cellDive.calculateTotalFOVdensity: Calculate density of markers in each full FOV

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

Description

Generate table of four columns: Sample, SPOT, Counts, Density

Usage

cellDive.calculateTotalFOVdensity(allDat, markerConfig, fovAreas, pp,
  updatedFOVarea, updatedComboTable, fovDensityPrefix = "")

Arguments

allDat	all Halo data
markerConfig	tibble of parsed marker configuration (value returned from getMarkerConfig)
fovAreas	tibble of areas for each FOV in each Sample (value returned from cellDive.calculateTotalFOVarea)
pp	list of all project parameters
updatedComboTable	logical indicating whether combo table was updated during current pipeline run
fovDensityPrefix	prefix added to prefix added to 'fov_density_file' and/or 'fov_density_dir' in names of pp list (leave "" if no prefix)
updatedFOVareas	logical indicating whether FOV areas were updated during current pipeline run

Value

list of three items: (1) dat = tibble of three columns: Sample, SPOT, Count, Density (2) updated = logical indicating whether a new density table was generated (TRUE) or an old one was loaded (FALSE) (3) pp = updated list of project parameters

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