Files in caitlinjones/halo
Development version of the package 'halo', which analyzes and visualizes Halo data

.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/constants.R R/exclusions.R
R/halodevTest/config/study_config.yaml
R/halodevTest/config/template_plot_config.yaml
R/interface.R R/marker_combo_table.R R/marker_counts.R R/melanoma_spatial.R R/old_functions.R R/plots.R R/process_meta.R R/spatial_util.R R/util.R R/validation.R README.md README_OLD.md
TEMPORARY_NOTES.txt
archive/counts.R archive/halo_pipeline.R archive/halo_pipeline_cohort1.R archive/mark_exclusions.R archive/old_halo_pipeline.R archive/pie_charts.R archive/spatial_plots.R archive/spatial_plots_2.R docs/analyses.md docs/config_files.md docs/pipeline.md docs/scripts.md
halo.Rproj
inst/extdata/template_configs/all_marker_sets_config.yaml
inst/extdata/template_configs/example_study_config.yaml
inst/extdata/template_configs/plot_config.yaml
inst/extdata/template_configs/template_marker_config.yaml
man/OLD_calculateInfiltrationDensity.Rd man/addMedianErrorBarValues.Rd man/addMissingMarkers.Rd man/assignCellType.Rd man/calcDistancesFromTumorBoundary.Rd man/calculateAreaTotalFOV.Rd man/calculateBandAreas.Rd man/calculateDensity.Rd man/calculateFOVStats.Rd man/calculateInfiltrationDensity.Rd man/calculateInterfaceArea.Rd man/calculateMarkerDensityTotalFOV.Rd man/cellDive.calculateInfiltrationArea.Rd man/cellDive.calculateInfiltrationDensity.Rd man/cellDive.calculateTotalFOVarea.Rd man/cellDive.calculateTotalFOVdensity.Rd man/cellDive.fillInMarkerComboInterpretations.Rd man/cellDive.getAllBoundaryAnnotations.Rd man/cellDive.initCombinedProject.Rd man/cellDive.loadAllData.Rd man/cellDive.loadStudyAnnotations.Rd man/cellDive.markExclusions.Rd man/cellDive.updateManifest.Rd man/cellDive.writeMarkerComboTables.Rd man/cleanBoundaries.Rd man/cleanBoundaries_OLD.Rd man/cleanData.Rd man/cleanMarkers.Rd man/computeBandAreasMC.Rd man/configureStudy.Rd man/convertBoundaryFilePaths.Rd man/convertCellMinMaxToMidpoints.Rd man/countMarkers.Rd man/densityBoxPlots.Rd man/distance.Rd man/flattenMetaData.Rd man/g_legend.Rd man/generateSobolGrid.Rd man/getAllCellTypeCombinations.Rd man/getAllCombos.Rd man/getAllDensityValues.Rd man/getAllFOVDensityValues.Rd man/getAllInfiltrationDensityValues.Rd man/getAllInfiltrationPlots.Rd man/getAllTotalFOVPlots.Rd man/getAreaPerBand.Rd man/getBandAssignments.Rd man/getBorderPaddingExclusions.Rd man/getBoundingBox.Rd man/getBoundingBoxL.Rd man/getCellTypes.Rd man/getComplexMarkerCombos.Rd man/getCustomColors.Rd man/getHaloExclusions.Rd man/getInfiltrationDensitySummary.Rd man/getLegend.Rd man/getMarkerColors.Rd man/getMarkerConfig.Rd man/getMarkerDensityTable.Rd man/getPlotTheme.Rd man/getSampleBandMaxY.Rd man/getSampleFromFileName.Rd man/getSheetOrder.Rd man/getStudyExclusions.Rd man/getTemplateCellTypeConfig.Rd man/getTemplateMarkerConfig.Rd man/getTemplatePlotConfig.Rd man/getTemplateStudyConfig.Rd man/getTotalDensityFillColors.Rd man/getTotalDensityPlots.Rd man/initializeProject.Rd man/interpretMarkerCombos.Rd man/joinBandArea.Rd man/joinBoundingBoxes.Rd man/loadHalo.Rd man/logParams.Rd man/makeDensityHeatmap.Rd man/makeSampleInfiltrationDensityPlots.Rd man/makeSampleTotalFOVDensityPlots.Rd man/markExclusions.Rd man/markerComboCounts.Rd man/markerComboWorkbook.Rd man/markerComboXLSX.Rd man/markerStatsFile.Rd man/markerStringToPredicate.Rd man/medianRow.Rd man/parseAnnotationXML.Rd man/plotCellTypeLocations.Rd man/plotExclusions.Rd man/plotInfiltrationDensity.Rd man/plotMarkerPercentages.Rd man/plotTotalFOVMarkerDensity.Rd man/printDensityPlots.Rd man/printInfiltrationDensityPlots.Rd man/printTotalDensityPlots.Rd man/printTotalFOVDensityPlots.Rd man/projectFileName.Rd man/readHaloAnnotations.Rd man/removeExcludedPoints.Rd man/removeExtraMarkers.Rd man/removeLegend.Rd man/sampleInfiltrationPlotsSingleFile.Rd man/splitByFov.Rd man/stackable.Rd man/summarizeByCellTypeDefinition.Rd man/summarizeFOVDataByCellTypeDefinition.Rd man/theta.Rd man/trimImage.Rd man/validateConfig.Rd man/validateExclusions.Rd man/validateSingleFOVFile.Rd man/writeExclusionReasons.Rd man/writeXLSXsheet.Rd scripts/add_marker_combo_interpretations.R scripts/calculate_distances.R scripts/combine_cohorts.R scripts/configure_halo_pipeline.R scripts/final_pipeline.R scripts/macrophage_pie_alternatives.R scripts/macrophage_pies.R scripts/macrophage_pies_total_FOV.R scripts/mark_exclusions.R test_starter.R
tests/config/plot_config.yaml
tests/config/study_config.yaml
tests/config/template_marker_config.yaml
tests/halodevTest/config/study_config.yaml
tests/halodevTest/file9dc2ea9d530
tests/halodevTest/file9dc6d382e4c
tests/run_test.sh
tests/testthat.R
caitlinjones/halo documentation built on Sept. 27, 2018, 9:28 p.m.