Man pages for caitlinjones/halo
Development version of the package 'halo', which analyzes and visualizes Halo data

addMedianErrorBarValuesAdd to data MAD min/max y-values for plotting median error...
addMissingMarkersAdd missing markers
assignCellTypeBased on MarkerCombinationAnnotation table from...
calcDistancesFromTumorBoundaryCalculate distances from each cell to nearest point on tumor...
calculateAreaTotalFOVCalculate total area in each FOV
calculateBandAreasCalculate area of interface bands, each defined as the...
calculateDensityCalculate density of set of markers (marker combinations)
calculateFOVStatsCalculate total area and density of entire FOVs
calculateInfiltrationDensityCalculate density of set of markers (marker combinations)
calculateInterfaceAreaCalculate total area and density of tumor interface
calculateMarkerDensityTotalFOVCalculate marker densities for full FOVs
cellDive.calculateInfiltrationAreaCalculate infiltration area
cellDive.calculateInfiltrationDensityCalculate infiltration density
cellDive.calculateTotalFOVareaCalculate area of each entire FOV
cellDive.calculateTotalFOVdensityCalculate density of markers in each full FOV
cellDive.fillInMarkerComboInterpretationsAdd columns Cell_Type and Cell_Subtype to marker counts file
cellDive.getAllBoundaryAnnotationsLoad and/or parse all Halo boundary annotations
cellDive.initCombinedProjectProcess and load any existing project data
cellDive.loadAllDataLoad data from each rda file into one table
cellDive.loadStudyAnnotationsLoad and parse all Sample+FOV annotations
cellDive.markExclusionsMark cells in *.rda file to be excluded from analysis
cellDive.updateManifestOverwrite manifest file with updated values
cellDive.writeMarkerComboTablesWrite XLSX table of counts for all marker combinations in all...
cleanBoundariesRemove exclusion boundaries that are contained in another one
cleanBoundaries_OLDRemove exclusion boundaries that are contained in another one
cleanDataClean data table
cleanMarkersClean marker file
computeBandAreasMCCompute band areas for each interface bin
configureStudyConfigure study
convertBoundaryFilePathsConvert shared drive path to server path, and add...
convertCellMinMaxToMidpointsReplace Min/Max X and Y coordinates from Halo with cell...
countMarkersGenerate a XLSX file of counts for all markers in a given...
densityBoxPlotsBox plots of densities showing differences between samples...
distanceDistance between points (L2-norm)
flattenMetaDataFlatten meta data for a single study
generateSobolGridGenerate data frame of random points (is it random???)
getAllCellTypeCombinationsGet all possible marker combinations for a certain cell...
getAllCombosGet all possible combinations of markers
getAllDensityValuesGet all absolute and percentage density values for complete...
getAllFOVDensityValuesGet all absolute and percentage density values for complete...
getAllInfiltrationDensityValuesCalculate absolute and percentage density values by Sample,...
getAllInfiltrationPlotsCreate and store all infiltration plots in a list to be...
getAllTotalFOVPlotsCreate and store all infiltration plots in a list to be...
getAreaPerBandCompute lattice of boundary bins
getBandAssignmentsGet counts of cells that fall within given distances of tumor...
getBorderPaddingExclusionsGet indices of cell to be excluded because they lie outside...
getBoundingBoxGet min and max X and Y coordinates of a FOV
getBoundingBoxLGet min and max X and Y coordinates of a FOV
getCellTypesMake list of all known cell types (marker combinations) given...
getComplexMarkerCombosBuild a list of all marker combinations described in...
getCustomColorsGet marker colors
getHaloExclusionsRemove points from data set that fall inside exclusion...
getInfiltrationDensitySummarySummarize infiltration by getting total density of all FOV in...
getLegendExtract a legend from a gplot
getMarkerColorsGet marker colors
getMarkerConfigParse marker config
getMarkerDensityTableGet a table of marker combination densities
getPlotThemeGet plot theme for a given type of halo plot
getSampleBandMaxYGet maximum density value from all Sample+Band combos in a...
getSampleFromFileNameExtract sample name from file name
getSheetOrderGet order of workbook sheets for final excel file
getStudyExclusionsGet indices of cells to be excluded because of reasons...
getTemplateCellTypeConfigGenerate a template marker configuration based on meta data
getTemplateMarkerConfigGenerate a template marker configuration based on meta data
getTemplatePlotConfigGenerate a template plot configuration based on marker...
getTemplateStudyConfigCreate a study config template
getTotalDensityFillColorsGet a named vector of colors to use on total density bar...
getTotalDensityPlotsBuild bar plot for total cell type density
g_legendGet legend from a gplot
initializeProjectBuild list of project parameters and values by reading...
interpretMarkerCombosInterpret marker combinations
joinBandAreaAdd columns for band area to existing tibble with a column of...
joinBoundingBoxesGet X and Y coordinates of box enclosing two existing boxes
loadHaloLoad data from *.rda file
logParamsLog project parameters
makeDensityHeatmapMake annotated heatmap of cell type densities
makeSampleInfiltrationDensityPlotsGenerate all infiltration density plots for a single sample
makeSampleTotalFOVDensityPlotsGenerate all infiltration density plots for a single sample
markerComboCountsFind all marker combinations existing in data and count cells...
markerComboWorkbookCreate XLSX workbook and style all sheets for marker combo...
markerComboXLSXGenerate XLSX file of all marker combinations represented in...
markerStatsFileGenerate name of output file for marker stats based on input...
markerStringToPredicateGenerate string for selecting markers based on positive or...
markExclusionsGiven a tibble of object analysis data, add a column EXCLUDE...
medianRowCreate median row
OLD_calculateInfiltrationDensityCalculate density of set of markers (marker combinations)
parseAnnotationXMLRecursively process an XML node for one FOV
plotCellTypeLocationsPlot location of given cell types within one FOV
plotExclusionsPlot cell locations of exclusions
plotInfiltrationDensityPlot and print absolute density or density percentages of...
plotMarkerPercentagesMake a grid of pie charts, one for each given marker showing...
plotTotalFOVMarkerDensityPlot and print absolute density or density percentages of...
printDensityPlotsPrint density plots
printInfiltrationDensityPlotsPrint density plots
printTotalDensityPlotsPrint bar charts showing marker densities for total FOVs
printTotalFOVDensityPlotsPrint plots of total FOV marker density plots
projectFileNameGenerate name of output file for marker stats based on input...
readHaloAnnotationsParse boundary annotations of a single FOV in a single XML...
removeExcludedPointsRemove points from data set that fall inside exclusion...
removeExtraMarkersRemove from data markers that are not in marker file
removeLegendRemove a legend from a gplot
sampleInfiltrationPlotsSingleFileOrganize and print multiple sample summaries on a page or two
splitByFovSplit data in *.rda file by FOV (SPOT)
stackableDetermine whether a set of markers is 'stackable' in a bar...
summarizeByCellTypeDefinitionSummarize positive/negative marker matrix by cell type...
summarizeFOVDataByCellTypeDefinitionSummarize density data by cell type definition
thetaCompute theta
trimImageRemove cells near edge of FOV from dataset
validateConfigValidate study configuration
validateExclusionsValidate data exclusions
validateSingleFOVFileMake sure list of unique FOVs contains only one element
writeExclusionReasonsAdd exclusion reasons to a vector of existing exclusion...
writeXLSXsheetShortcut to write a XLSX file
caitlinjones/halo documentation built on Sept. 27, 2018, 9:28 p.m.