getMarkerDensityTable: Get a table of marker combination densities

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

Description

Generate a table of cell type densities

Usage

getMarkerDensityTable(markers, dat = NULL, outDir = getwd(),
  dataFiles = NULL, annotationsDirs = NULL, haloAnnotations = NULL,
  areaFiles = NULL, densityFiles = NULL, sampleOrder = NULL,
  writeCSVfiles = FALSE, pad = 20, byBand = TRUE,
  maxDistanceFromInterface = 360, bandWidth = 10, markerSetName = NULL,
  sortByMarker = NULL, funcMarker = NULL, maxG = 5, calcFOVarea = FALSE)

Arguments

dat	tibble containing halo data, specifically Sample, UUID, SPOT, Marker, Xmin/max, Ymin/max, ValueType, Value
outDir	if writeCSVfiles=T, directory to which these files will be written
dataFiles	vector of *.rda files containing Halo data for a single sample
annotationsDirs	vector of directories containing *.annotations files, XML files of boundary annotations from Halo; order must correspond to order of dataFiles
writeCSVfiles	logical; write CSV files, one of density values and one of area values; default=TRUE
pad	amount to trim from each FOV
byBand	logical indicating whether to break down density by distance from tumor interface; default=FALSE
maxDistanceFromInterface	include only those cells within this distance from tumor interface
bandWidth	width of each band around tumor interface, to be used when byBand is TRUE; default=10
sortByMarker	sort FOVs by density of this marker (cell type)in ascending order; default=NULL
funcMarker	character string of functional marker to plot on top of every other marker
maxG	maximum factor of 10 to use for generating random points on grid [ REWORD??? ]

Value

tibble containing density for all markers in all samples

caitlinjones/halo documentation built on May 7, 2019, 8 a.m.