psSubpathway (version 0.1.0)

plotheatmap: 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", phentype = "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. Only subpathway with lower fdr are ploted. (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 ploted.when it is negative, plot low-expression subpathways.

phentype

Parameter `phentype` is useful only when `plotSubSEA` is TRUE. `phentype` 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,`phentype="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.

Value

a heatmap

Details

plotheatmap

plot a subpathway heat map according to the user's set conditions.

Examples

# NOT RUN {
# 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",phentype="all")
# plot significant down-regulation subpathway heat map specific for each breast cancer subtype.
plotheatmap(Subspwresult,plotSubSEA=TRUE,fdr.th=0.01,SES="negative",phentype="all")
# plot basal subtype specific significant subpathway heat map.
plotheatmap(Subspwresult,plotSubSEA=TRUE,fdr.th=0.01,SES="all",phentype="Basal")
# plot adrenocortical cancer disease stages specific significant subpathway heat map.
plotheatmap(DCspwresult,plotSubSEA=FALSE,fdr.th=0.01)
# }