caOmicsV-package | caOmicsV bioMatrix and bioNetCircos Layout Plot |
Methods to Get caOmicsV BioMatrix Plot Parameters | |
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 |
caOmicsV | caOmicsV bioMatrix and bioNetCircos Layout 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 |
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 Layout |
eraseBioNetNode | Erase Background of All Nodes on caOmicsV bioNetCircos Layout |
getBezierCurve | Calculate x and y Coordinates for A Quadratic Bezier Curve |
getBioMatrixBasePositions | Methods to Get caOmicsV BioMatrix Plot Parameters |
getBioMatrixColumnPadding | Methods to Get caOmicsV BioMatrix Plot Parameters |
getBioMatrixDataAreaWidth | Methods to Get caOmicsV BioMatrix Plot Parameters |
getBioMatrixDataRowTop | Get y Coordinate for Top of A Row on bioMatrix Layout |
getBioMatrixGeneLabelWidth | Methods to Get caOmicsV BioMatrix Plot Parameters |
getBioMatrixGeneNumber | Methods to Get caOmicsV BioMatrix Plot Parameters |
getBioMatrixLegendHeight | Methods to Get caOmicsV BioMatrix Plot Parameters |
getBioMatrixPhenotypeNumber | Methods to Get caOmicsV BioMatrix Plot Parameters |
getBioMatrixPlotAreaHeigth | Methods to Get caOmicsV BioMatrix Plot Parameters |
getBioMatrixPlotAreaWidth | Methods to Get caOmicsV BioMatrix Plot Parameters |
getBioMatrixRemarkWidth | Methods to Get caOmicsV BioMatrix Plot Parameters |
getBioMatrixRowPadding | Methods to Get caOmicsV BioMatrix Plot Parameters |
getBioMatrixSampleHeight | Methods to Get caOmicsV BioMatrix Plot Parameters |
getBioMatrixSampleIDHeight | Methods to Get caOmicsV BioMatrix Plot Parameters |
getBioMatrixSampleNumber | Methods to Get caOmicsV BioMatrix Plot Parameters |
getBioMatrixSampleWidth | Methods to Get caOmicsV BioMatrix Plot Parameters |
getBioMatrixSummaryWidth | Methods to Get caOmicsV BioMatrix Plot Parameters |
getBioNetBasePositions | Methods to Get caOmicsV BioNetCircos Plot Parameters |
getBioNetGraph | Methods to Get caOmicsV BioNetCircos Plot Parameters |
getBioNetNodeLinkLine | Get X and Y Coordinates for An Arrow between Two Nodes |
getBioNetNodePaddingScale | Methods to Get caOmicsV BioNetCircos Plot Parameters |
getBioNetNodeParameters | Methods to Get caOmicsV BioNetCircos Plot Parameters |
getBioNetNodePlotAreaBoundary | Methods to Get caOmicsV BioNetCircos Plot Parameters |
getBioNetNodeRadius | Methods to Get caOmicsV BioNetCircos Plot Parameters |
getBioNetPlotAreaWidth | Methods to Get caOmicsV BioNetCircos Plot Parameters |
getBioNetPlotLocations | Get bioNetCircos Plot Locations |
getBioNetPlotSampleWidth | Methods to Get caOmicsV BioNetCircos Plot Parameters |
getBioNetPlotTotalSample | Methods to Get caOmicsV BioNetCircos Plot Parameters |
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 Information |
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 bioNewCircos Layout |
resetBioNetNodePlotAreaBoundary | Update Node Plot Area Boundary on caOmicsV bioNetCircos Layout |
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 bioNetCircor Layout |
setBioNetNodeLayout | Set up Layout for the igraph Object |
setBioNetPlotAreaBackground | Set up Plot Area Background for Nodes of caOmicsV bioNetCircos Layout |
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 Plot |
sortClinicalData | Sort Clinical Data by a Column |
sortOmicsDataByColumn | Sort Omics Data by Column Header |
sortOmicsDataByRow | Sort Omics Data by Row |