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
