Mercurial > repos > md-anderson-bioinformatics > heat_map_creation_advanced

comparison heatmap_advanced.sh @ 7:c5489978071a draft

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Uploaded
author insilico-bob
date Tue, 28 Jan 2020 15:33:09 -0500
parents 1f13d304ddbd
children c1be063b2454
comparison
equal deleted inserted replaced
6:1f13d304ddbd 7:c5489978071a
57 ctr=0 57 ctr=0
58 for i in "$@"; do 58 for i in "$@"; do
59 if [ $ctr -gt 1 ] 59 if [ $ctr -gt 1 ]
60 then 60 then
61 currParm=$(cut -d'|' -f1 <<< $i) 61 currParm=$(cut -d'|' -f1 <<< $i)
62 if [ $currParm != "matrix_files" ] && [ $currParm != "row_configuration" ] && [ $currParm != "col_configuration" ] && [ $currParm != "classification" ] && [ $currParm != "attribute" ] 62 if [ $currParm != "matrix_files" ] && [ $currParm != "row_configuration" ] && [ $currParm != "col_configuration" ] && [ $currParm != "classification" ] && [ $currParm != "attribute" ] && [ $currParm != "chm_name" ]
63 then 63 then
64 #Parse pipe-delimited parameter parameter 64 #Parse pipe-delimited parameter parameter
65 parmJson=$parmJson' "'$(cut -d'|' -f1 <<< $i)'":"'$(cut -d'|' -f2 <<< $i)'",' 65 parmJson=$parmJson' "'$(cut -d'|' -f1 <<< $i)'":"'$(cut -d'|' -f2 <<< $i)'",'
66 fi
67 if [ $currParm = "chm_name" ]
68 then
69 currVal=$(cut -d'|' -f2 <<< $i)
70 currEdit=$(echo "$currVal" | sed 's/\//_/g')
71 parmJson=$parmJson' "'$(cut -d'|' -f1 <<< $i)'":"'$currEdit'",'
66 fi 72 fi
67 if [ $currParm = "row_configuration" ] 73 if [ $currParm = "row_configuration" ]
68 then 74 then
69 rowOrder=$(cut -d'|' -f3 <<< $i) 75 rowOrder=$(cut -d'|' -f3 <<< $i)
70 rowDistance=$(cut -d'|' -f5 <<< $i) 76 rowDistance=$(cut -d'|' -f5 <<< $i)
316 if [ $currParm = "classification" ] 322 if [ $currParm = "classification" ]
317 then 323 then
318 classIter=$((classIter+1)) 324 classIter=$((classIter+1))
319 className=$(cut -d'|' -f3 <<< $i) 325 className=$(cut -d'|' -f3 <<< $i)
320 #Parse pipe-delimited 3-part classification bar parameter 326 #Parse pipe-delimited 3-part classification bar parameter
321 classJson=$classJson' {"'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'","'$(cut -d'|' -f8 <<< $i)'":"'$(cut -d'|' -f9 <<< $i)'","'$(cut -d'|' -f12 <<< $i)'":"'$(cut -d'|' -f13 <<< $i)'","'$(cut -d'|' -f14 <<< $i)'":"'$(cut -d'|' -f15 <<< $i)'"' 327 if [[ -z "$className" ]]; then
328 className="covar"$classIter
329 fi
330 classJson=$classJson' {"'$(cut -d'|' -f2 <<< $i)'":"'$className'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'","'$(cut -d'|' -f8 <<< $i)'":"'$(cut -d'|' -f9 <<< $i)'","'$(cut -d'|' -f12 <<< $i)'":"'$(cut -d'|' -f13 <<< $i)'","'$(cut -d'|' -f14 <<< $i)'":"'$(cut -d'|' -f15 <<< $i)'"'
322 classCat=$(cut -d'|' -f7 <<< $i) 331 classCat=$(cut -d'|' -f7 <<< $i)
323 classColorType=$(cut -d'_' -f2 <<< $classCat) 332 classColorType=$(cut -d'_' -f2 <<< $classCat)
324 classJson=$classJson',' 333 classJson=$classJson','
325 classHeight=$(cut -d'|' -f11 <<< $i) 334 classHeight=$(cut -d'|' -f11 <<< $i)
326 heightErrorVal=0 335 heightErrorVal=0
355 then 364 then
356 echo $output; 365 echo $output;
357 if [ `echo "$output" | grep -c "Inf in foreign function call"` -gt 0 ] 366 if [ `echo "$output" | grep -c "Inf in foreign function call"` -gt 0 ]
358 then 367 then
359 echo ""; 368 echo "";
360 echo "NOTE 1: This error can occur when a covariate file has inadvertently been selected as an Input Matrix. Check your Input Matrix entry."; 369 echo "";
361 echo "NOTE 2: This error can occur when there is no variation in a data rows or columns in the input matrix. Try a different distance measure or remove rows/columns without variation."; 370 echo "R CLUSTERING: Error in clustering the matrix provided (View Details stdout). "
371 echo "Note: This error can occur when:"
372 echo " 1. There is invalid numeric data in the matrix provided. Try using Matrix Manipulation tools to fix invalid data.";
373 echo " 2. There is no variation in a row or column in the matrix. Try a different distance measure or remove rows/columns without variation using Matrix Manipulation tools.";
374 echo " 3. A covariate file has inadvertently been selected as an Input Matrix. Check your Input Matrix entry.";
362 fi 375 fi
363 exit $rc; 376 exit $rc;
364 fi 377 fi
365 378
366 #Call java program to generate NGCHM viewer files. 379 #Call java program to generate NGCHM viewer files.