comparison CHM.R @ 38:605ec840a06b draft

Uploaded

37:f2272e907f1b

### rowCut - For rows the number of classifications to automatically generate based on dendrogram into a classification file.  0 for turned off.
### colCut - For columns the number of classifications to automatically generate based on dendrogram into a classification file.  0 for turned off.

performDataOrdering<-function(dataFile, rowOrderMethod, rowDistanceMeasure, rowAgglomerationMethod, colOrderMethod, colDistanceMeasure, colAgglomerationMethod,rowOrderFile, colOrderFile, rowDendroFile, colDendroFile, rowCut, colCut)
{ 
   dataMatrix = read.table(dataFile, header=TRUE, sep = "\t", row.names = 1, as.is=TRUE, na.strings=c("NA","N/A","-","?"))
   rowOrder <-  createOrdering(dataMatrix, rowOrderMethod, "row", rowDistanceMeasure, rowAgglomerationMethod)  
   if (rowOrderMethod == "Hierarchical") {
      writeHCDataTSVs(rowOrder, rowDendroFile, rowOrderFile)
   }

   colnames(data)<-c("A", "B", "Height")
   write.table(data, file = outputHCDataFileName, append = FALSE, quote = FALSE, sep = "\t", row.names=FALSE)
 
   data=matrix(,length(uDend$labels),2);
   for (i in 1:length(uDend$labels)) {
      data[i,1] = uDend$labels[i];
      data[i,2] = which(uDend$order==i);
   }
   colnames(data)<-c("Id", "Order")
   write.table(data, file = outputHCOrderFileName, append = FALSE, quote = FALSE, sep = "\t", row.names=FALSE)

38:605ec840a06b

### rowCut - For rows the number of classifications to automatically generate based on dendrogram into a classification file.  0 for turned off.
### colCut - For columns the number of classifications to automatically generate based on dendrogram into a classification file.  0 for turned off.

performDataOrdering<-function(dataFile, rowOrderMethod, rowDistanceMeasure, rowAgglomerationMethod, colOrderMethod, colDistanceMeasure, colAgglomerationMethod,rowOrderFile, colOrderFile, rowDendroFile, colDendroFile, rowCut, colCut)
{ 
   dataMatrix = read.table(dataFile, header=TRUE, sep = "\t", check.names = FALSE, row.names = 1, as.is=TRUE, na.strings=c("NA","N/A","-","?"))
   rowOrder <-  createOrdering(dataMatrix, rowOrderMethod, "row", rowDistanceMeasure, rowAgglomerationMethod)  
   if (rowOrderMethod == "Hierarchical") {
      writeHCDataTSVs(rowOrder, rowDendroFile, rowOrderFile)
   }

   colnames(data)<-c("A", "B", "Height")
   write.table(data, file = outputHCDataFileName, append = FALSE, quote = FALSE, sep = "\t", row.names=FALSE)
 
   data=matrix(,length(uDend$labels),2);
   for (i in 1:length(uDend$labels)) {
   	  print(uDend$labels[i])
      data[i,1] = uDend$labels[i];
      data[i,2] = which(uDend$order==i);
   }
   colnames(data)<-c("Id", "Order")
   write.table(data, file = outputHCOrderFileName, append = FALSE, quote = FALSE, sep = "\t", row.names=FALSE)