createTanimotoBaseline: Creates the plot for all jaccard coefficients amongst the...

In epos: Epilepsy Ontologies' Similarities

Description

Creates the plot for all jaccard coefficients amongst the three epilepsy ontologies

Usage

createTanimotoBaseline(neuroepso, neuroesso, neuroepi, dneuromaxk)

Arguments

neuroepso	list of neuro drug names co-occurring with epso
neuroesso	list of neuro drug names co-occurring with esso
neuroepi	list of neuro drug names co-occurring with epi
dneuromaxk	object returned from TopKLists::calculate.maxk

Value

jaccardepilepsyplot the ggplot object

Examples

utils::data(rawDrugNamesCoOcEpSO, package="epos")
utils::data(rawDrugNamesCoOcESSO, package="epos")
utils::data(rawDrugNamesCoOcEPILONT, package="epos")
utils::data(rawDrugNamesCoOcEPISEM, package="epos")
atchashda <-
  readAtcMapIntoHashMapDrugNamesAtcCodes(
    system.file("extdata", "db-atc.map", package = "epos"), "\t")
atchashaa <-
  readAtcMapIntoHashMapAtcCodesAtcNames(
    system.file("extdata", "db-atc.map", package = "epos"), "\t")
atchashsec <-
  readSecondLevelATC(
    system.file("extdata", "atc-secondlevel.map", package = "epos"), "\t")
tepso <- rawDrugNamesCoOcEpSO
tesso <- rawDrugNamesCoOcESSO
tepi <- rawDrugNamesCoOcEPILONT
tepisem <- rawDrugNamesCoOcEPISEM
tfenics <- rawDrugNamesCoOcFENICS

neuroepso <- filterNeuroDrugs(tepso, atchashda)
neuroesso <- filterNeuroDrugs(tesso, atchashda)
neuroepi <- filterNeuroDrugs(tepi, atchashda)
neuroepisem <- filterNeuroDrugs(tepisem, atchashda)
neurofenics <- filterNeuroDrugs(tfenics, atchashda)

dneuro <-
  data.frame(EpSO = neuroepso[1:210],
             ESSO = neuroesso[1:210],
             EPILONT = neuroepi[1:210],
             EPISEM = neuroepisem[1:210],
             FENICS = neurofenics[1:210])
dneuromaxk <- TopKLists::calculate.maxK(dneuro, 5, 5, 5)
tanimotobaseline <- createTanimotoBaseline(neuroepso, neuroesso, neuroepi, dneuromaxk)

epos documentation built on Feb. 20, 2021, 9:09 a.m.