Mercurial > repos > md-anderson-bioinformatics > heat_map_creation_advanced
comparison CHM_Advanced.R @ 6:1f13d304ddbd draft
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author | insilico-bob |
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date | Thu, 20 Jun 2019 11:36:53 -0400 |
parents | 8893ea2915cc |
children |
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5:15c71ed09efa | 6:1f13d304ddbd |
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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="")) |