getBioNetParameters {caOmicsV} | R Documentation

## 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.

### Author(s)

Henry Zhang

### 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()

[Package caOmicsV version 1.20.0 Index]