## ----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='stringdb::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)