caOmicsV: Visualization of multi-dimentional cancer genomics data

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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.

Author
Henry Zhang
Date of publication
None
Maintainer
Henry Zhang <hzhang@mail.nih.gov>
License
GPL (>=2.0)
Version
1.4.0

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