exportNetworkToCytoscape: Export network to Cytoscape

Description Usage Arguments Details Value Author(s) See Also

View source: R/exportFunctions.R

Description

This function exports a network in edge and node list files in a format suitable for importing to Cytoscape.

Usage

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exportNetworkToCytoscape(
   adjMat,
   edgeFile = NULL,
   nodeFile = NULL,
   weighted = TRUE,
   threshold = 0.5,
   nodeNames = NULL,
   altNodeNames = NULL,
   nodeAttr = NULL,
   includeColNames = TRUE)

Arguments

adjMat

adjacency matrix giving connection strengths among the nodes in the network.

edgeFile

file name of the file to contain the edge information.

nodeFile

file name of the file to contain the node information.

weighted

logical: should the exported network be weighted?

threshold

adjacency threshold for including edges in the output.

nodeNames

names of the nodes. If not given, dimnames of adjMat will be used.

altNodeNames

optional alternate names for the nodes, for example gene names if nodes are labeled by probe IDs.

nodeAttr

optional node attribute, for example module color. Can be a vector or a data frame.

includeColNames

logical: should column names be included in the output files? Note that Cytoscape can read files both with and without column names.

Details

If the corresponding file names are supplied, the edge and node data is written to the appropriate files. The edge and node data is also returned as return value (see below).

Value

A list with the following componens:

egdeData

a data frame containing the edge data, with one row per edge

nodeData

a data frame containing the node data, with one row per node

Author(s)

Peter Langfelder

See Also

exportNetworkToVisANT


WGCNA documentation built on Aug. 5, 2017, 5:05 p.m.