$classifications Class $tdir/COfile.txt.cut col_categorical"
41 fi
42
43 #now add the user provided classification files
44 for i in "$@"; do
45 if [ $count -gt 16 ]
46 then
47 classifications=$classifications' '$i
48 fi
49 count=$((count+1))
50 done
51 echo "classifications " $classifications
52 echo "${11} " ${11}
53 #call java program to generate NGCHM viewer files. 144 #call java program to generate NGCHM viewer files.
54 java -jar $tooldir/GalaxyMapGen.jar "${1}" "${2}" "${3}" DataLayer1 $4 linear ${15} ${16} $5 $6 $7 $tdir/ROfile.txt $tdir/RDfile.txt $8 $9 ${10} $tdir/COfile.txt $tdir/CDfile.txt ${11} $classifications 145 java -jar $tooldir/GalaxyMapGen.jar "$parmJson"
55 #clean up tempdir 146 #clean up tempdir
56 rm -rf $tdir 147 rm -rf $tdir