diff heatmap_advanced.sh @ 1:603f99d9e776 draft

Version 2.2.1 embedded viewer

--- a/heatmap_advanced.sh	Tue Aug 08 14:01:05 2017 -0400
+++ b/heatmap_advanced.sh	Tue Dec 05 14:59:26 2017 -0500
@@ -1,21 +1,35 @@
-echo $1 $2 $3 $4 $5 $6 $7 $8 $9 ${10} ${11} ${12} ${13} ${14} ${15} ${16} ${17} ${18} ${19}
-
-#run python to validate the input matrix and covariate files (if any)
-#output="$(python  ${11}/mda_heatmap_gen.py $@)"
-output=$(python  ${11}/mda_heatmap_gen.py "$@")
-rc=$?;
-echo $output;
-if [ $rc != 0 ]
-then
-  exit $rc;
-fi
+#echo "1: " $1 
+#echo "2: " $2 
+#echo "3: " $3 
+#echo "4: " $4 
+#echo "5: " $5 
+#echo "6: " $6 
+#echo "7: " $7 
+#echo "8: " $8 
+#echo "9: " $9 
+#echo "10: " ${10} 
+#echo "11: " ${11}  
+#echo "12: " ${12} 
+#echo "13: " ${13} 
+#echo "14: " ${14}  
+#echo "15: " ${15}  
+#echo "16: " ${16}  
+#echo "17: " ${17}  
+#echo "18: " ${18} 
+#echo "19: " ${19} 
+#echo "20: " ${20} 
+#echo "21: " ${21} 
+#echo "22: " ${22} 
+#echo "23: " ${23} 
+#echo "23: " ${24} 
+#echo $1 $2 $3 $4 $5 $6 $7 $8 $9 ${10} ${11} ${12} ${13} ${14} ${15} ${16} ${17} ${18} ${19} ${20} ${21} ${22} ${23}
 
 #create temp directory for row and col order and dendro files.
-tdir=${11}/$(date +%y%m%d%M%S)
+tdir=${12}/$(date +%y%m%d%M%S)
 echo $tdir
 mkdir $tdir
 #run R to cluster matrix
-output="$(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} ${15} 2>&1)"
+output="$(R --slave --vanilla --file=${12}/CHM_Advanced.R --args $4 $5 $6 $7 $8 $9 ${10} $tdir/ROfile.txt $tdir/COfile.txt $tdir/RDfile.txt $tdir/CDfile.txt ${13} ${14} ${15} ${16} 2>&1)"
 rc=$?;
 if [ $rc != 0 ]
 then
@@ -24,35 +38,39 @@
   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
-
+ 
 #there are a variable number of triplicate parameters for classification bars
 count=0
 classifications=''
 
 #if row cut was done, add that autogenerated classification
-if [ ${12} -gt 1 ]
+if [ ${13} -gt 1 ]
 then
-  classifications="Class $tdir/ROfile.txt.cut row_categorical"
+  classifications="Class $tdir/ROfile.txt.cut row_categorical color_plot"
 fi
 
 #if col cut was done, add that autogenerated classification
-if [ ${13} -gt 1 ]
+if [ ${14} -gt 1 ]
 then
-  classifications="$classifications Class $tdir/COfile.txt.cut col_categorical"
+  classifications="$classifications Class $tdir/COfile.txt.cut col_categorical  color_plot"
 fi
 
 #now add the user provided classification files 
 for i in "$@"; do
-  if [ $count -gt 15 ]
+  if [ $count -gt 20 ]
   then
+#    echo "class entry: " $i
     classifications=$classifications' '$i
   fi
   count=$((count+1))
 done
+#echo "classifications: " $classifications
+
 #call java program to generate NGCHM viewer files.
-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
+java -jar ${12}/GalaxyMapGen.jar "${1}" "${2}" "${3}" DataLayer1 $4 linear ${15} ${16} $5 $6 $7 $tdir/ROfile.txt $tdir/RDfile.txt "${17}" "${19}" $8 $9 ${10} $tdir/COfile.txt $tdir/CDfile.txt "${18}" "${20}" ${11} "${21}" $classifications  
 #clean up tempdir
 rm -rf $tdir