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

Functions

bioMatrixLegend Man page
biomatrixPlotDemoData Man page
bioNetCircosPlot Man page
bioNetLegend Man page
bionetPlotDemoData Man page
CA_OMICS_ENV Man page
CA_OMICS_NAME Man page
CA_OMICS_NA_STRING Man page
caOmicsV Man page
caOmicsV-package Man page
CNVDemoData Man page
convertToZScores Man page
drawBioNetNodeBackground Man page
eraseBioNetNode Man page
getBezierCurve Man page
getBioMatrixDataRowTop Man page
getBioNetNodeLinkLine Man page
getBioNetPlotLocations Man page
getBioNetSamplePlotPosition Man page
getCaOmicsVColors Man page
getCaOmicsVPlotTypes Man page
getDefaultNaStrings Man page
getHeatmapColorScales Man page
getPlotDataSet Man page
getPlotOmicsData Man page
getPlotSampleData Man page
getPlotSummaryData Man page
getRelatedPlotData Man page
initializeBioMatrixPlot Man page
initializeBioNetCircos Man page
labelBioNetNodeNames Man page
linkBioNetNodes Man page
linkBioNetSamples Man page
methylDemoData Man page
miRNA Man page
miRNADemoData Man page
plotBioMatrix Man page
plotBioMatrixBars Man page
plotBioMatrixBinaryData Man page
plotBioMatrixCategoryData Man page
plotBioMatrixHeatmap Man page
plotBioMatrixRowNames Man page
plotBioMatrixSampleData Man page
plotBioMatrixSampleNames Man page
plotBioNetBars Man page
plotBioNetCircos Man page
plotBioNetHeatmap Man page
plotBioNetLines Man page
plotBioNetPoints Man page
plotBioNetPolygons Man page
plotHeatmapColorScale Man page
resetBioNetNodePlotAreaBoundary Man page
RNA2miRNA Man page
RNASeq Man page
RNASeqDemoData Man page
sampleDemoData Man page
setBioMatrixBaseCoordinates Man page
setBioMatrixPlotArea Man page
setBioMatrixPlotParameters Man page
setBioNetCircosBasePlotPositions Man page
setBioNetNodeLayout Man page
setBioNetPlotAreaBackground Man page
setBioNetPlotParameters Man page
setCaOmicsVColors Man page
setDefaultNaStrings Man page
showBioMatrixPlotLayout Man page
showBioNetNodesLayout Man page
showSupportedBioNetCircosPlotType Man page
sortClinicalData Man page
sortOmicsDataByColumn Man page
sortOmicsDataByRow Man page

Files

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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