Plot Autofluorescence Identification Gate — gate.af.identify.plot • AutoSpectral

This function plots the sample being used to identify intrusive autofluorescence in the single-stained controls. The input data are expected to be PCA projections of the unstained sample with an accompanying region to identify the low-autofluorescence cell region.

Usage

gate.af.identify.plot(
  gate.data,
  samp,
  gate.region,
  gate.bound.density,
  asp,
  color.palette = "rainbow"
)

Arguments

gate.data: Matrix containing autofluorescence data points.
samp: Sample identifier.
gate.region: Dataframe containing region boundary information.
gate.bound.density: Density (e.g., from MASS:kde2d) information
asp: The AutoSpectral parameter list. Prepare using get.autospectral.param
color.palette: Optional character string defining the viridis color palette to be used for the fluorophore traces. Default is rainbow, which will be similar to FlowJo or SpectroFlo. Other pptions are the viridis color options: magma, inferno, plasma, viridis, cividis, rocket, mako and turbo.

Value

Saves the plot as a JPEG file in the specified directory.