getBioMatrixParameters {caOmicsV} | R Documentation

## Methods to Get caOmicsV BioMatrix Plot Parameters

### Description

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

### Usage

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

### Value

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).

### Author(s)

Henry Zhang

### Examples

        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()

[Package caOmicsV version 1.20.0 Index]