createXGMMLR Documentation

createXGMML

Description

Creates a Cytoscape xgmml readable file.

Usage

  createXGMML(gr, node.label, cwName = "test",
    node.form = NULL, edge.form = NULL, attributes = NULL,
    path)

Arguments

gr

a graphNEL object generated by edge matrices provided by reac2cor.

node.label

a character vector containing the name of each node.

cwName

Cytoscape window name.

node.form

data.frame containing the names of the nodes in the first column, and TRUE/FALSE vectors for graph parameters in the additional columns. The column name should have the parameter type, color and shape and the value in the format "color.#FF0000".

edge.form

data.frame containing the names of the nodes in the first column, and TRUE/FALSE vectors for graph parameters in the additional columns. The column name should have the parameter type, color, width and style, and the value in the format "color.#FF0000".

attributes

classification table created by export.class.table function.

path

system path to save the file.

Value

Cytoscape xgmml readable file.