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Last data update: 2014.03.03

R: caOmicsV bioNetCircos Layout Plot

bioNetCircosPlot

R Documentation

caOmicsV bioNetCircos Layout Plot

Description

Plot one track of caOmics data on each node of a biological network. Supported plot types include polygon, bar, points, heatmap, and lines.

Usage

    bioNetCircosPlot(dataValues=NULL, plotType="polygon", outer, inner, 
            plotColors=NULL, maxValue=NULL, minValue=NULL)

Arguments

`dataValues`	an numeric matrix with columns for samples and rows for genes
`plotType`	character vector for plot type, supporting polygon, points, and lines.
`outer`	non-negative numeric, outer location of a data track
`inner`	non-negative numeric, inner location of a data track
`plotColors`	character vector specifying colors for plot items
`maxValue`	numeric, the biggest value of plot data or user defined top threshold. Set to NULL to use the biggest value in dataset.
`minValue`	numeric, the smallest value of plot data or user defined bottom threshold. Set to NULL to use the smallest value in dataset.

Value

None

Author(s)

Henry Zhang

Examples

    data(bionetPlotDemoData)
    expr <- bionetPlotDemoData$heatmapData[[1]]
    bioNet <- bc3net(expr) 
    initializeBioNetCircos(bioNet, totalSamples=60)
    showBioNetNodesLayout()

    binaryData <- bionetPlotDemoData$binaryData[[1]]
    sampleColors <- c(rep("blue", ncol(binaryData)))
    plotType <- "points"
    inner <- 2
    outer <- 3
    bioNetCircosPlot(binaryData, plotType, outer, inner, sampleColors)

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.

R is a collaborative project with many contributors.
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(caOmicsV)
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

Loading required package: bc3net
Loading required package: c3net
Loading required package: infotheo
Loading required package: Matrix
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/caOmicsV/bioNetCircosPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: bioNetCircosPlot
> ### Title: caOmicsV bioNetCircos Layout Plot
> ### Aliases: bioNetCircosPlot
> ### Keywords: methods
> 
> ### ** Examples
> 
>     data(bionetPlotDemoData)
>     expr <- bionetPlotDemoData$heatmapData[[1]]
>     bioNet <- bc3net(expr) 
>     initializeBioNetCircos(bioNet, totalSamples=60)
>     showBioNetNodesLayout()
> 
>     binaryData <- bionetPlotDemoData$binaryData[[1]]
>     sampleColors <- c(rep("blue", ncol(binaryData)))
>     plotType <- "points"
>     inner <- 2
>     outer <- 3
>     bioNetCircosPlot(binaryData, plotType, outer, inner, sampleColors)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>