Man pages for hzhanghenry/caOmicsV
Visualization of multi-dimentional cancer genomics data
| 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.biomatrix.eset | Demo Dataset for caOmicsV bioMatrix Plot |
| caOmicsV.bionet.eset | Demo Dataset for caOmicsV bioNetCircos Plot |
| 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 |
| getESet | Prepare Data Set for caOmicsV Plot |
| 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 |
