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

## -----------------------------------------------------------------------------
# if(!"RCy3" %in% installed.packages()){
#     install.packages("BiocManager")
#     BiocManager::install("RCy3")
# }
# library(RCy3)

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

## -----------------------------------------------------------------------------
# openSession()  #Closes current session (without saving) and opens a sample session file

## -----------------------------------------------------------------------------
# mapped.cols <- mapTableColumn('name','Yeast','Ensembl','Entrez Gene')

## -----------------------------------------------------------------------------
# mapped.cols[1:3,] #first three entries

## -----------------------------------------------------------------------------
# #available in Cytoscape 3.7.0 and above
# installApp('STRINGapp')

## -----------------------------------------------------------------------------
# string.cmd = 'string disease query disease="breast cancer" cutoff=0.9 species="Homo sapiens" limit=150'
# commandsGET(string.cmd)
# 
# # for more information on string commands:
# # commandsHelp('string')
# # commandsHelp('string disease query')

## -----------------------------------------------------------------------------
# mapped.cols <- mapTableColumn('stringdb::canonical name','Human','Uniprot-TrEMBL','Ensembl')

## -----------------------------------------------------------------------------
# #available in Cytoscape 3.7.0 and above
# installApp('WikiPathways')

## -----------------------------------------------------------------------------
# wp.cmd = 'wikipathways import-as-pathway id="WP254"'
# commandsGET(wp.cmd)
# 
# # for more information on wikipathways commands:
# # commandsHelp('wikipathways')
# # commandsHelp('wikipathways import-as-pathway')
# 

## -----------------------------------------------------------------------------
# mapped.cols <- mapTableColumn('XrefId','Human','Entrez Gene','Ensembl')

## -----------------------------------------------------------------------------
# only.mapped.cols <- mapped.cols[complete.cases(mapped.cols), 'Ensembl', drop=FALSE]
# colnames(only.mapped.cols) <- 'XrefId'
# loadTableData(only.mapped.cols,table.key.column = 'SUID')

## -----------------------------------------------------------------------------
# ?mapTableColumn

## -----------------------------------------------------------------------------
# #available in Cytoscape 3.7.0 and above
# installApp('BridgeDb')

## -----------------------------------------------------------------------------
# commandsHelp('bridgedb')