dseaPlotActmap: Plot drug Activity Map

In bigomics/SPACEconnect: Stratified Perturbation Analysis by Correlation Enrichment of connectivity

Plot drug Activity Map

Description

Plot drug Activity Map

Usage

dseaPlotActmap(dsea, drugs, method = "GSEA", contr, nterms = 50, nfc = 20)

Arguments

dsea	drugs set enrichment analysis object as output of getActiveDSEA
drugs	a list of drugs enrichment stats and annotations the output of computePeturbEnrichment()
method	the computation methods of Enrichment, either using GSEA algorithm or the rank correlation.
contr	is a character string represent the two compared conditions(contrast) as it is provided from the fold-change matrix
nterms	integer
nfc	integer

Value

plot of drug activity map

Examples

# from the data-sets provided as examples within the package load the .rda files
#DrugsAnnot, mDrugEnrich, mFC
dsea = getActiveDSEA(mDrugEnrich, DrugsAnnot, mFC, contr = colnames(mFC)[1])
drugs= computePeturbEnrichment(mFC = mFC, mDrugEnrich = mDrugEnrich, DrugsAnnot = DrugsAnnot,
methods = "GSEA", nprune = 250, contrast = NULL)
dseaPlotActmap (dsea, drugs, method = "GSEA", contr=colnames(mFC)[1], nterms = 50, nfc=20)

bigomics/SPACEconnect documentation built on March 19, 2022, 3:39 a.m.