caOmicsV (version 1.2.0)

getBioNetParameters: Methods to Get caOmicsV BioNetCircos Plot Parameters

Description

Methods for retrieving plot parameters of caOmicsV bioNetCircos layout stored in caOmicsV environment. The bioNetCircos layout must be initialized first.

Usage

getBioNetBasePositions()
    getBioNetGraph()
    getBioNetNodePaddingScale()
    getBioNetNodeParameters()
    getBioNetNodePlotAreaBoundary()
    getBioNetNodeRadius()
    getBioNetPlotAreaWidth()
    getBioNetPlotSampleWidth()
    getBioNetPlotTotalSample()

Value

• getBioNetBasePositions() returns numeric matrix containing x and y coordinates of points on a circular line with radius of 1 and degrees of text rotation on each point.

  getBioNetGraph() returns an igraph object which representing a biological network built with user's inputs.

  getBioNetNodePaddingScale() returns a numeric value for padding between two nodes.

  getBioNetNodeParameters() returns a list containing totalSamples, sampleWidth, nodeRadius, nodePadding, plotAreaWidth, inner, and outer boundary of plot area.

  getBioNetNodePlotAreaBoundary() returns a numeric vector for outer and inner boundary of a node on caOmicsV bioNetCircos layout.

  getBioNetNodeRadius() returns the numeric value for radius of a node on caOmicsV bioNetCircos layout.

  getBioNetPlotAreaWidth() returns the width of bioNetCircos layout plot area.

  getBioNetPlotSampleWidth() returns total points a sample will need on a circular track.

  getBioNetPlotTotalSample() returns the total number of samples to be plotted on each node.

Examples

data(bionetPlotDemoData)
    expr <- bionetPlotDemoData$heatmapData[[1]]
    bioNet <- bc3net(expr) 
    initializeBioNetCircos(bioNet)

    positions   <- getBioNetBasePositions()
    bioGraph    <- getBioNetGraph()
    paddScale   <- getBioNetNodePaddingScale()
    nodeParams  <- getBioNetNodeParameters()
    plotBound   <- getBioNetNodePlotAreaBoundary()
    nodeRadius  <- getBioNetNodeRadius()
    areaWidth   <- getBioNetPlotAreaWidth()
    sampleWidth <- getBioNetPlotSampleWidth()
    numOfSample <- getBioNetPlotTotalSample()