Plot Pre-defined Gate on Sample

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 = 10000,
  raster.bins = 256L
)

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

Minimum number of points required to render density contours. Below this threshold only the rasterised scatter layer is shown. Default is 1e4.

raster.bins

Number of pixels on each axis of the rasterised scatter image. Higher values give finer detail at the cost of a little extra memory. Default is 256L.

Value

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