README.md

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

transomics2cytoscape

Introduction

Visualization of trans-omic networks helps biological interpretation by illustrating pathways where the signals are transmitted.

To characterize signals that go across multiple omic layers, Yugi and colleagues have proposed a method for network visualization by stacking multiple 2D pathways in a 3D space.

The 3D network visualization was realized by VANTED. However, the visualization relies on time-consuming manual operation. Here we propose transomics2cytoscape, an R package that automatically creates 3D network visualization in combination with Cytoscape, Cy3D App, and Cytoscape Automation.

Installation

install.packages("devtools")
devtools::install_github("ecell/transomics2cytoscape")

and also you need to install Cytoscape.

Example

1. Run Cytoscape Desktop
2. Run R[Studio].
3. Run the following R code. This will import multiple networks and integrate the networks to a 3D space.

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)

Then, you should have a 3D view with layered networks and transomic interactions between them. (Note that you need to perform operations such as zooming out or adjusting the camera angle.)

Please see ./vignettes/transomics2cytoscape.Rmd for more information.

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