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

## -----------------------------------------------------------------------------
#  BiocManager::install("transomics2cytoscape")

## ----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", "yugi2014.tsv",
#      package = "transomics2cytoscape")
#  stylexml <- system.file("extdata", "yugi2014styles.xml",
#      package = "transomics2cytoscape")
#  suid <- create3Dnetwork(networkDataDir, networkLayers, stylexml)
#  
#  layer1to2 <- system.file("extdata", "kinase2enzyme_gene2rea.tsv",
#      package = "transomics2cytoscape")
#  suid <- createTransomicEdges(suid, layer1to2)
#  
#  layer2to3 <- system.file("extdata", "allosteric.tsv",
#      package = "transomics2cytoscape")
#  suid <- createTransomicEdges(suid, layer2to3)

## -----------------------------------------------------------------------------
#  ecnum <- system.file("extdata", "allosteric_ecnumber.tsv",
#      package = "transomics2cytoscape")
#  ec2reaction(ecnum, 8, "allosteric.tsv")