inst/doc/rWikiPathways-and-RCy3.R

In rWikiPathways: rWikiPathways - R client library for the WikiPathways API

## ---- echo = FALSE------------------------------------------------------------
knitr::opts_chunk$set(
  eval=FALSE
)

## -----------------------------------------------------------------------------
#  if(!"rWikiPathways" %in% installed.packages()){
#      if (!requireNamespace("BiocManager", quietly=TRUE))
#          install.packages("BiocManager")
#      BiocManager::install("rWikiPathways")
#  }
#  library(rWikiPathways)
#  if(!"RCy3" %in% installed.packages()){
#      if (!requireNamespace("BiocManager", quietly=TRUE))
#          install.packages("BiocManager")
#      BiocManager::install("RCy3")
#  }
#  library(RCy3)

## -----------------------------------------------------------------------------
#  cytoscapePing()

## -----------------------------------------------------------------------------
#  gbm.pathways <- findPathwaysByText('Glioblastoma') # many pathways returned
#  human.gbm.pathways <- gbm.pathways %>%
#    dplyr::filter(species == "Homo sapiens") # just the human gbm  pathways

## -----------------------------------------------------------------------------
#  human.gbm.wpids <- human.gbm.pathways$id

## -----------------------------------------------------------------------------
#  commandsRun(paste0('wikipathways import-as-pathway id=',human.gbm.wpids[1]))

## -----------------------------------------------------------------------------
#  openSession()
#  net.data <- getTableColumns(columns=c('name','degree.layout','COMMON'))
#  max.gene <- net.data[which.max(unlist(net.data['degree.layout'])),]
#  max.gene

## -----------------------------------------------------------------------------
#  mcm1.pathways <-unique(findPathwayIdsByXref('YMR043W','En'))
#  commandsRun(paste0('wikipathways import-as-pathway id=', mcm1.pathways[1]))

## -----------------------------------------------------------------------------
#  selectNodes('MCM1','name')