createNetworkForCytoscape: Create network and load it into Cytoscape

In adeschen/gprofiler2cytoscape: From functional enrichment results to biological networks

Create network and load it into Cytoscape

Description

Create network from gprofiler2 results and load it into Cytoscape

Usage

createNetworkForCytoscape(nodeEdgeInfo, title, collection)

Arguments

nodeEdgeInfo	a TODO
title	a character string representing the name assigned to the network.
collection	a character string representing the collection name assigned to the network.

Value

TRUE

Author(s)

Astrid Deschênes

Examples

## Loading dataset containing result from an enrichment analysis done with
## gprofiler2
data(parentalNapaVsDMSOEnrichment)

## Only retained the GO Molecular Function results
results <- parentalNapaVsDMSOEnrichment$result[
        parentalNapaVsDMSOEnrichment$result$source == "GO:MF", ]

## Extract node and edge information
information <- enrichViewNet:::extractInformationWhenIntersection(
        gostResults=results)
    
## The creation of the network can only be done when Cytoscape
## is up and running
## A network using GO - Molecular Function enriched terms will be
## generated and loaded into Cytoscape
if (enrichViewNet:::isCytoscapeRunning()) {
    enrichViewNet:::createNetworkForCytoscape(nodeEdgeInfo=information, 
        title="Test", collection="New Collection")
}

adeschen/gprofiler2cytoscape documentation built on Nov. 4, 2024, 3:16 p.m.