## ---- echo = FALSE--------------------------------------------------------- knitr::opts_chunk$set( eval=FALSE ) ## ----setup, include=FALSE-------------------------------------------------- # knitr::opts_chunk$set(echo = TRUE) ## -------------------------------------------------------------------------- # if(!"RCy3" %in% installed.packages()){ # install.packages("BiocManager") # BiocManager::install("RCy3") # } # library(RCy3) ## -------------------------------------------------------------------------- # installApp('STRINGapp') ## -------------------------------------------------------------------------- # string.cmd = 'string disease query disease="breast cancer"' # commandsRun(string.cmd) # string.net<-getNetworkSuid() #grab handle on network for future reference ## -------------------------------------------------------------------------- # createDegreeFilter('degree filter', c(0,2), 'IS_NOT_BETWEEN') ## -------------------------------------------------------------------------- # createSubnetwork(subnetwork.name ='Breast cancer: highly connected nodes') ## -------------------------------------------------------------------------- # createColumnFilter(filter.name='disease score filter', column='disease score', 4, 'GREATER_THAN', network = string.net) ## -------------------------------------------------------------------------- # createSubnetwork(subnetwork.name ='Breast cancer: high disease score') ## -------------------------------------------------------------------------- # createCompositeFilter('combined filter', c('degree filter','disease score filter'), network = string.net) # createSubnetwork(subnetwork.name ='final subnetwork') ## -------------------------------------------------------------------------- # layoutNetwork('force-directed defaultSpringCoefficient=5E-6') ## -------------------------------------------------------------------------- # applyFilter('combined filter', hide=TRUE, network = string.net)