Man pages for caitlinjones/halo
Development version of the package 'halo', which analyzes and visualizes Halo data
| addMedianErrorBarValues | Add to data MAD min/max y-values for plotting median error... |
| addMissingMarkers | Add missing markers |
| assignCellType | Based on MarkerCombinationAnnotation table from... |
| calcDistancesFromTumorBoundary | Calculate distances from each cell to nearest point on tumor... |
| calculateAreaTotalFOV | Calculate total area in each FOV |
| calculateBandAreas | Calculate area of interface bands, each defined as the... |
| calculateDensity | Calculate density of set of markers (marker combinations) |
| calculateFOVStats | Calculate total area and density of entire FOVs |
| calculateInfiltrationDensity | Calculate density of set of markers (marker combinations) |
| calculateInterfaceArea | Calculate total area and density of tumor interface |
| calculateMarkerDensityTotalFOV | Calculate marker densities for full FOVs |
| cellDive.calculateInfiltrationArea | Calculate infiltration area |
| cellDive.calculateInfiltrationDensity | Calculate infiltration density |
| cellDive.calculateTotalFOVarea | Calculate area of each entire FOV |
| cellDive.calculateTotalFOVdensity | Calculate density of markers in each full FOV |
| cellDive.fillInMarkerComboInterpretations | Add columns Cell_Type and Cell_Subtype to marker counts file |
| cellDive.getAllBoundaryAnnotations | Load and/or parse all Halo boundary annotations |
| cellDive.initCombinedProject | Process and load any existing project data |
| cellDive.loadAllData | Load data from each rda file into one table |
| cellDive.loadStudyAnnotations | Load and parse all Sample+FOV annotations |
| cellDive.markExclusions | Mark cells in *.rda file to be excluded from analysis |
| cellDive.updateManifest | Overwrite manifest file with updated values |
| cellDive.writeMarkerComboTables | Write XLSX table of counts for all marker combinations in all... |
| cleanBoundaries | Remove exclusion boundaries that are contained in another one |
| cleanBoundaries_OLD | Remove exclusion boundaries that are contained in another one |
| cleanData | Clean data table |
| cleanMarkers | Clean marker file |
| computeBandAreasMC | Compute band areas for each interface bin |
| configureStudy | Configure study |
| convertBoundaryFilePaths | Convert shared drive path to server path, and add... |
| convertCellMinMaxToMidpoints | Replace Min/Max X and Y coordinates from Halo with cell... |
| countMarkers | Generate a XLSX file of counts for all markers in a given... |
| densityBoxPlots | Box plots of densities showing differences between samples... |
| distance | Distance between points (L2-norm) |
| flattenMetaData | Flatten meta data for a single study |
| generateSobolGrid | Generate data frame of random points (is it random???) |
| getAllCellTypeCombinations | Get all possible marker combinations for a certain cell... |
| getAllCombos | Get all possible combinations of markers |
| getAllDensityValues | Get all absolute and percentage density values for complete... |
| getAllFOVDensityValues | Get all absolute and percentage density values for complete... |
| getAllInfiltrationDensityValues | Calculate absolute and percentage density values by Sample,... |
| getAllInfiltrationPlots | Create and store all infiltration plots in a list to be... |
| getAllTotalFOVPlots | Create and store all infiltration plots in a list to be... |
| getAreaPerBand | Compute lattice of boundary bins |
| getBandAssignments | Get counts of cells that fall within given distances of tumor... |
| getBorderPaddingExclusions | Get indices of cell to be excluded because they lie outside... |
| getBoundingBox | Get min and max X and Y coordinates of a FOV |
| getBoundingBoxL | Get min and max X and Y coordinates of a FOV |
| getCellTypes | Make list of all known cell types (marker combinations) given... |
| getComplexMarkerCombos | Build a list of all marker combinations described in... |
| getCustomColors | Get marker colors |
| getHaloExclusions | Remove points from data set that fall inside exclusion... |
| getInfiltrationDensitySummary | Summarize infiltration by getting total density of all FOV in... |
| getLegend | Extract a legend from a gplot |
| getMarkerColors | Get marker colors |
| getMarkerConfig | Parse marker config |
| getMarkerDensityTable | Get a table of marker combination densities |
| getPlotTheme | Get plot theme for a given type of halo plot |
| getSampleBandMaxY | Get maximum density value from all Sample+Band combos in a... |
| getSampleFromFileName | Extract sample name from file name |
| getSheetOrder | Get order of workbook sheets for final excel file |
| getStudyExclusions | Get indices of cells to be excluded because of reasons... |
| getTemplateCellTypeConfig | Generate a template marker configuration based on meta data |
| getTemplateMarkerConfig | Generate a template marker configuration based on meta data |
| getTemplatePlotConfig | Generate a template plot configuration based on marker... |
| getTemplateStudyConfig | Create a study config template |
| getTotalDensityFillColors | Get a named vector of colors to use on total density bar... |
| getTotalDensityPlots | Build bar plot for total cell type density |
| g_legend | Get legend from a gplot |
| initializeProject | Build list of project parameters and values by reading... |
| interpretMarkerCombos | Interpret marker combinations |
| joinBandArea | Add columns for band area to existing tibble with a column of... |
| joinBoundingBoxes | Get X and Y coordinates of box enclosing two existing boxes |
| loadHalo | Load data from *.rda file |
| logParams | Log project parameters |
| makeDensityHeatmap | Make annotated heatmap of cell type densities |
| makeSampleInfiltrationDensityPlots | Generate all infiltration density plots for a single sample |
| makeSampleTotalFOVDensityPlots | Generate all infiltration density plots for a single sample |
| markerComboCounts | Find all marker combinations existing in data and count cells... |
| markerComboWorkbook | Create XLSX workbook and style all sheets for marker combo... |
| markerComboXLSX | Generate XLSX file of all marker combinations represented in... |
| markerStatsFile | Generate name of output file for marker stats based on input... |
| markerStringToPredicate | Generate string for selecting markers based on positive or... |
| markExclusions | Given a tibble of object analysis data, add a column EXCLUDE... |
| medianRow | Create median row |
| OLD_calculateInfiltrationDensity | Calculate density of set of markers (marker combinations) |
| parseAnnotationXML | Recursively process an XML node for one FOV |
| plotCellTypeLocations | Plot location of given cell types within one FOV |
| plotExclusions | Plot cell locations of exclusions |
| plotInfiltrationDensity | Plot and print absolute density or density percentages of... |
| plotMarkerPercentages | Make a grid of pie charts, one for each given marker showing... |
| plotTotalFOVMarkerDensity | Plot and print absolute density or density percentages of... |
| printDensityPlots | Print density plots |
| printInfiltrationDensityPlots | Print density plots |
| printTotalDensityPlots | Print bar charts showing marker densities for total FOVs |
| printTotalFOVDensityPlots | Print plots of total FOV marker density plots |
| projectFileName | Generate name of output file for marker stats based on input... |
| readHaloAnnotations | Parse boundary annotations of a single FOV in a single XML... |
| removeExcludedPoints | Remove points from data set that fall inside exclusion... |
| removeExtraMarkers | Remove from data markers that are not in marker file |
| removeLegend | Remove a legend from a gplot |
| sampleInfiltrationPlotsSingleFile | Organize and print multiple sample summaries on a page or two |
| splitByFov | Split data in *.rda file by FOV (SPOT) |
| stackable | Determine whether a set of markers is 'stackable' in a bar... |
| summarizeByCellTypeDefinition | Summarize positive/negative marker matrix by cell type... |
| summarizeFOVDataByCellTypeDefinition | Summarize density data by cell type definition |
| theta | Compute theta |
| trimImage | Remove cells near edge of FOV from dataset |
| validateConfig | Validate study configuration |
| validateExclusions | Validate data exclusions |
| validateSingleFOVFile | Make sure list of unique FOVs contains only one element |
| writeExclusionReasons | Add exclusion reasons to a vector of existing exclusion... |
| writeXLSXsheet | Shortcut to write a XLSX file |
