## ----echo = FALSE------------------------------------------------------------- knitr::opts_chunk$set( eval=FALSE ) ## ----setup-------------------------------------------------------------------- # # suppressPackageStartupMessages(library(dplyr)) # # suppressPackageStartupMessages(library(RCy3)) # # suppressPackageStartupMessages(library(KEGGREST)) # # Sys.setenv(LANGUAGE="en_US.UTF-8") # library(transomics2cytoscape) # networkDataDir <- tempfile(); dir.create(networkDataDir) # # networkLayers <- system.file("extdata/usecase1", "yugi2014.tsv", # package = "transomics2cytoscape") # stylexml <- system.file("extdata/usecase1", "yugi2014.xml", # package = "transomics2cytoscape") # suid <- create3Dnetwork(networkDataDir, networkLayers, stylexml) # # layer1to2 <- system.file("extdata/usecase1", "k2e.tsv", # package = "transomics2cytoscape") # suid <- createTransomicEdges(suid, layer1to2) # # layer3to2 <- system.file("extdata/usecase1", "allosteric_ecnumber.tsv", # package = "transomics2cytoscape") # ec2reaction(layer3to2, 6, "allosteric_ec2rea.tsv") # suid <- createTransomicEdges(suid, "allosteric_ec2rea.tsv") ## ----------------------------------------------------------------------------- # ecnum <- system.file("extdata", "allosteric_ecnumber.tsv", # package = "transomics2cytoscape") # ec2reaction(ecnum, 6, "allosteric_ec2rea.tsv") ## ----------------------------------------------------------------------------- # networkDataDir <- tempfile(); dir.create(networkDataDir) # tfs <- system.file("extdata/usecase2", "TFs.sif", # package = "transomics2cytoscape") # file.copy(tfs, networkDataDir) # networkLayers <- system.file("extdata/usecase2", "kokaji2020.tsv", # package = "transomics2cytoscape") # stylexml <- system.file("extdata/usecase2", "Kokaji2020styles.xml", # package = "transomics2cytoscape") # suid <- create3Dnetwork(networkDataDir, networkLayers, stylexml) # # layer1to2 <- system.file("extdata/usecase2", "s2t_name_updated.tsv", # package = "transomics2cytoscape") # suid <- createTransomicEdges(suid, layer1to2) # # layer2to3 <- system.file("extdata/usecase2", "t2e_name_updated.tsv", # package = "transomics2cytoscape") # suid <- createTransomicEdges(suid, layer2to3) # # layer3to4 <- system.file("extdata/usecase2", "e2r_updated.tsv", # package = "transomics2cytoscape") # ec2reaction(layer3to4, 6, "e2r_updated_ec2rea.tsv") # suid <- createTransomicEdges(suid, "e2r_updated_ec2rea.tsv") # # layer5to4 <- system.file("extdata/usecase2", "m2r_updated.tsv", # package = "transomics2cytoscape") # ec2reaction(layer5to4, 6, "m2r_updated_ec2rea.tsv") # suid <- createTransomicEdges(suid, "m2r_updated_ec2rea.tsv") ## ----------------------------------------------------------------------------- # sessionInfo()