Plot Pre-defined Gate on Sample — gate.sample.plot • AutoSpectral

This function plots a pre-defined gate on a sample, using ggplot2 and other necessary packages.

Usage

gate.sample.plot(
  samp,
  gate.data,
  gate.marker,
  gate.boundary,
  scatter.and.channel.label,
  control.type,
  asp,
  color.palette = "mako",
  max.points = 50000,
  gate.color = "darkgoldenrod1",
  switch.n = 20000
)

Arguments

samp: Sample identifier.
gate.data: Matrix containing gate data points.
gate.marker: Vector containing gate marker names.
gate.boundary: List containing gate boundary information.
scatter.and.channel.label: Named vector mapping scatter and channel labels.
control.type: Type of control: beads or cells. Deprecated.
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 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.
max.points: Number of points to plot (speeds up plotting). Default is 5e4.
gate.color: Color to plot the gate boundary line, default is darkgoldenrod1.
switch.n: Number of points to trigger the switch to using slower but more robust density plotting. Default is 1e4.

Value

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