comparison CHM.R @ 32:16593e40c2cd draft

Version 2.0.5

31:e01b833f5d43

{ 
   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)
      writeHCCut(rowOrder, rowCut, paste(rowOrderFile,".cut", sep=""))
   } else {
      writeOrderTSV(rowOrder, rownames(dataMatrix), rowOrderFile)
   }

   colOrder <-  createOrdering(dataMatrix, colOrderMethod, "col", colDistanceMeasure, colAgglomerationMethod)  
   if (colOrderMethod == "Hierarchical") {
      writeHCDataTSVs(colOrder, colDendroFile, colOrderFile)
      writeHCCut(colOrder, colCut, paste(colOrderFile,".cut", sep=""))
   } else {
      writeOrderTSV(colOrder, colnames(dataMatrix), colOrderFile)
   }
}

#creates output files for hclust ordering
writeHCDataTSVs<-function(uDend, outputHCDataFileName, outputHCOrderFileName)

 
   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)
}

#creates order file for non-clustering methods
writeOrderTSV<-function(newOrder, originalOrder, outputHCOrderFileName)
{
   data=matrix(,length(originalOrder),2);
   for (i in 1:length(originalOrder)) {
      data[i,1] = originalOrder[i];
      data[i,2] = which(newOrder==originalOrder[i]);
   }
   colnames(data)<-c("Id", "Order")
   write.table(data, file = outputHCOrderFileName, append = FALSE, quote = FALSE, sep = "\t", row.names=FALSE)
}

32:16593e40c2cd

{ 
   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)
   }

   colOrder <-  createOrdering(dataMatrix, colOrderMethod, "col", colDistanceMeasure, colAgglomerationMethod)  
   if (colOrderMethod == "Hierarchical") {
      writeHCDataTSVs(colOrder, colDendroFile, colOrderFile)
      writeHCCut(colOrder, colCut, paste(colOrderFile,".cut", sep=""))
   }
}

#creates output files for hclust ordering
writeHCDataTSVs<-function(uDend, outputHCDataFileName, outputHCOrderFileName)

 
   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)
}