cellDive.calculateInfiltrationArea: Calculate infiltration area

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

Description

Generate table with columns: Sample, SPOT, Band, Area

Usage

cellDive.calculateInfiltrationArea(allDat, pp, haloAnnotations,
  updatedExclusions)

Arguments

allDat	tibble of all halo data
pp	list of all project parameters
haloAnnotations	list of parsed halo annotations organized by sample and then by FOV
updatedExclusions	logical indicating whether exclusions (haloAnnotations) were updated during current run of the pipeline

Value

list of three items: (1) dat = list where area = table of Sample,SPOT,Area and bandAssignments = table of 0/1 for each marker in each cell, plus a column "Band" indicating roughly how far the cell lies from a tumor interface (2) updated = logical indicating whether table being returned was generated (TRUE) or loaded from existing file (FALSE) (3) pp = updated list of project parameters

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