initializeBioNetCircos {caOmicsV} | R Documentation

## Initialize caOmicsV bioNetCircos Layout Plot

### Description

Set up parameters for layout of caOmicsV bioNetCircos plot including total number of samples, default width of a sample on a circos track , node radius, padding width between two nodes, plot area of each node, default x and y coordinates of points on a circle with radius of 1, and node layout.

### Usage

        initializeBioNetCircos(bioNet, totalSamples=100, sampleWidth=100,
        nodeRadius=1, nodePadding=1, plotAreaWidth=1,
        layout=layout.fruchterman.reingold(bioNet))

### Arguments

`bioNet` | an igraph object
`totalSamples` | non-negative numeric, total number of samples to be plotted
`sampleWidth` | non-negative numeric, total number of points to represent a sample on a circular track.
`nodeRadius` | non-negative numeric, radius of a node on biological network.
`nodePadding` | non-negative numeric, padding width between two node on biological network.
`plotAreaWidth` | non-negative numeric, outside boundary of plot area of a node, relative to node radius, default 1 (same as nodeRadius)
`layout` | two dimentional numeric matrix, node layout of the igraph returned by igraph layout method

### Value

None

### Author(s)

Henry Zhang

### Examples

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

        initializeBioNetCircos(bioNet, totalSamples=100, sampleWidth=100,
                nodeRadius=1, nodePadding=1, plotAreaWidth=1,
                layout=layout.fruchterman.reingold(bioNet))

[Package caOmicsV version 1.20.0 Index]