CA_OMICS_ENV            caOmicsV Environment
CA_OMICS_NAME           The Name of caOmicsV Environment
CA_OMICS_NA_STRING      The Default NA String Used by caOmicsV Package
CNVDemoData             Demo Data Set for Copy Number Variation
RNA2miRNA               Paired miRNA and Genes with Negative
                        Correlation Coefficients
RNASeq                  An Sample of RNASeq Data Set
RNASeqDemoData          RNASeq Demo Data Set
bioMatrixLegend         Plot Legend on caOmicsV bioMatrix Layout
bioNetCircosPlot        caOmicsV bioNetCircos Layout Plot
bioNetLegend            Draw Legend for caOmicsV bioNet Plot
biomatrixPlotDemoData   Demo Data for caOmicsV bioMatrix Plot
bionetPlotDemoData      Demo Dataset for caOmicsV bioNetCircos Plot
caOmicsV-package        caOmicsV bioMatrix and bioNetCircos Layout Plot
convertToZScores        Calculate z-scores for A Data Matrix
drawBioNetNodeBackground
                        Draw Background for A Data Track On Nodes of
                        caOmicsV bioNet Layout
eraseBioNetNode         Erase Background of All Nodes on caOmicsV
                        bioNetCircos Layout
getBezierCurve          Calculate x and y Coordinates for A Quadratic
                        Bezier Curve
getBioMatrixBasePositions
                        Methods to Retrieve bioMatrix Layout Parameters
getBioMatrixBasePositions

    getBioMatrixColumnPadding

    getBioMatrixDataAreaWidth

    getBioMatrixGeneLabelWidth

    getBioMatrixGeneNumber

    getBioMatrixLegendHeight

    getBioMatrixPhenotypeNumber

    getBioMatrixPlotAreaHeigth

    getBioMatrixPlotAreaWidth

    getBioMatrixRemarkWidth

    getBioMatrixSummaryWidth

    getBioMatrixRowPadding

    getBioMatrixSampleHeight

    getBioMatrixSampleIDHeight

    getBioMatrixSampleNumber

    getBioMatrixSampleWidth
                        Methods to Get caOmicsV BioMatrix Plot
                        Parameters
getBioMatrixDataRowTop
                        Get y Coordinate for Top of A Row on bioMatrix
                        Layout
getBioNetBasePositions
                        Methods to Retrieve bioNet Layout Parameters
getBioNetBasePositions

    getBioNetGraph

    getBioNetNodePaddingScale

    getBioNetNodeParameters

    getBioNetNodePlotAreaBoundary

    getBioNetNodeRadius

    getBioNetPlotAreaWidth

    getBioNetPlotSampleWidth

    getBioNetPlotTotalSample
                        Methods to Get caOmicsV BioNetCircos Plot
                        Parameters
getBioNetNodeLinkLine   Get X and Y Coordinates for An Arrow between
                        Two Nodes
getBioNetPlotLocations
                        Get bioNetCircos Plot Locations
getBioNetSamplePlotPosition
                        Calculate x and y Coordinates for Each Sample
                        on Default Node
getCaOmicsVColors       Get Default Colors Used by caOmicsV Plot
getCaOmicsVPlotTypes    Get Plot Types Supported by caOmicsV Package
getDefaultNaStrings     Default NA String
getHeatmapColorScales   Get caOmicsV Heatmap Color Scales
getPlotDataSet          Prepare Data Set for caOmicsV Plot
getPlotOmicsData        Extract Subset from A Data Frame
getPlotSampleData       Extract Subset of Sample Information
getPlotSummaryData      Extract Summary Subset for Plotting
getRelatedPlotData      Extract subset from A Data Frame Based on
                        Relational Information
initializeBioMatrixPlot
                        Set Up Parameters for caOmicsV bioMatrix Plot
                        Layout
initializeBioNetCircos
                        Initialize caOmicsV bioNetCircos Layout Plot
labelBioNetNodeNames    Label Names for Each Node on Network Graph
linkBioNetNodes         Draw A Customized Arrow between Two Nodes
linkBioNetSamples       Link Two samples Inside a Node with Quadratic
                        Bezier Curve
methylDemoData          Methylation Demo Data Set
miRNA                   Selected miRNA Read Counts
miRNADemoData           miRNASeq Demo Data Set
plotBioMatrix           Default Plot Method for caOmicsV bioMatrix
                        Layout Plot
plotBioMatrixBars       Bar Plot on caOmicsV bioMatrix Layout
plotBioMatrixBinaryData
                        Binary Data Plot on caOmicsV bioMatrix Layout
plotBioMatrixCategoryData
                        Plot Category Data on caOmicsV bioMatrix Layout
plotBioMatrixHeatmap    Heatmap Plot on caOmicsV bioMatrix Layout
plotBioMatrixRowNames   Plot Row Names on caOmicsV bioMatrix Layout
plotBioMatrixSampleData
                        Plot Sample Data on caOmicsV bioMatrix Layout
plotBioMatrixSampleNames
                        Label Sample Names on the Top of caOmicsV
                        bioMatrix Layout
plotBioNetBars          Bar Plot on caOmicsV bioNetCircos Layout
plotBioNetCircos        Default Plot Method for caOmicsV bioNetCircos
                        Layout
plotBioNetHeatmap       Heatmap Plot for Each Node on caOmicsV
                        bioNetCircos Layout
plotBioNetLines         Line Plot on caOmicsV bioNetCircos Layout
plotBioNetPoints        Point Plot on caOmicsV bioNetCircos Layout
plotBioNetPolygons      Polygon Plot on caOmicsV bioNetCircos Layout
plotHeatmapColorScale   Plot Heatmap Color Scale for both caOmicsV
                        bioMatrix and bioNewCircos Layout
resetBioNetNodePlotAreaBoundary
                        Update Node Plot Area Boundary on caOmicsV
                        bioNetCircos Layout
sampleDemoData          Sample Tissue Type Demo Data Set
setBioMatrixBaseCoordinates
                        Set up Base Coordinates for caOmicsV bioMatrix
                        Layout
setBioMatrixPlotArea    Set up Plot Area for caOimcsV bioMatrix Layout
setBioMatrixPlotParameters
                        Set up Plot Parameters for caOmicsV bioMatrix
                        Layout
setBioNetCircosBasePlotPositions
                        Set up Default Plot Positions for a Node on
                        caOmicsV bioNetCircor Layout
setBioNetNodeLayout     Set up Layout for the igraph Object
setBioNetPlotAreaBackground
                        Set up Plot Area Background for Nodes of
                        caOmicsV bioNetCircos Layout
setBioNetPlotParameters
                        Initialize Plot Parameters for caOmicsV
                        bioNetCircos Plot
setCaOmicsVColors       Set up Default Plot Colors for caOmicsV Plot
setDefaultNaStrings     Set up Default NA Strings for caOmicsV Package
showBioMatrixPlotLayout
                        Display caOmicsV bioMatrix Layout
showBioNetNodesLayout   Display Nodes Layout of caOmicsV bioNetCircos
                        Plot
showSupportedBioNetCircosPlotType
                        Display the Plot Types Supported by caOmicsV
                        bioNetCircos Plot
sortClinicalData        Sort Clinical Data by a Column
sortOmicsDataByColumn   Sort Omics Data by Column Header
sortOmicsDataByRow      Sort Omics Data by Row
