create3Dnetwork: Create 3D network view for transomics visualization.

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

Description

Import multiple KEGG pathways and integrate the pathways into Cy3D renderer

Usage

create3Dnetwork(networkDataDir, networkLayers, transomicEdges, stylexml)

Arguments

networkDataDir	Path of a directory to put the network files of the second column of networkLayers TSV.
networkLayers	Path of a TSV file with the 3 columns (layer index, the network file name in networkDataDir, Z-height of the network).
transomicEdges	Path of a TSV file with the 5 columns (layer index of a source node, name or KEGG object ID that the source node should have, layer index of a target node, name or KEGG object ID that the target node should have, interaction type).
stylexml	Path of a XML file for Cytoscape style

Value

A SUID of the 3D network.

Author(s)

Kozo Nishida

Examples

## Not run: 
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)

## End(Not run)

transomics2cytoscape documentation built on Nov. 8, 2020, 8:14 p.m.