comparison heatmap.sh @ 41:8acca16f3921 draft

Uploaded

40:8f8ab332a050

ctr=0
for i in "$@"; do
	if [ $ctr -gt 1 ]
	then
		currParm=$(cut -d'|' -f1 <<< $i)
		if [ $currParm != "matrix_files" ] && [ $currParm != "row_configuration" ] && [ $currParm != "col_configuration" ] && [ $currParm != "classification" ]
		then
			#Parse pipe-delimited parameter parameter
			parmJson=$parmJson' "'$(cut -d'|' -f1 <<< $i)'":"'$(cut -d'|' -f2 <<< $i)'",'
	  	fi
		if [ $currParm = "row_configuration" ]
		then
			rowOrder=$(cut -d'|' -f3 <<< $i)
			rowDistance=$(cut -d'|' -f5 <<< $i)

	currParm=$(cut -d'|' -f1 <<< $i)
	if [ $currParm = "classification" ]
	then
		classIter=$((classIter+1))
		#Parse pipe-delimited 3-part classification bar parameter
		classJson=$classJson' {"'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'"'
		classCat=$(cut -d'|' -f7 <<< $i)
		classColorType=$(cut -d'_' -f2 <<< $classCat)
		classJson=$classJson','
		classJson=$classJson' "position":"'$(cut -d'_' -f1 <<< $classCat)'","color_map": {"type":"'$classColorType'"}}'
		if [ $classIter -lt $classSize ]		

then
  echo $output;
  if [ `echo "$output" | grep -c "Inf in foreign function call"` -gt 0 ]
  then
    echo "";
    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.";
    echo "This error may also be caused when a covariate file has inadvertently been selected as an Input Matrix.  Check your Input Matrix entry.";
  fi
  exit $rc;
fi

#call java program to generate NGCHM viewer files.

41:8acca16f3921

ctr=0
for i in "$@"; do
	if [ $ctr -gt 1 ]
	then
		currParm=$(cut -d'|' -f1 <<< $i)
		if [ $currParm != "matrix_files" ] && [ $currParm != "row_configuration" ] && [ $currParm != "col_configuration" ] && [ $currParm != "classification" ] && [ $currParm != "chm_name" ]
		then
			#Parse pipe-delimited parameter parameter
			parmJson=$parmJson' "'$(cut -d'|' -f1 <<< $i)'":"'$(cut -d'|' -f2 <<< $i)'",'
	  	fi
		if [ $currParm = "chm_name" ]
		then
			currVal=$(cut -d'|' -f2 <<< $i)
			currEdit=$(echo "$currVal"  | sed 's/\//_/g')		
			parmJson=$parmJson' "'$(cut -d'|' -f1 <<< $i)'":"'$currEdit'",'
	  	fi
		if [ $currParm = "row_configuration" ]
		then
			rowOrder=$(cut -d'|' -f3 <<< $i)
			rowDistance=$(cut -d'|' -f5 <<< $i)

	currParm=$(cut -d'|' -f1 <<< $i)
	if [ $currParm = "classification" ]
	then
		classIter=$((classIter+1))
		#Parse pipe-delimited 3-part classification bar parameter
		className=$(cut -d'|' -f3 <<< $i)
		if [[ -z "$className" ]]; then
		   className="covar"$classIter
		fi
		classJson=$classJson' {"'$(cut -d'|' -f2 <<< $i)'":"'$className'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'"'
		classCat=$(cut -d'|' -f7 <<< $i)
		classColorType=$(cut -d'_' -f2 <<< $classCat)
		classJson=$classJson','
		classJson=$classJson' "position":"'$(cut -d'_' -f1 <<< $classCat)'","color_map": {"type":"'$classColorType'"}}'
		if [ $classIter -lt $classSize ]		

then
  echo $output;
  if [ `echo "$output" | grep -c "Inf in foreign function call"` -gt 0 ]
  then
    echo "";
    echo "R CLUSTERING: Error in clustering the matrix provided (View Details - stdout).   "
    echo "Note: This error can occur when:"
    echo "   1. There is invalid numeric data in the matrix provided. Try using Matrix Manipulation tools to fix invalid data.";
    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.";
    echo "   3. A covariate file has inadvertently been selected as an Input Matrix.  Check your Input Matrix entry.";
  fi
  exit $rc;
fi

#call java program to generate NGCHM viewer files.