plotSubSEScurve: Plot subtype set sample enrichment score curve graph

In psSubpathway: Flexible Identification of Phenotype-Specific Subpathways

Plot subtype set sample enrichment score curve graph

Description

Draw a sample enrichment score curve graph of a single or all subtypes.

Usage

plotSubSEScurve(inputdata, spwid = "", phenotype = "all")

Arguments

inputdata	A list of result data generated by function 'SubSEA' or 'DCSA'.
spwid	The subpathway id which the user wants to plot.
phenotype	The 'phenotype“ specifies which phenotypic phenotype set enrichment curve is drawn for subpathway. When 'phenotype="all"' (default), the phenotype set enrichment score curve graph of subpathway under all phenotypes is drawn.

Details

plotSubSEScurve

Plot a phenotype set enrichment score curve graph of a subpathway under all phenotypes or specified phenotype, including the location of the maximum enrichment score (ES) and the leading-edge subset. This function can only be used for the results of the 'SubSEA' function.

Value

a plot

an enrichment score curve graph

Author(s)

Xudong Han, Junwei Han, Qingfei Kong

Examples

# get the results of the SubSEA function for breast cancer subtypes.
Subspwresult<-get("Subspwresult")
# plot enrichment score curve of the subpathway 00120_9 in all breast cancer subtypes.
plotSubSEScurve(Subspwresult,spwid="00120_9",phenotype="all")
# plot enrichment score curve of the subpathway 00120_9 in the basal breast cancer subtypes.
plotSubSEScurve(Subspwresult,spwid="00120_9",phenotype="Basal")

psSubpathway documentation built on Aug. 9, 2023, 5:09 p.m.