bioNetCircosPlot: caOmicsV bioNetCircos Layout Plot

In hzhanghenry/caOmicsV: Visualization of multi-dimentional cancer genomics data

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)

hzhanghenry/caOmicsV documentation built on May 17, 2019, 10:07 p.m.