exportWCNetwork: exportWCNetwork

In noriakis/wcGeneSummary: visualization and interpretation of textual information from omics summary data through network analysis

exportWCNetwork

Description

Export wordcloud networks to Cytoscape.js

Usage

exportWCNetwork(
  g,
  geneList,
  dir = "network",
  colors = NULL,
  sizeMin = 50,
  sizeMax = 200,
  wcScale = 20,
  keyType = "SYMBOL",
  orgDb = org.Hs.eg.db,
  wcArgs = list(),
  numWords = 50
)

Arguments

g	igraph (node name corresponding to gene cluster name)
geneList	named list of gene IDs
dir	directory to output the files, default to current directory
colors	color palettes to use for each cluster named list, or random palette will be assigned if NULL
sizeMin	minimum scale size for nodes
sizeMax	maximum scale size for nodes
wcScale	scaling size for wordcloud
keyType	type of gene IDs (default to SYMBOL)
orgDb	annotation database
wcArgs	parameters for ggwordcloud
numWords	number of words

Details

The function exports the wordcloud network by providing the gene cluster network. Node size will be the number of genes in the cluster. By default use cola layout, and see below for the parameters of the layout. (https://github.com/cytoscape/cytoscape.js-cola) If "strength" attribute is in the edge of igraph object, the parameter is used to size the edge width.

Value

export the Cytoscape.js network

Examples

g <- igraph::graph_from_edgelist(rbind(c("ME1","ME2")))
gl <- list("ME1"=c("PNKP","IRF3","MCM5"), "ME2"=c("IRF3","ERCC2","TP53"))
exportWCNetwork(g, gl)

noriakis/wcGeneSummary documentation built on May 31, 2024, 4:42 p.m.