WGCNA_MEs_traitCorrelationHeatmap: Heatmap showing correlation among MEs and traits.

In Tong-Chen/YSX: For Yishengxin Training

Description

Heatmap showing correlation among MEs and traits.

Usage

WGCNA_MEs_traitCorrelationHeatmap(MEs_col, traitData, saveplot = NULL, ...)

Arguments

MEs_col	Module epigenes generated in WGCNA_saveModuleAndMe.
traitData	Sample attributes data frame. Or the "traitData" generated in WGCNA_readindata.
saveplot	Save plot to given file "a.pdf", "b.png".
...	Additional parameters given to plot output (pdf, png,...) like "width", "height", .etc.

Examples

df = generateAbundanceDF(nSample=30, nGrp=3, sd=5)
datExpr <- WGCNA_dataFilter(df)
datExpr <- WGCNA_sampleClusterDetectOutlier(datExpr)
power <- WGCNA_softpower(datExpr)
net <- WGCNA_coexprNetwork(datExpr, power)
WGCNA_saveModuleAndMe(net, datExpr)

#2
exprMat <- "test.file"
wgcnaL <- WGCNA_readindata(exprMat)

traitData <- 'trait.file'
wgcnaL <- WGCNA_readindata(exprMat, traitData)
datExpr <- wgcnaL$datExpr
WGCNA_dataCheck(datExpr)
datExpr <- WGCNA_dataFilter(datExpr)
datExpr <- WGCNA_sampleClusterDetectOutlier(datExpr)
# datExpr <- WGCNA_sampleClusterDetectOutlier(datExpr, traitColors=wgcnaL$traitColors)
power <- WGCNA_softpower(datExpr)
net <- WGCNA_coexprNetwork(datExpr, power)
MEs_col <- WGCNA_saveModuleAndMe(net, datExpr)
WGCNA_MEs_traitCorrelationHeatmap(MEs_col, traitData=wgcnaL$traitData)

Tong-Chen/YSX documentation built on Jan. 25, 2021, 2:49 a.m.