| plotSubSEScurve {psSubpathway} | R Documentation |
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")