WGCNA_ModuleGeneTraitHeatmap: Plot gene module relationship and correlation with traits.

In Tong-Chen/YSX: For Yishengxin Training

Description

Plot gene module relationship and correlation with traits.

Usage

WGCNA_ModuleGeneTraitHeatmap(
  datExpr,
  traitData = NULL,
  net,
  corType = "bicor",
  prefix = "ehbio",
  saveplot = NULL,
  ...
)

Arguments

datExpr	Expression data. A matrix (preferred) or data frame in which columns are genes and rows ar samples. NAs are allowed, but not too many. See checkMissingData below and details.
traitData	Sample attributes data frame. Or the "traitData" generated in WGCNA_readindata.
net	WGCNA_coexprNetwork or blockwiseModules returned WGCNA object.
corType	character string specifying the correlation to be used. Allowed values are (unique abbreviations of) "pearson" and "bicor", corresponding to Pearson and bidweight midcorrelation, respectively. Missing values are handled using the pairwise.complete.obs option.
prefix	prefix for output files.
saveplot	Save plot to given file "a.pdf", "b.png".
...	Additional parameters given to plot output (pdf, png,...) like "width", "height", .etc.

Value

A dataframe geneTraitCor

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)
cyt <- WGCNA_cytoscape(net, power, datExpr)
hubgene <- WGCNA_hubgene(cyt)

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

traitData <- 'trait.file'
wgcnaL <- WGCNA_readindata(exprMat, traitData)
datExpr <- wgcnaL$datExpr
traitData <- wgcnaL$traitData
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=traitData)
cyt <- WGCNA_cytoscape(net, power, datExpr)
hubgene <- WGCNA_hubgene(cyt)
WGCNA_moduleTraitPlot(MEs_col, traitData=traitData)
geneTraitCor <- WGCNA_ModuleGeneTraitHeatmap(datExpr, traitData, net)

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