inst/doc/transomics2cytoscape.R

In transomics2cytoscape: A tool set for 3D Trans-Omic network visualization with Cytoscape

## ---- 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)
#  sif <- system.file("extdata","galFiltered.sif",package="RCy3")
#  file.copy(sif, networkDataDir)
#  networkLayers <- system.file("extdata", "networkLayers.tsv",
#      package = "transomics2cytoscape")
#  transomicEdges <- system.file("extdata", "transomicEdges.tsv",
#      package = "transomics2cytoscape")
#  stylexml <- system.file("extdata", "transomics.xml",
#      package = "transomics2cytoscape")
#  create3Dnetwork(networkDataDir, networkLayers, transomicEdges, stylexml)

## ----sessionInfo, echo=FALSE--------------------------------------------------
#  sessionInfo()