Mercurial > repos > md-anderson-bioinformatics > heat_map_creation_advanced

comparison CHM_Advanced.R @ 6:1f13d304ddbd draft

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author insilico-bob
date Thu, 20 Jun 2019 11:36:53 -0400
parents 8893ea2915cc
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5:15c71ed09efa 6:1f13d304ddbd
15 ### rowCut - For rows the number of classifications to automatically generate based on dendrogram into a classification file. 0 for turned off. 15 ### rowCut - For rows the number of classifications to automatically generate based on dendrogram into a classification file. 0 for turned off.
16 ### colCut - For columns the number of classifications to automatically generate based on dendrogram into a classification file. 0 for turned off. 16 ### colCut - For columns the number of classifications to automatically generate based on dendrogram into a classification file. 0 for turned off.
17 17
18 performDataOrdering<-function(dataFile, rowOrderMethod, rowDistanceMeasure, rowAgglomerationMethod, colOrderMethod, colDistanceMeasure, colAgglomerationMethod,rowOrderFile, colOrderFile, rowDendroFile, colDendroFile, rowCut, colCut) 18 performDataOrdering<-function(dataFile, rowOrderMethod, rowDistanceMeasure, rowAgglomerationMethod, colOrderMethod, colDistanceMeasure, colAgglomerationMethod,rowOrderFile, colOrderFile, rowDendroFile, colDendroFile, rowCut, colCut)
19 { 19 {
20 dataMatrix = read.table(dataFile, header=TRUE, sep = "\t", row.names = 1, as.is=TRUE, na.strings=c("NA","N/A","-","?")) 20 dataMatrix = read.table(dataFile, header=TRUE, sep = "\t", check.names = FALSE, row.names = 1, as.is=TRUE, na.strings=c("NA","N/A","-","?"))
21 rowOrder <- createOrdering(dataMatrix, rowOrderMethod, "row", rowDistanceMeasure, rowAgglomerationMethod) 21 rowOrder <- createOrdering(dataMatrix, rowOrderMethod, "row", rowDistanceMeasure, rowAgglomerationMethod)
22 if (rowOrderMethod == "Hierarchical") { 22 if (rowOrderMethod == "Hierarchical") {
23 writeHCDataTSVs(rowOrder, rowDendroFile, rowOrderFile) 23 writeHCDataTSVs(rowOrder, rowDendroFile, rowOrderFile)
24 if (rowCut != 0) { 24 if (rowCut != 0) {
25 writeHCCut(rowOrder, rowCut, paste(rowOrderFile,".cut", sep="")) 25 writeHCCut(rowOrder, rowCut, paste(rowOrderFile,".cut", sep=""))