plotEnrichment: Plotting functions for enrichment lists

In epos: Epilepsy Ontologies' Similarities

Plotting functions for enrichment lists

Description

Plotting functions for enrichment lists

Usage

plotEnrichment(enepso, enesso, enepi, enepisem, enfenics, enspace, k)

Arguments

enepso	list with enrichment for EpSO
enesso	list with enrichment for ESSO
enepi	list with enrichment for EPILONT
enepisem	list with enrichment for EPISEM
enfenics	list with enrichment for FENICS
enspace	list with enrichment for the combined ranked list
k	numeric value for the length to be plotted

Value

the plot object

Examples

utils::data(rawDrugNamesCoOcEpSO, package="epos")
utils::data(rawDrugNamesCoOcESSO, package="epos")
utils::data(rawDrugNamesCoOcEPILONT, package="epos")
utils::data(rawDrugNamesCoOcEPISEM, package="epos")
utils::data(rawDrugNamesCoOcFENICS, package="epos")
atchashda <-
    readAtcMapIntoHashMapDrugNamesAtcCodes(
        system.file("extdata", "db-atc.map", package = "epos"), "\t")
epso <- rawDrugNamesCoOcEpSO
neuroepso <- filterNeuroDrugs(epso, atchashda)
esso <- rawDrugNamesCoOcESSO
neuroesso   <- filterNeuroDrugs(esso, atchashda)
epi <- rawDrugNamesCoOcEPILONT
neuroepi    <- filterNeuroDrugs(epi, atchashda)
episem <- rawDrugNamesCoOcEPISEM
neuroepisem <- filterNeuroDrugs(episem, atchashda)
fenics <- rawDrugNamesCoOcFENICS
neurofenics <- filterNeuroDrugs(fenics, atchashda)
mx <- max(
    c(length(neuroepso), length(neuroesso), length(neuroepi),
      length(neuroepisem), length(neurofenics)))
dneuro <-
  data.frame(EpSO = c(neuroepso, rep("", (mx-length(neuroepso)))),
             ESSO = c(neuroesso, rep("", (mx-length(neuroesso)))),
             EPILONT = c(neuroepi, rep("", (mx-length(neuroepi)))),
             EPISEM = c(neuroepisem, rep("", (mx-length(neuroepisem)))),
             FENICS = c(neurofenics, rep("", (mx-length(neurofenics)))))
dneuromaxk <- TopKLists::calculate.maxK(dneuro, L=5, d=5, v=5)
neurospace <- as.character(dneuromaxk$topkspace)
enepso <- calcEnrichment(neuroepso)
enesso <- calcEnrichment(neuroesso)
enepi <- calcEnrichment(neuroepi)
enepisem <- calcEnrichment(neuroepisem)
enfenics <- calcEnrichment(neurofenics)
enspace <- calcEnrichment (neurospace)
p <- plotEnrichment(enepso, enesso, enepi, enepisem, enfenics, enspace, dneuromaxk$maxK)

epos documentation built on May 29, 2024, 3:49 a.m.