initializeBioNetCircos: Initialize caOmicsV bioNetCircos Layout Plot

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

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)) 

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