caOmicsV: Visualization of multi-dimentional cancer genomics data
Version 1.6.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorHenry Zhang
Bioconductor views Network RNASeq Visualization
Date of publicationNone
MaintainerHenry Zhang <hzhang@mail.nih.gov>
LicenseGPL (>=2.0)
Version1.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("caOmicsV")

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

CA_OMICS_ENV Man page
CA_OMICS_NAME Man page
CA_OMICS_NA_STRING Man page
CNVDemoData Man page
RNA2miRNA Man page
RNASeq Man page
RNASeqDemoData Man page
bioMatrixLegend Man page Source code
bioNetCircosPlot Man page Source code
bioNetLegend Man page Source code
biomatrixPlotDemoData Man page
bionetPlotDemoData Man page
caOmicsV Man page
caOmicsV-package Man page
convertToZScores Man page Source code
drawBioNetNodeBackground Man page Source code
eraseBioNetNode Man page Source code
getBezierCurve Man page Source code
getBioMatrixBasePositions Source code
getBioMatrixColumnPadding Source code
getBioMatrixDataAreaWidth Source code
getBioMatrixDataRowTop Man page Source code
getBioMatrixGeneLabelWidth Source code
getBioMatrixGeneNumber Source code
getBioMatrixLegendHeight Source code
getBioMatrixPhenotypeNumber Source code
getBioMatrixPlotAreaHeigth Source code
getBioMatrixPlotAreaWidth Source code
getBioMatrixRemarkWidth Source code
getBioMatrixRowPadding Source code
getBioMatrixSampleHeight Source code
getBioMatrixSampleIDHeight Source code
getBioMatrixSampleNumber Source code
getBioMatrixSampleWidth Source code
getBioMatrixSummaryWidth Source code
getBioNetBasePositions Source code
getBioNetGraph Source code
getBioNetNodeLinkLine Man page Source code
getBioNetNodePaddingScale Source code
getBioNetNodeParameters Source code
getBioNetNodePlotAreaBoundary Source code
getBioNetNodeRadius Source code
getBioNetPlotAreaWidth Source code
getBioNetPlotLocations Man page Source code
getBioNetPlotSampleWidth Source code
getBioNetPlotTotalSample Source code
getBioNetSamplePlotPosition Man page Source code
getCaOmicsVColors Man page Source code
getCaOmicsVPlotTypes Man page Source code
getDefaultNaStrings Man page Source code
getHeatmapColorScales Man page Source code
getPlotDataSet Man page Source code
getPlotOmicsData Man page Source code
getPlotSampleData Man page Source code
getPlotSummaryData Man page Source code
getRelatedPlotData Man page Source code
initializeBioMatrixPlot Man page Source code
initializeBioNetCircos Man page Source code
labelBioNetNodeNames Man page Source code
linkBioNetNodes Man page Source code
linkBioNetSamples Man page Source code
methylDemoData Man page
miRNA Man page
miRNADemoData Man page
plotBioMatrix Man page Source code
plotBioMatrixBars Man page Source code
plotBioMatrixBinaryData Man page Source code
plotBioMatrixCategoryData Man page Source code
plotBioMatrixHeatmap Man page Source code
plotBioMatrixRowNames Man page Source code
plotBioMatrixSampleData Man page Source code
plotBioMatrixSampleNames Man page Source code
plotBioNetBars Man page Source code
plotBioNetCircos Man page Source code
plotBioNetHeatmap Man page Source code
plotBioNetLines Man page Source code
plotBioNetPoints Man page Source code
plotBioNetPolygons Man page Source code
plotHeatmapColorScale Man page Source code
resetBioNetNodePlotAreaBoundary Man page Source code
sampleDemoData Man page
setBioMatrixBaseCoordinates Man page Source code
setBioMatrixPlotArea Man page Source code
setBioMatrixPlotParameters Man page Source code
setBioNetCircosBasePlotPositions Man page Source code
setBioNetNodeLayout Man page Source code
setBioNetPlotAreaBackground Man page Source code
setBioNetPlotParameters Man page Source code
setCaOmicsVColors Man page Source code
setDefaultNaStrings Man page Source code
showBioMatrixPlotLayout Man page Source code
showBioNetNodesLayout Man page Source code
showSupportedBioNetCircosPlotType Man page Source code
sortClinicalData Man page Source code
sortOmicsDataByColumn Man page Source code
sortOmicsDataByRow Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/caOmicsV.R
R/caOmicsV.bioMatrix.R
R/caOmicsV.bioNetCircos.R
build
build/vignette.rds
data
data/CNVDemoData.RData
data/RNA2miRNA.RData
data/RNASeq.RData
data/RNASeqDemoData.RData
data/biomatrixPlotDemoData.RData
data/bionetPlotDemoData.RData
data/methylDemoData.RData
data/miRNA.RData
data/miRNADemoData.RData
data/sampleDemoData.RData
demo
demo/00Index
demo/caOmicsV.biomatrix.layout.demo.R
demo/caOmicsV.bionetcircos.layout.demo.R
inst
inst/NEWS
inst/doc
inst/doc/Introduction_to_caOmicsV.R
inst/doc/Introduction_to_caOmicsV.Rnw
inst/doc/Introduction_to_caOmicsV.pdf
man
man/CA_OMICS_ENV.Rd
man/CA_OMICS_NAME.Rd
man/CA_OMICS_NA_STRING.Rd
man/CNVDemoData.Rd
man/RNA2miRNA.Rd
man/RNASeq.Rd
man/RNASeqDemoData.Rd
man/bioMatrixLegend.Rd
man/bioNetCircosPlot.Rd
man/bioNetLegend.Rd
man/biomatrixPlotDemoData.Rd
man/bionetPlotDemoData.Rd
man/caOmicsV-package.Rd
man/convertToZScores.Rd
man/drawBioNetNodeBackground.Rd
man/eraseBioNetNode.Rd
man/getBezierCurve.Rd
man/getBioMatrixDataRowTop.Rd
man/getBioMatrixPlotParameters.Rd
man/getBioNetNodeLinkLine.Rd
man/getBioNetParameters.Rd
man/getBioNetPlotLocations.Rd
man/getBioNetSamplePlotPosition.Rd
man/getCaOmicsVColors.Rd
man/getCaOmicsVPlotTypes.Rd
man/getDefaultNaStrings.Rd
man/getHeatmapColorScales.Rd
man/getPlotDataSet.Rd
man/getPlotOmicsData.Rd
man/getPlotSampleData.Rd
man/getPlotSummaryData.Rd
man/getRelatedPlotData.Rd
man/initializeBioMatrixPlot.Rd
man/initializeBioNetCircos.Rd
man/labelBioNetNodeNames.Rd
man/linkBioNetNodes.Rd
man/linkBioNetSamples.Rd
man/methylDemoData.Rd
man/miRNA.Rd
man/miRNADemoData.Rd
man/plotBioMatrix.Rd
man/plotBioMatrixBars.Rd
man/plotBioMatrixBinaryData.Rd
man/plotBioMatrixCategoryData.Rd
man/plotBioMatrixHeatmap.Rd
man/plotBioMatrixRowNames.Rd
man/plotBioMatrixSampleData.Rd
man/plotBioMatrixSampleNames.Rd
man/plotBioNetBars.Rd
man/plotBioNetCircos.Rd
man/plotBioNetHeatmap.Rd
man/plotBioNetLines.Rd
man/plotBioNetPoints.Rd
man/plotBioNetPolygons.Rd
man/plotHeatmapColorScale.Rd
man/resetBioNetNodePlotAreaBoundary.Rd
man/sampleDemoData.Rd
man/setBioMatrixBaseCoordinates.Rd
man/setBioMatrixPlotArea.Rd
man/setBioMatrixPlotParameters.Rd
man/setBioNetCircosBasePlotPositions.Rd
man/setBioNetNodeLayout.Rd
man/setBioNetPlotAreaBackground.Rd
man/setBioNetPlotParameters.Rd
man/setCaOmicsVColors.Rd
man/setDefaultNaStrings.Rd
man/showBioMatrixPlotLayout.Rd
man/showBioNetNodesLayout.Rd
man/showSupportedBioNetCircosPlotType.Rd
man/sortClinicalData.Rd
man/sortOmicsDataByColumn.Rd
man/sortOmicsDataByRow.Rd
vignettes
vignettes/Introduction_to_caOmicsV.Rnw
caOmicsV documentation built on May 20, 2017, 10:07 p.m.