Get Gated Flow Expression Data — get.gated.flow.expression.data • AutoSpectral

Retrieves gated flow cytometry expression data for specified samples, removing out-of-range events and applying gating boundaries.

Usage

get.gated.flow.expression.data(
  samp,
  file.name,
  control.dir,
  scatter.and.spectral.channel,
  spectral.channel,
  set.resolution,
  flow.gate,
  gate.list,
  scatter.param,
  scatter.and.channel.label,
  asp,
  apply.gate,
  color.palette = "mako"
)

Arguments

samp: The sample identifier.
file.name: A vector of file names for the samples.
control.dir: The directory containing the control files.
scatter.and.spectral.channel: A vector of scatter and spectral channels.
spectral.channel: A vector of spectral channels.
set.resolution: The resolution limit for the spectral channels.
flow.gate: A list of flow gates for the samples.
gate.list: A list of gating boundaries.
scatter.param: A vector of scatter parameters.
scatter.and.channel.label: A label for scatter and channel.
asp: The AutoSpectral parameter list.
apply.gate: Logical, whether to apply a scatter gate (supplied to gate.list).
color.palette: Optional character string defining the viridis color palette to be used for the fluorophore traces. Default is mako. Use rainbow to be similar to FlowJo or SpectroFlo. Other options are the viridis color options: magma, inferno, plasma, viridis, cividis, rocket, mako and turbo.

Value

A matrix with the gated expression data.