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# transomics2cytoscape [![DOI](]( [![BioC Release Build Status](]( - Bioconductor Release Build [![BioC Dev Build Status](]( - 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]( 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 1. Install Cytoscape from 2. Install transomics2cytoscape (see ## 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)