Description Usage Value Author(s) Examples
Methods for retrieving plot parameters of caOmicsV bioNetCircos layout stored in caOmicsV environment. The bioNetCircos layout must be initialized first.
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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.
Henry Zhang
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | 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()
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