https://github.com/ecell/transomics2cytoscape

Get and integrate the pathways to create a 3D transomics network visualization
https://github.com/ecell/transomics2cytoscape

Last synced: about 2 months ago
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Get and integrate the pathways to create a 3D transomics network visualization

• Host: GitHub
• URL: https://github.com/ecell/transomics2cytoscape
• Owner: ecell
• Created: 2019-10-16T02:41:53.000Z (about 5 years ago)
• Default Branch: devel
• Last Pushed: 2024-10-28T14:21:52.000Z (about 2 months ago)
• Last Synced: 2024-10-28T17:14:48.766Z (about 2 months ago)
• Language: R
• Homepage:
• Size: 58.7 MB
• Stars: 5
• Watchers: 9
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: NEWS

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README

        
# transomics2cytoscape

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8201898.svg)](https://doi.org/10.5281/zenodo.8201898)

[![BioC Release Build Status](http://bioconductor.org/shields/build/release/bioc/transomics2cytoscape.svg)](http://bioconductor.org/checkResults/release/bioc-LATEST/transomics2cytoscape/) - Bioconductor Release Build

[![BioC Dev Build Status](http://bioconductor.org/shields/build/devel/bioc/transomics2cytoscape.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/transomics2cytoscape/) - Bioconductor Dev Build

## 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](https://pubmed.ncbi.nlm.nih.gov/25131207/)

by stacking multiple 2D pathways in a 3D space.

The 3D network visualization was realized by [VANTED](https://www.cls.uni-konstanz.de/software/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](http://apps.cytoscape.org/apps/cy3d), and

[Cytoscape Automation](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1758-4).

## Installation

1. Install Cytoscape from https://cytoscape.org/

2. Install transomics2cytoscape (see https://www.bioconductor.org/packages/release/bioc/html/transomics2cytoscape.html)

## Example

1. Run Cytoscape (If Cytoscape is already running, you don't need to run it anymore. transomics2cytoscape works only when 1 Cytoscape [window] is up.)

2. Run R.

3. Run the following R code. This will import multiple networks and integrate the networks to a 3D space. (This will take a few minutes.)

```R

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)

```

Next Run the following R code. This will add edges between the network layers. (This code execution finishes faster than before.)

```

layer1to2 <- system.file("extdata/usecase1", "k2e.tsv",

                            package = "transomics2cytoscape")

suid <- createTransomicEdges(suid, layer1to2)

layer2to3 <- system.file("extdata/usecase1", "allosteric_ec2rea.tsv", package = "transomics2cytoscape")

suid <- createTransomicEdges(suid, layer2to3)

```

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.)

![allosteric_result](man/figures/yugi2014.png)