API for caitlinjones/halo
Development version of the package 'halo', which analyzes and visualizes Halo data
| Global functions | |
|---|---|
| DATE | Source code |
| OLD_calculateInfiltrationDensity | Man page Source code |
| addMedianErrorBarValues | Man page Source code |
| addMissingMarkers | Man page Source code Source code |
| addNegatives | Source code |
| areaBB | Source code |
| assignCellType | Man page Source code |
| boundaryToSpatialPolygon | Source code |
| boundingBoxToPath | Source code |
| boundingBoxToRect | Source code |
| calcDistancesFromTumorBoundary | Man page Source code |
| calculateAreaTotalFOV | Man page Source code |
| calculateBandAreas | Man page Source code |
| calculateDensity | Man page |
| calculateFOVStats | Man page |
| calculateInfiltrationDensity | Man page Source code |
| calculateInterfaceArea | Man page Source code |
| calculateMarkerDensityTotalFOV | Man page Source code |
| cc | Source code |
| cellDive.calculateInfiltrationArea | Man page Source code |
| cellDive.calculateInfiltrationDensity | Man page Source code |
| cellDive.calculateTotalFOVarea | Man page Source code |
| cellDive.calculateTotalFOVdensity | Man page Source code |
| cellDive.fillInMarkerComboInterpretations | Man page Source code |
| cellDive.getAllBoundaryAnnotations | Man page Source code |
| cellDive.initCombinedProject | Man page Source code |
| cellDive.loadAllData | Man page Source code |
| cellDive.loadStudyAnnotations | Man page Source code |
| cellDive.markExclusions | Man page Source code |
| cellDive.updateManifest | Man page Source code |
| cellDive.writeMarkerComboTables | Man page Source code |
| cleanBoundaries | Man page Source code |
| cleanBoundaries_OLD | Man page Source code |
| cleanData | Man page Source code Source code |
| cleanMarkers | Man page Source code Source code |
| clipSPBoundaryToBB | Source code |
| clipSPBoundaryToBBWithDraw | Source code |
| computeBandAreasMC | Man page Source code |
| computeMultiMarkerTable | Source code Source code |
| configureStudy | Man page Source code |
| convertBoundaryFilePaths | Man page Source code |
| convertCellMinMaxToMidpoints | Man page Source code |
| countMarkers | Man page Source code Source code |
| densityBoxPlots | Man page Source code |
| distance | Man page Source code |
| drawBoundaries | Source code |
| drawBoundary | Source code |
| drawBoundingBox | Source code |
| expandClippedPathToOuterBox | Source code |
| flattenMetaData | Man page Source code |
| g_legend | Man page |
| generateSobolGrid | Man page Source code |
| getAllCellTypeCombinations | Man page Source code |
| getAllCombos | Man page Source code |
| getAllDensityValues | Man page |
| getAllFOVDensityValues | Man page Source code |
| getAllHaloAnnotations | Source code |
| getAllInfiltrationDensityValues | Man page Source code |
| getAllInfiltrationPlots | Man page Source code |
| getAllTotalFOVPlots | Man page Source code |
| getAreaPerBand | Man page Source code |
| getBandAssignments | Man page Source code |
| getBorderPaddingExclusions | Man page Source code |
| getBoundingBox | Man page Source code |
| getBoundingBoxL | Man page Source code |
| getCellTypes | Man page Source code |
| getComplexMarkerCombos | Man page Source code |
| getCustomColors | Man page |
| getDriftExclusions | Source code |
| getHaloExclusions | Man page Source code |
| getInfiltrationDensitySummary | Man page Source code |
| getLegend | Man page Source code |
| getMarkerColors | Man page |
| getMarkerConfig | Man page Source code |
| getMarkerDensityTable | Man page Source code |
| getPlotTheme | Man page Source code |
| getSDIR | Source code |
| getSampleBandMaxY | Man page Source code |
| getSampleFromFileName | Man page Source code |
| getSheetOrder | Man page Source code Source code |
| getStudyExclusions | Man page Source code |
| getTemplateCellTypeConfig | Man page Source code |
| getTemplateMarkerConfig | Man page |
| getTemplatePlotConfig | Man page Source code |
| getTemplateStudyConfig | Man page Source code |
| getTotalDensityFillColors | Man page |
| getTotalDensityPlots | Man page |
| getTotalSampleDensitySummary | Source code |
| gridArrangeSharedLegend | Source code |
| initializeProject | Man page Source code |
| interfaceSide | Source code |
| interpretMarkerCombos | Man page Source code |
| intersectWithBoundingBox | Source code |
| joinBandArea | Man page Source code |
| joinBoundingBoxes | Man page Source code |
| len | Source code |
| loadHalo | Man page Source code Source code |
| logParams | Man page Source code |
| makeDensityHeatmap | Man page Source code |
| makeSampleInfiltrationDensityPlots | Man page Source code |
| makeSampleTotalFOVDensityPlots | Man page Source code |
| markExclusions | Man page Source code |
| markerComboCounts | Man page Source code |
| markerComboWorkbook | Man page Source code |
| markerComboXLSX | Man page Source code |
| markerStatsFile | Man page Source code Source code |
| markerStringToPredicate | Man page Source code |
| markerStringToSelectRE | Source code |
| medianRow | Man page Source code Source code |
| padBoundingBox | Source code |
| parseAnnotationXML | Man page Source code |
| plotCellTypeLocations | Man page Source code |
| plotExclusions | Man page Source code |
| plotFOV | Source code |
| plotFOV0 | Source code |
| plotFOV1 | Source code |
| plotInfiltrationDensity | Man page Source code |
| plotMarkerPercentages | Man page |
| plotTotalFOVMarkerDensity | Man page Source code |
| pointsInPolygon | Source code |
| pointsInsidePolygonList | Source code |
| printDensityPlots | Man page |
| printInfiltrationDensityPlots | Man page Source code |
| printTotalDensityPlots | Man page |
| printTotalFOVDensityPlots | Man page Source code |
| projectFileName | Man page Source code |
| readHaloAnnotations | Man page Source code |
| removeExcludedPoints | Man page Source code |
| removeExtraMarkers | Man page Source code Source code |
| removeLegend | Man page Source code |
| removeNegativeMarkers | Source code |
| sampleInfiltrationPlotsSingleFile | Man page Source code |
| splitByFov | Man page Source code |
| stackable | Man page Source code |
| subDivideLongSegments | Source code |
| summarizeByCellTypeDefinition | Man page Source code |
| summarizeFOVDataByCellTypeDefinition | Man page Source code |
| theta | Man page Source code |
| trimDFToBB | Source code |
| trimImage | Man page Source code Source code |
| tty.width | Source code |
| validateConfig | Man page Source code |
| validateExclusions | Man page Source code |
| validateSingleFOVFile | Man page Source code Source code |
| write.xls | Source code |
| writeExclusionReasons | Man page Source code |
| writeXLSXsheet | Man page Source code Source code |
