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caOmicsV (version 1.2.0)

Visualization of multi-dimentional cancer genomics data

Description

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.

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Version

Version

1.2.0

License

GPL (>=2.0)

Maintainer

Hongen Zhang

Last Published

February 15th, 2017

Functions in caOmicsV (1.2.0)

getBioMatrixParameters

Methods to Get caOmicsV BioMatrix Plot Parameters

linkBioNetSamples

Link Two samples Inside a Node with Quadratic Bezier Curve

plotBioMatrixRowNames

Plot Row Names on caOmicsV bioMatrix Layout

Prepare Data Set for caOmicsV Plot

getPlotSampleData

Extract Subset of Sample Information

plotBioMatrixSampleData

Plot Sample Data on caOmicsV bioMatrix Layout

plotBioMatrixBinaryData

Binary Data Plot on caOmicsV bioMatrix Layout

plotBioMatrixCategoryData

Plot Category Data on caOmicsV bioMatrix Layout

plotBioMatrixSampleNames

Label Sample Names on the Top of caOmicsV bioMatrix Layout

Demo Data Set for Copy Number Variation

setBioMatrixPlotArea

Set up Plot Area for caOimcsV bioMatrix Layout

sortClinicalData

Sort Clinical Data by a Column

plotBioNetLines

Line Plot on caOmicsV bioNetCircos Layout

showBioNetNodesLayout

Display Nodes Layout of caOmicsV bioNetCircos Plot

An Sample of RNASeq Data Set

RNASeq Demo Data Set

Selected miRNA Read Counts

showBioMatrixPlotLayout

Display caOmicsV bioMatrix Layout

setBioNetPlotParameters

Initialize Plot Parameters for caOmicsV bioNetCircos Plot

plotBioMatrixBars

Bar Plot on caOmicsV bioMatrix Layout

getDefaultNaStrings

Default NA String

Bar Plot on caOmicsV bioNetCircos Layout

getBioNetSamplePlotPosition

Calculate x and y Coordinates for Each Sample on Default Node

bioMatrixLegend

Plot Legend on caOmicsV bioMatrix Layout

initializeBioNetCircos

Initialize caOmicsV bioNetCircos Layout Plot

linkBioNetNodes

Draw A Customized Arrow between Two Nodes

resetBioNetNodePlotAreaBoundary

Update Node Plot Area Boundary on caOmicsV bioNetCircos Layout

setBioNetCircosBasePlotPositions

Set up Default Plot Positions for a Node on caOmicsV bioNetCircor Layout

setCaOmicsVColors

Set up Default Plot Colors for caOmicsV Plot

The Name of caOmicsV Environment

Draw Legend for caOmicsV bioNet Plot

getRelatedPlotData

Extract subset from A Data Frame Based on Relational Information

getCaOmicsVPlotTypes

Get Plot Types Supported by caOmicsV Package

bionetPlotDemoData

Demo Dataset for caOmicsV bioNetCircos Plot

plotBioNetCircos

Default Plot Method for caOmicsV bioNetCircos Layout

plotBioNetPoints

Point Plot on caOmicsV bioNetCircos Layout

setBioNetNodeLayout

Set up Layout for the igraph Object

setBioMatrixBaseCoordinates

Set up Base Coordinates for caOmicsV bioMatrix Layout

setBioNetPlotAreaBackground

Set up Plot Area Background for Nodes of caOmicsV bioNetCircos Layout

plotHeatmapColorScale

Plot Heatmap Color Scale for both caOmicsV bioMatrix and bioNewCircos Layout

showSupportedBioNetCircosPlotType

Display the Plot Types Supported by caOmicsV bioNetCircos Plot

sortOmicsDataByRow

Sort Omics Data by Row

caOmicsV Environment

bioNetCircosPlot

caOmicsV bioNetCircos Layout Plot

convertToZScores

Calculate z-scores for A Data Matrix

getCaOmicsVColors

Get Default Colors Used by caOmicsV Plot

initializeBioMatrixPlot

Set Up Parameters for caOmicsV bioMatrix Plot Layout

sortOmicsDataByColumn

Sort Omics Data by Column Header

setDefaultNaStrings

Set up Default NA Strings for caOmicsV Package

Calculate x and y Coordinates for A Quadratic Bezier Curve

eraseBioNetNode

Erase Background of All Nodes on caOmicsV bioNetCircos Layout

getPlotOmicsData

Extract Subset from A Data Frame

getBioNetNodeLinkLine

Get X and Y Coordinates for An Arrow between Two Nodes

getPlotSummaryData

Extract Summary Subset for Plotting

labelBioNetNodeNames

Label Names for Each Node on Network Graph

setBioMatrixPlotParameters

Set up Plot Parameters for caOmicsV bioMatrix Layout

Paired miRNA and Genes with Negative Correlation Coefficients

caOmicsV-package

caOmicsV bioMatrix and bioNetCircos Layout Plot

CA_OMICS_NA_STRING

The Default NA String Used by caOmicsV Package

Methylation Demo Data Set

miRNASeq Demo Data Set

plotBioMatrixHeatmap

Heatmap Plot on caOmicsV bioMatrix Layout

plotBioNetPolygons

Polygon Plot on caOmicsV bioNetCircos Layout

Default Plot Method for caOmicsV bioMatrix Layout Plot

Sample Tissue Type Demo Data Set

getHeatmapColorScales

Get caOmicsV Heatmap Color Scales

biomatrixPlotDemoData

Demo Data for caOmicsV bioMatrix Plot

getBioMatrixDataRowTop

Get y Coordinate for Top of A Row on bioMatrix Layout

getBioNetPlotLocations

Get bioNetCircos Plot Locations

getBioNetParameters

Methods to Get caOmicsV BioNetCircos Plot Parameters

plotBioNetHeatmap

Heatmap Plot for Each Node on caOmicsV bioNetCircos Layout

drawBioNetNodeBackground

Draw Background for A Data Track On Nodes of caOmicsV bioNet Layout