Unmix All FCS Files in a Directory — unmix.folder • AutoSpectral

This function unmixes all FCS files in a specified directory using the provided spectra and method, and saves the unmixed FCS files to an output directory of the user's choice.

Usage

unmix.folder(
  fcs.dir,
  spectra,
  asp,
  flow.control,
  method = c("AutoSpectral", "OLS", "WLS", "Poisson", "FastPoisson"),
  weighted = FALSE,
  weights = NULL,
  af.spectra = NULL,
  spectra.variants = NULL,
  output.dir = NULL,
  file.suffix = NULL,
  include.raw = FALSE,
  include.imaging = TRUE,
  use.dist0 = TRUE,
  divergence.threshold = 10000,
  divergence.handling = "Balance",
  balance.weight = 0.5,
  speed = c("fast", "medium", "slow"),
  parallel = FALSE,
  threads = NULL,
  verbose = TRUE,
  n.variants = NULL,
  chunk.size = 2e+06,
  pipeline = c("legacy", "joint"),
  n.passes = 1L,
  n.af.passes = 1L,
  cell.weight = if (asp$cytometer == "ID7000") TRUE else FALSE,
  noise.floor = 125,
  alpha = 0.5,
  collinear.threshold = 0.5,
  joint.pair.resolution = TRUE,
  refine.af.quantile = 0.5,
  ...
)

Arguments

fcs.dir: Directory (file path) containing FCS files to be unmixed.
spectra: A matrix containing the spectral data. Fluorophores in rows, detectors in columns.
asp: The AutoSpectral parameter list. Prepare using get.autospectral.param.
flow.control: A list containing flow cytometry control parameters.
method: A character string specifying the unmixing method to use. The default as of version 1.0.0 is now AutoSpectral to avoid confusion. To use AutoSpectral unmixing, you must provide at least af.spectra to perform autofluorescence extraction (on a per-cell basis). To also optimize fluorophore spectra, provide spectra.variants. To perform other types of unmixing, select from the options: OLS, WLS, Poisson or FastPoisson. FastPoisson requires installation of AutoSpectralRcpp.
weighted: Logical, whether to use ordinary or weighted least squares unmixing as the base algorithm in AutoSpectral legacy pipeline unmixing. Default is FALSE and will use OLS.
weights: Optional numeric vector of weights (one per fluorescent detector). Default is NULL, in which case weighting will be done by channel means (Poisson variance). Only used for WLS.
af.spectra: Spectral signatures of autofluorescences, normalized between 0 and 1, with fluorophores in rows and detectors in columns. Prepare using get.af.spectra. Required for AutoSpectral unmixing. Default is NULL and will thus provoke failure if no spectra are provided and AutoSpectral is selected.
spectra.variants: Named list (names are fluorophores) carrying matrices of spectral signature variations for each fluorophore. Prepare using get.spectral.variants. Default is NULL. Used for AutoSpectral unmixing. Required for per-cell fluorophore optimization.
output.dir: A character string specifying the directory to save the unmixed FCS file. Default is NULL, which will use ./AutoSpectral_unmixed.
file.suffix: A character string to append to the output file name. Default is NULL.
include.raw: A logical value indicating whether to include raw expression data in the written FCS file. Default is FALSE to provide smaller output files.
include.imaging: A logical value indicating whether to include imaging parameters in the written FCS file. Default is TRUE.
use.dist0: Legacy pipeline argument. Logical, controls whether the selection of the optimal AF signature for each cell is determined by the minimization of potential AF spillover into the fluorophore channels (use.dist0 = TRUE) or by which unmixing minimizes the per-cell residual (use.dist0 = FALSE). Default is TRUE. Used for legacy AutoSpectral unmixing.
divergence.threshold: Numeric. Used for FastPoisson only. Threshold to trigger reversion towards WLS unmixing when Poisson result diverges for a given point. To be deprecated.
divergence.handling: String. How to handle divergent cells from Poisson IRLS. Options are NonNeg (non-negativity will be enforced), WLS (revert to WLS initial unmix) or Balance (WLS and NonNeg will be averaged). Default is Balance. To be deprecated.
balance.weight: Numeric. Weighting to average non-convergent cells. Used for Balance option under divergence.handling. Default is 0.5. To be deprecated.
speed: Selector for the precision-speed trade-off in AutoSpectral per-cell fluorophore optimization. Options are fast, medium and slow, with the default being fast. As of version 1.0.0, the backend for how this works has changed. Spectral variants and AF signatures are now pre-screened per cell to identify likely candidates, so brute force testing of all variants is no longer required. So, speed controls the number of variants to be tested per cell, with fast testing a single variant, medium testing 3 variants, and slow testing 10 variants. While this is now implemented in pure R in AutoSpectral, installation of AutoSpectralRcpp is strongly encouraged for faster processing.
parallel: Logical, default is TRUE, which enables parallel processing for per-cell unmixing methods.
threads: Numeric, defaults to a single thread for sequential processing (parallel=FALSE) or all available cores if parallel=TRUE.
verbose: Logical, controls messaging. Default is TRUE. Set to FALSE to have it shut up.
n.variants: Numeric, used for legacy AutoSpectral pipeline unmixing. Number of variants to test per cell. Allows explicit control over the number used, as opposed to speed, which selects from pre-defined choices. Providing a numeric value to n.variants will override speed, allowing up to n.variants (or the max available) variants to be tested. The default is NULL, in which case n.variants will be ignored.
chunk.size: Numeric, number of events to use per chunk of unmixing. Used to manage memory when processing large FCS files. As a rough guide, you will need approximately 10x the size of the raw FCS file on disk as available memory. Default is set at 2e6 events, assuming ~20GB memory available.
pipeline: Character, one of "legacy" (default) or "joint". Passed to unmix.autospectral.rcpp(). "joint" uses the new covariance-weighted joint per-cell pipeline; "legacy" reproduces the behaviour of AutoSpectral prior to version 1.6.0.
n.passes: Integer, default 1L. Number of joint optimisation passes per cell. Only used when pipeline = "joint". Set higher for some improvement in unmixing with high spillover datasets.
n.af.passes: Integer, default 1L. Number of autofluorescence extraction passes per cell. Only used when pipeline = "joint". Passed to unmix.autospectral.rcpp().
cell.weight: Logical, default FALSE. Applies per-cell detector weighting to the joint unmixing solve. Only used when pipeline = "joint". Passed to unmix.autospectral.rcpp(). Useful for ID7000 files.
noise.floor: Numeric, default 125. Lower clamp on the denominator of the per-cell detector weights when cell.weight = TRUE. Only used when pipeline = "joint". Passed to unmix.autospectral.rcpp().
alpha: Numeric, default 0.5. Weighting for balancing residual and covariance spillover minimization. Only used when pipeline = "joint". Passed to unmix.autospectral.rcpp().
collinear.threshold: Numeric, default 0.5. Cosine similarity value to trigger conflict assessment for collinear fluorophore variants. Only used when pipeline = "joint". Passed to unmix.autospectral.rcpp().
joint.pair.resolution: Logical, default TRUE. Whether to perform conflict-resolution for collinear fluorophore pairs. Only used when pipeline = "joint". Passed to unmix.autospectral.rcpp().
refine.af.quantile: Numeric, default 0.5. Fraction of cells taken forward for additional AF passes (see n.af.passes). Only used when pipeline = "joint". Passed to unmix.autospectral.rcpp().
...: Ignored. Previously used for deprecated arguments such as calculate.error.

Value

None. Saves the unmixed FCS files to the specified output directory.