DE_heatmap: Plot differentially expressed genes with a heatmap

In kmuench/DESeqAid: DESeqAid: Kristin's favorite functions for her DESeq-based differential expression pipelines

Description

This function makes a pretty heatmap illustrating how your genes are clustering.

Usage

DE_heatmap(rawCounts, sampleTable, factorsToPlot, sampleTableNameCol,
  myWidth, myHeight, myFilename, myColors, myAnnotationColors,
  rowsplit = NULL)

Arguments

rawCounts	A dataframe representing counts in your dataset. Could be normalized (rlog(DESeqobject)) or not (counts(DESeqObject))
sampleTable	Sample table used to import data in DESeq's DESeqDataSetFromHTSeqCount function
factorsToPlot	character list of sampleTable column names you want to plot alongside heatmap
sampleTableNameCol	the column of sampleTable with the sample names you want plotted. MUST MATCH COLNAMES OF rawCounts
myWidth	Width of svg output in inches
myHeight	Height of svg output in inches
myFilename	Name of svg file output
myColors	Color brewer palatte, or character vector of colors. This feeds into "colors" flag of pheatmap. Check out RColorBrewer for more colors
rowsplit	If you want clustering, indicate a number where you want the split to occur in the rows

Examples

DE_heatmap(myData_moduleGenes, sampleTable_plus, c('Genotype', 'PCR_integration', 'plas_backbone', 'plas_shp', 'transcripts_shp'), 
'DESeqAnalysisID', 30,15, 'Expression_YlOrRed.png', myColors =  colorRampPalette(rev(brewer.pal(n = 7, name = "YlOrRd")))(100))

kmuench/DESeqAid documentation built on Oct. 14, 2020, 4:45 a.m.