export2cytoscapeR Documentation

export2cytoscape

Description

Exports a graph to Cytoscape with optional node and edge attributes.

Usage

  export2cytoscape(gr, node.label, cwName = "test",
    node.form = NULL, edge.form = NULL, cpdInfo = NULL,
    classTable = NULL, pos = NULL)

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".

cpdInfo

matrix of pathway information, with pathway code, name and the counting how many nodes each pathway has.

classTable

matrix of classification generated by export.class.table. If the user provides this matrix the information is sent to Cytoscape as node attributes, and the user can visualize it in the data panel.

pos

node position list given by get.kgml.positions function.

Value

Exports a graph to Cytoscape window, with additional parameters.