plotheatmap {psSubpathway} | R Documentation |
Plot a heatmap
Description
Plot a heatmap of subpathway activity profile based on the parameters set by the user.
Usage
plotheatmap(
inputdata,
plotSubSEA = TRUE,
fdr.th = 1,
SES = "positive",
phenotype = "all"
)
Arguments
inputdata |
A list of result data generated by function 'SubSEA' or 'DCSA'. |
plotSubSEA |
Determine the inputdata is the result data of function 'SubSEA' (default:plotSubSEA=TRUE) or 'DCSA' (plotSubSEA=FLASE). |
fdr.th |
Cutoff value for FDR. The only subpathway with lower FDR is plotted. (default: 1). |
SES |
Parameter 'SES' is useful only when 'plotSubSEA' is TRUE. When 'plotSubSEA=TRUE',if 'SES' is positive, the subpathway with high-expression will be plotted. when it is negative, plot low-expression subpathways. |
phenotype |
Parameter 'phenotype' is useful only when 'plotSubSEA' is TRUE. 'phenotype' decides which phenotypic significant subpathways to screen (which phenotypic result is applied to parameter 'fdr.th' and 'SES'.) and plot a heat map of these subpathways.By default,'phenotype="all"' which will screen the subpathways of all phenotypes and plot a heat map. When the user wants to plot a subpathway heat map of the specified phenotype, this parameter should be set to the name of the phenotype. |
Details
plotheatmap
The subpathways are screened according to the conditions set by the user and a heat map of the activity of these subpathways is drawn.
Value
a heatmap
Author(s)
Xudong Han, Junwei Han, Qingfei Kong
Examples
# load depend package.
library(pheatmap)
# get the Subspwresult which is the result of SubSEA function.
Subspwresult<-get("Subspwresult")
# get the DCspwresult which is the result of DCSA function.
DCspwresult<-get("DCspwresult")
# plot significant up-regulation subpathway heat map specific for each breast cancer subtype.
plotheatmap(Subspwresult,plotSubSEA=TRUE,fdr.th=0.01,SES="positive",phenotype="all")
# plot significant down-regulation subpathway heat map specific for each breast cancer subtype.
plotheatmap(Subspwresult,plotSubSEA=TRUE,fdr.th=0.01,SES="negative",phenotype="all")
# plot basal subtype specific significant subpathway heat map.
plotheatmap(Subspwresult,plotSubSEA=TRUE,fdr.th=0.01,SES="all",phenotype="Basal")
# plot adrenocortical cancer disease stages specific significant subpathway heat map.
plotheatmap(DCspwresult,plotSubSEA=FALSE,fdr.th=0.01)