# Visualization of multi-dimentional cancer genomics data

## Documentation for package ‘caOmicsV’ version 1.25.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

caOmicsV-package | caOmicsV bioMatrix and bioNetCircos Layout Plot
bioMatrixLegend | Plot Legend on caOmicsV bioMatrix Layout
biomatrixPlotDemoData | Demo Data for caOmicsV bioMatrix Plot
bioNetCircosPlot | caOmicsV bioNetCircos Layout Plot
bioNetLegend | Draw Legend for caOmicsV bioNet Plot
bionetPlotDemoData | Demo Dataset for caOmicsV bioNetCircos Plot
caOmicsV | caOmicsV bioMatrix and bioNetCircos Layout Plot
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
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
getBioMatrixColumnPadding | Methods to Retrieve bioMatrix Layout Parameters
getBioMatrixDataAreaWidth | Methods to Retrieve bioMatrix Layout Parameters
getBioMatrixDataRowTop | Get y Coordinate for Top of A Row on bioMatrix Layout
getBioMatrixGeneLabelWidth | Methods to Retrieve bioMatrix Layout Parameters
getBioMatrixGeneNumber | Methods to Retrieve bioMatrix Layout Parameters
getBioMatrixLegendHeight | Methods to Retrieve bioMatrix Layout Parameters
getBioMatrixPhenotypeNumber | Methods to Retrieve bioMatrix Layout Parameters
getBioMatrixPlotAreaHeigth | Methods to Retrieve bioMatrix Layout Parameters
getBioMatrixPlotAreaWidth | Methods to Retrieve bioMatrix Layout Parameters
getBioMatrixRemarkWidth | Methods to Retrieve bioMatrix Layout Parameters
getBioMatrixRowPadding | Methods to Retrieve bioMatrix Layout Parameters
getBioMatrixSampleHeight | Methods to Retrieve bioMatrix Layout Parameters
getBioMatrixSampleIDHeight | Methods to Retrieve bioMatrix Layout Parameters
getBioMatrixSampleNumber | Methods to Retrieve bioMatrix Layout Parameters
getBioMatrixSampleWidth | Methods to Retrieve bioMatrix Layout Parameters
getBioNetBasePositions | Methods to Retrieve bioNet Layout Parameters
getBioNetBasePositions getBioNetGraph getBioNetNodePaddingScale getBioNetNodeParameters getBioNetNodePlotAreaBoundary getBioNetNodeRadius getBioNetPlotAreaWidth getBioNetPlotSampleWidth getBioNetPlotTotalSample | Methods to Get caOmicsV BioNetCircos Plot Parameters
getBioNetGraph | Methods to Retrieve bioNet Layout Parameters
getBioNetNodeLinkLine | Get X and Y Coordinates for An Arrow between Two Nodes
getBioNetNodePaddingScale | Methods to Retrieve bioNet Layout Parameters
getBioNetNodeParameters | Methods to Retrieve bioNet Layout Parameters
getBioNetNodePlotAreaBoundary | Methods to Retrieve bioNet Layout Parameters
getBioNetNodeRadius | Methods to Retrieve bioNet Layout Parameters
getBioNetPlotAreaWidth | Methods to Retrieve bioNet Layout Parameters
getBioNetPlotLocations | Get bioNetCircos Plot Locations
getBioNetPlotSampleWidth | Methods to Retrieve bioNet Layout Parameters
getBioNetPlotTotalSample | Methods to Retrieve bioNet Layout Parameters
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
RNA2miRNA | Paired miRNA and Genes with Negative Correlation Coefficients
RNASeq | An Sample of RNASeq Data Set
RNASeqDemoData | RNASeq Demo Data Set
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