getBioMatrixPlotParameters: Methods to Get caOmicsV BioMatrix Plot Parameters
In caOmicsV: Visualization of multi-dimentional cancer genomics data

Description Usage Value Author(s) Examples

Get methods to retrieve parameters for caOmicsV bioMatrix layout plot stored in caOmicsV environment. bioMatrix layout must be initialized first.

    getBioMatrixBasePositions()
    getBioMatrixColumnPadding()
    getBioMatrixDataAreaWidth()
    getBioMatrixGeneLabelWidth()
    getBioMatrixGeneNumber()
    getBioMatrixLegendHeight()
    getBioMatrixPhenotypeNumber()
    getBioMatrixPlotAreaHeigth()
    getBioMatrixPlotAreaWidth()
    getBioMatrixRemarkWidth()
    getBioMatrixSummaryWidth()
    getBioMatrixRowPadding()
    getBioMatrixSampleHeight()
    getBioMatrixSampleIDHeight()
    getBioMatrixSampleNumber()
    getBioMatrixSampleWidth()

getBioMatrixBasePositions() returns a numeric matrix of defult x and y coordinates of rectangles for each samples at a row.

getBioMatrixColumnPadding() returns a non-negative numeric value in inch for padding between two samples, default 0.025.

getBioMatrixDataAreaWidth() returns a non-negative numeric value in inch for width of data plot area, total samples times the sum of sample width and columnPadding.

getBioMatrixDataRowTop() returns y coordinate for the top of a sample row.

getBioMatrixGeneLabelWidth() returns a non-negative numeric value in inch for length of left labels (gene names).

getBioMatrixGeneNumber() returns total number of genes to be plotted.

getBioMatrixLegendHeight() returns a non-negative numeric value in inch for the height of legend area.

getBioMatrixPhenotypeNumber() returns total number of phenotypes.

getBioMatrixPlotAreaHeigth() returns a non-negative numeric value in inch representing the height of all plot areas (sample name area, data plot area, and legend area).

getBioMatrixPlotAreaWidth() returns a non-negative numeric value in inch for width of all plot areas (left labels (gene names), data plot area, and right labels).

getBioMatrixRemarkWidth() returns a non-negative numeric value in inch for width on the right side of data plot, usually for second gene labels.

getBioMatrixSummaryWidth() returns a non-negative numeric value in inch for width on the right side of data plot area to plot summary data plot.

getBioMatrixRowPadding() returns a non-negative numeric value in inch for height of padding between two rows.

getBioMatrixSampleHeight() returns a non-negative numeric value in inch for height of a sample row.

getBioMatrixSampleIDHeight() returns a non-negative numeric value in inch for height of sample labels (on the top of phenotype plot area).

getBioMatrixSampleNumber() returns the total number of samples in plot datasets.

getBioMatrixSampleWidth() returns a non-negative numeric value in inch for width of a rectangle (sample).

Henry Zhang

    initializeBioMatrixPlot()

    positions      <- getBioMatrixBasePositions()
    colPadding     <- getBioMatrixColumnPadding()
    dataAreaWidth  <- getBioMatrixDataAreaWidth()
    geneNameWidth  <- getBioMatrixGeneLabelWidth()
    numOfGenes     <- getBioMatrixGeneNumber()
    legendHeight   <- getBioMatrixLegendHeight()
    numOfFeatures  <- getBioMatrixPhenotypeNumber()
    dataAreaHeight <- getBioMatrixPlotAreaHeigth()
    plotAreaWidth  <- getBioMatrixPlotAreaWidth()
    sumAreaWidth   <- getBioMatrixRemarkWidth()
    rowPadding     <- getBioMatrixRowPadding()
    sampleHeight   <- getBioMatrixSampleHeight()
    sampleIDHeight <- getBioMatrixSampleIDHeight()
    numOfSamples   <- getBioMatrixSampleNumber()
    sampleWidth    <- getBioMatrixSampleWidth()