## ---- 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')