Make SpatialMap from FCS files

Parse standard CODEX output

Works for standard (Akoya / Enable) input. Specifically, a zipped directory or directory containing .csv files with fluorescence values and cell data, compensated using FlowJo. Each CSV corresponds to a Region, and these regions are described by the metadata_file.

Usage

makeSpatialMapFromFCS(
  data_dir,
  metadata_file,
  pattern_match = NULL,
  cell_channel_name = "DAPI",
  blank_channel_name = "Blank",
  empty_channel_name = "Empty",
  projectName = NULL,
  projectSummary = NULL,
  activeRegions = NULL,
  settings = NULL
)

Arguments

data_dir

A data directory containing CSV files

metadata_file

A metadata file, one row for each sample

pattern_match

A grep pattern for input files in data_dir

cell_channel_name

Name of the nuclear segmentation channel

blank_channel_name

Name of blank channel

empty_channel_name

Name of empty channels

projectName

The project name

projectSummary

A description of the project

activeRegions

Whether to set activeRegions here

settings

Any SM settings