Skip to contents

Get Autofluorescence Spectra

Source: R/get_af_spectra.R
get.af.spectra.Rd

Extracts autofluorescence spectra from an unstained samples. Intended for use with unmix.autospectral. Uses FlowSOM (EmbedSOM) clustering for rapid identification of cells with similar AF profiles.

Usage

get.af.spectra(
  unstained.sample,
  asp,
  spectra,
  som.dim = 10,
  figures = TRUE,
  plot.dir = NULL,
  table.dir = NULL,
  title = "Autofluorescence spectra",
  verbose = TRUE,
  refine = FALSE,
  problem.quantile = 0.99,
  remove.contaminants = TRUE,
  parallel = TRUE,
  threads = if (parallel) 0 else 1,
  heatmap.color.palette = "viridis",
  spectral.trace.color.palette = NULL,
  af.fill.color = "red",
  af.line.color = "black"
)

Arguments

unstained.sample

Path and file name for a unstained sample FCS file. The sample type and processing (protocol) method should match the fully stained samples to which the AF will be applied, ideally.

asp

The AutoSpectral parameter list.

spectra

Spectral signatures of fluorophores, normalized between 0 and 1, with fluorophores in rows and detectors in columns.

som.dim

Number of x and y dimensions for the SOM. Default is 10.

figures

Logical, whether to plot the spectral traces and heatmap for the AF signatures. Default is TRUE.

plot.dir

Directory (folder) where the plots will be saved. Default is NULL, which inherits from asp$figure.af.dir.

table.dir

Directory (folder) where the spectra csv file will be saved. Default is NULL, which inherits from asp$table.af.dir.

title

Title for the output spectral plots and csv file. Default is Autofluorescence spectra.

verbose

Logical, controls messaging. Default is TRUE.

refine

Logical, default is FALSE. Controls whether to perform a second round of autofluorescence measurement on "problem cells", which are those with the highest spillover, as defined by problem.quantile. When FALSE, behavior is identical to versions of AutoSpectral prior to 1.0.0. If you are working with samples containing complex autofluorescence, e.g., tissues or tumors, using refine=TRUE will improve autofluorescence extraction in the unmixing at the cost of an increase in unmixing time. The increase in time will depend on the method used to assign autofluorescence spectra per cell (residual based assignment is very fast) and whether you have installed AutoSpectralRcpp, which will speed up assignment and unmixing.

problem.quantile

Numeric, default 0.99. The quantile for determining which cells will be considered "problematic" after unmixing with per-cell AF extraction. Cells in the problem.quantile or above with respect to total signal in the fluorophore (non-AF) channels after per-cell AF extraction will be used to determine additional autofluorescence spectra, using a second round of clustering and modulation of the previously selected autofluorescence spectra. A value of 0.99 means the top 1% of cells, those farthest from zero, will be selected for further investigation.

remove.contaminants

Logical, default is TRUE. A QC check is performed to exclude any autofluorescence spectra that are nearly identical to the fluorophore signatures in spectra. This helps deal with low-level contamination of unstained samples by single-stained control samples, which happens sometimes. To include these AF spectra, which can mess up unmixing if they are really fluorophore spectra, set FALSE.

parallel

Logical, default is TRUE, which enables parallel processing for per-cell AF identification. Used when refine=TRUE.

threads

Numeric, defaults to a single thread for sequential processing (parallel=FALSE) or all available cores if parallel=TRUE.Used when refine=TRUE.

heatmap.color.palette

Optional character string defining the viridis color palette to be used for the fluorophore traces. Default is viridis. Options are the viridis color options: magma, inferno, plasma, viridis, cividis, rocket, mako and turbo.

spectral.trace.color.palette

Optional character string defining the color palette to be used for the AF traces. Default is NULL, in which case default R Brewer colors will be assigned automatically. Options are the viridis color options: magma, inferno, plasma, viridis, cividis, rocket, mako and turbo.

af.fill.color

Color for the shaded region indicating the range of variation in the autofluorescence. Feeds to fill in geom_ribbon. Default is "red".

af.line.color

Color for the line representing the median autofluorescence spectrum. Default is "black".

Value

A matrix of autofluorescence spectra.

References

Van Gassen S et al. (2015). "FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data." Cytometry Part A, 87(7), 636-645. doi:10.1002/cyto.a.22625 Wehrens R, Kruisselbrink J (2018). “Flexible Self-Organizing Maps in kohonen 3.0.” Journal of Statistical Software, 87(7), 1-18. doi:10.18637/jss.v087.i07