Computes colors for vertices according to their attributes.

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

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

Arguments

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, plotClusterProbs, plotClusters; plotCytoscape, plotCytoscapeGML; plotNetwork; plotPathClassifier; plotPaths

Examples

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

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(NetPathMiner)
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/NetPathMiner/colorVertexByAttr.Rd_%03d_medium.png", width=480, height=480)
> ### Name: colorVertexByAttr
> ### Title: Computes colors for vertices according to their attributes.
> ### Aliases: colorVertexByAttr
> 
> ### ** Examples
> 
> data("ex_kgml_sig")
>   v.colors <- colorVertexByAttr(ex_kgml_sig, "pathway")
>   plotNetwork(ex_kgml_sig, vertex.color=v.colors)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>