caOmicsV: Visualization of multi-dimentional cancer genomics data

caOmicsV package provides methods to visualize multi-dimentional cancer genomics data including of patient information, gene expressions, DNA methylations, DNA copy number variations, and SNP/mutations in matrix layout or network layout.

AuthorHenry Zhang
Date of publicationNone
MaintainerHenry Zhang <hzhang@mail.nih.gov>
LicenseGPL (>=2.0)
Version1.4.0

View on Bioconductor

Man pages

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

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

caOmicsV-package: caOmicsV bioMatrix and bioNetCircos Layout Plot

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...

eraseBioNetNode: Erase Background of All Nodes on caOmicsV bioNetCircos Layout

getBezierCurve: Calculate x and y Coordinates for A Quadratic Bezier Curve

getBioMatrixDataRowTop: Get y Coordinate for Top of A Row on bioMatrix Layout

getBioMatrixPlotParameters: Methods to Get caOmicsV BioMatrix Plot Parameters

getBioNetNodeLinkLine: Get X and Y Coordinates for An Arrow between Two Nodes

getBioNetParameters: Methods to Get caOmicsV BioNetCircos Plot Parameters

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...

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...

resetBioNetNodePlotAreaBoundary: Update Node Plot Area Boundary on caOmicsV bioNetCircos...

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...

setBioNetNodeLayout: Set up Layout for the igraph Object

setBioNetPlotAreaBackground: Set up Plot Area Background for Nodes of caOmicsV...

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...

sortClinicalData: Sort Clinical Data by a Column

sortOmicsDataByColumn: Sort Omics Data by Column Header

sortOmicsDataByRow: Sort Omics Data by Row

Files in this package

caOmicsV/DESCRIPTION
caOmicsV/NAMESPACE
caOmicsV/R
caOmicsV/R/caOmicsV.R caOmicsV/R/caOmicsV.bioMatrix.R caOmicsV/R/caOmicsV.bioNetCircos.R
caOmicsV/build
caOmicsV/build/vignette.rds
caOmicsV/data
caOmicsV/data/CNVDemoData.RData
caOmicsV/data/RNA2miRNA.RData
caOmicsV/data/RNASeq.RData
caOmicsV/data/RNASeqDemoData.RData
caOmicsV/data/biomatrixPlotDemoData.RData
caOmicsV/data/bionetPlotDemoData.RData
caOmicsV/data/methylDemoData.RData
caOmicsV/data/miRNA.RData
caOmicsV/data/miRNADemoData.RData
caOmicsV/data/sampleDemoData.RData
caOmicsV/demo
caOmicsV/demo/00Index
caOmicsV/demo/caOmicsV.biomatrix.layout.demo.R
caOmicsV/demo/caOmicsV.bionetcircos.layout.demo.R
caOmicsV/inst
caOmicsV/inst/NEWS
caOmicsV/inst/doc
caOmicsV/inst/doc/Introduction_to_caOmicsV.R
caOmicsV/inst/doc/Introduction_to_caOmicsV.Rnw
caOmicsV/inst/doc/Introduction_to_caOmicsV.pdf
caOmicsV/man
caOmicsV/man/CA_OMICS_ENV.Rd caOmicsV/man/CA_OMICS_NAME.Rd caOmicsV/man/CA_OMICS_NA_STRING.Rd caOmicsV/man/CNVDemoData.Rd caOmicsV/man/RNA2miRNA.Rd caOmicsV/man/RNASeq.Rd caOmicsV/man/RNASeqDemoData.Rd caOmicsV/man/bioMatrixLegend.Rd caOmicsV/man/bioNetCircosPlot.Rd caOmicsV/man/bioNetLegend.Rd caOmicsV/man/biomatrixPlotDemoData.Rd caOmicsV/man/bionetPlotDemoData.Rd caOmicsV/man/caOmicsV-package.Rd caOmicsV/man/convertToZScores.Rd caOmicsV/man/drawBioNetNodeBackground.Rd caOmicsV/man/eraseBioNetNode.Rd caOmicsV/man/getBezierCurve.Rd caOmicsV/man/getBioMatrixDataRowTop.Rd caOmicsV/man/getBioMatrixPlotParameters.Rd caOmicsV/man/getBioNetNodeLinkLine.Rd caOmicsV/man/getBioNetParameters.Rd caOmicsV/man/getBioNetPlotLocations.Rd caOmicsV/man/getBioNetSamplePlotPosition.Rd caOmicsV/man/getCaOmicsVColors.Rd caOmicsV/man/getCaOmicsVPlotTypes.Rd caOmicsV/man/getDefaultNaStrings.Rd caOmicsV/man/getHeatmapColorScales.Rd caOmicsV/man/getPlotDataSet.Rd caOmicsV/man/getPlotOmicsData.Rd caOmicsV/man/getPlotSampleData.Rd caOmicsV/man/getPlotSummaryData.Rd caOmicsV/man/getRelatedPlotData.Rd caOmicsV/man/initializeBioMatrixPlot.Rd caOmicsV/man/initializeBioNetCircos.Rd caOmicsV/man/labelBioNetNodeNames.Rd caOmicsV/man/linkBioNetNodes.Rd caOmicsV/man/linkBioNetSamples.Rd caOmicsV/man/methylDemoData.Rd caOmicsV/man/miRNA.Rd caOmicsV/man/miRNADemoData.Rd caOmicsV/man/plotBioMatrix.Rd caOmicsV/man/plotBioMatrixBars.Rd caOmicsV/man/plotBioMatrixBinaryData.Rd caOmicsV/man/plotBioMatrixCategoryData.Rd caOmicsV/man/plotBioMatrixHeatmap.Rd caOmicsV/man/plotBioMatrixRowNames.Rd caOmicsV/man/plotBioMatrixSampleData.Rd caOmicsV/man/plotBioMatrixSampleNames.Rd caOmicsV/man/plotBioNetBars.Rd caOmicsV/man/plotBioNetCircos.Rd caOmicsV/man/plotBioNetHeatmap.Rd caOmicsV/man/plotBioNetLines.Rd caOmicsV/man/plotBioNetPoints.Rd caOmicsV/man/plotBioNetPolygons.Rd caOmicsV/man/plotHeatmapColorScale.Rd caOmicsV/man/resetBioNetNodePlotAreaBoundary.Rd caOmicsV/man/sampleDemoData.Rd caOmicsV/man/setBioMatrixBaseCoordinates.Rd caOmicsV/man/setBioMatrixPlotArea.Rd caOmicsV/man/setBioMatrixPlotParameters.Rd caOmicsV/man/setBioNetCircosBasePlotPositions.Rd caOmicsV/man/setBioNetNodeLayout.Rd caOmicsV/man/setBioNetPlotAreaBackground.Rd caOmicsV/man/setBioNetPlotParameters.Rd caOmicsV/man/setCaOmicsVColors.Rd caOmicsV/man/setDefaultNaStrings.Rd caOmicsV/man/showBioMatrixPlotLayout.Rd caOmicsV/man/showBioNetNodesLayout.Rd caOmicsV/man/showSupportedBioNetCircosPlotType.Rd caOmicsV/man/sortClinicalData.Rd caOmicsV/man/sortOmicsDataByColumn.Rd caOmicsV/man/sortOmicsDataByRow.Rd
caOmicsV/vignettes
caOmicsV/vignettes/Introduction_to_caOmicsV.Rnw

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