colorVertexByAttr: Computes colors for vertices according to their attributes.

Description Usage Arguments Value Author(s) See Also Examples

View source: R/plotPath.R

Description

This function returns a list of colors for vertices, assigned similar colors if they share a common attribute (ex: in the same pathway, etc).

Usage

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colorVertexByAttr(graph, attr.name, col.palette = palette())

Arguments

graph

An annotated igraph object.

attr.name

The attribute name (ex: "pathway") by which vertices will be colored. Complex attributes, where a vertex belongs to more than one group, are supported.

col.palette

A color palette, or a palette generating function (ex:

col.palette=rainbow

).

Value

A list of colors (in HEX format) for vertices.

Author(s)

Ahmed Mohamed

See Also

Other Plotting methods: layoutVertexByAttr, plotAllNetworks, plotClassifierROC, plotClusterMatrix, plotCytoscapeGML, plotNetwork, plotPathClassifier, plotPaths

Examples

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  data("ex_kgml_sig")
  v.colors <- colorVertexByAttr(ex_kgml_sig, "pathway")
  plotNetwork(ex_kgml_sig, vertex.color=v.colors)

NetPathMiner documentation built on Nov. 8, 2020, 8:20 p.m.