WGCNA_moduleTraitPlot: Module-trait heatmap

In Tong-Chen/YSX: For Yishengxin Training

Description

Module-trait heatmap

Usage

WGCNA_moduleTraitPlot(
  MEs_col,
  traitData = NULL,
  corType = "bicor",
  saveplot = NULL,
  prefix = "ehbio",
  angle_x = 90,
  up_color = c("red", "white", "blue"),
  down_color = c("green", "white"),
  ...
)

Arguments

MEs_col	Module epigenes generated in WGCNA_saveModuleAndMe.
traitData	Sample attributes data frame. Or the "traitData" generated in WGCNA_readindata.
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.
saveplot	Save plot to given file "a.pdf", "b.png".
prefix	prefix for output files.
angle_x	Rotation angle for x-axis labels
up_color	Vector of colours to use for upper triangles (which representing pearson correlations values).
down_color	Vector of colours to use for lower triangles (which representing significance p-values).
...	Additional parameters given to plot output (pdf, png,...) like "width", "height", .etc.

Value

A dataframe.

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)

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