summarizeByCellTypeDefinition: Summarize positive/negative marker matrix by cell type...

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

Description

Get cell counts and densities by cell definition rather than marker combination

Usage

summarizeByCellTypeDefinition(assignments, bandArea, config, plotConfigFile)

Arguments

assignments	table of 0s and 1s, where columns are markers (may be pos or neg) and each row is a unique cell; zero indicates cell is NOT positive for that marker (note, if marker name is negative a zero means the opposite) and one indicates positivity
bandArea	table indicating calculated area for each sample, fov and band
config	parsed marker config of info for each cell type definition including marker combinations (result of getMarkerConfig())
plotConfigFile	full path to file containing plot options including colors for cell types

Value

list of two items: den=density table, config=updated config to represent summary info

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