Network diffusion analysis

Expand node selection using network propagation algorithms generating the expanded network for a core of genes and the network plot of this subnetwork.

diffusion(object, cond, genes, cyPath, name = "top_diffusion", label = TRUE)

Arguments

object

CeTF object resulted from runAnalysis function.
cond

Which conditions to be used to perform the diffusion analysis. The options are: network1 (1th condition) and network2 (2th condition).
genes

A single gene or a vector of characters indicating which genes will be used to perform diffusion analysis.
cyPath

System path of Cytoscape software (see details for further informations).
name

Network output name (default: top_diffusion)
label

If label is TRUE, shows the names of nodes (default: TRUE).

Value

Returns a list with the plot of the network and a table with the diffusion network.

Details

To perform the diffusion analysis is necessary to install the latest Cytoscape software version (https://cytoscape.org/).

The cyPath argument varies depending on the operating system used, for example:

  1. For Windows users: C:/Program Files/Cytoscape_v3.8.0/Cytoscape.exe

  2. For Linux users: /home/user/Cytoscape_v3.8.0/Cytoscape

  3. For macOS users: /Applications/Cytoscape_v3.8.0/cytoscape.sh

Examples

if (FALSE) { 
data(CeTFdemo)

result <- diffusion(object = CeTFdemo, 
                    cond = 'network1', 
                    genes = c('ENSG00000185591', 'ENSG00000179094'), 
                    cyPath = 'C:/Program Files/Cytoscape_v3.7.2/Cytoscape.exe', 
                    name = 'top_diffusion',
                    label = TRUE)
}