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Do Gate

Source: R/do_gate.r
do.gate.Rd

Performs gating on scatter parameters and returns a vector with the points describing the gate boundary.

The gating proceeds in three steps:

  • Defines bounds from the region of scatter space the data actually occupies, then trims those bounds further

  • Defines a region around the target maximum found within the bounds

  • Defines a gate around the target maximum, only within that region

The method uses numerical search of maxima over estimated densities and Voronoi tessellations to improve density estimation around maxima.

When region.auto is TRUE in the relevant default.gate.param.cells / default.gate.param.beads entry (the default), the bounds are computed with get.scatter.occupancy(), a density-relative method that is robust to a handful of extreme events and to cytometers with a much larger theoretical scatter range than any one sample occupies. scatter.data.min.x / scatter.data.max.x / scatter.data.min.y / scatter.data.max.y still apply as an outer sanity ceiling, and become the working bounds again if region.auto is set to FALSE.

Usage

do.gate(
  gate.data,
  viability.gate,
  large.gate,
  samp,
  scatter.and.channel.label,
  control.type,
  asp,
  color.palette = "plasma",
  max.points = 50000,
  gate.color = "darkgoldenrod1"
)

Arguments

gate.data

A data frame containing the gate data.

viability.gate

A logical vector indicating the viability gate.

large.gate

A logical vector indicating the large gate.

samp

A sample identifier.

scatter.and.channel.label

A label for scatter and channel.

control.type

The type of control used, either "beads" or "cells".

asp

The AutoSpectral parameter list, prepared using get.autospectral.param.

color.palette

Optional character string defining the viridis color palette to be used for the fluorophore traces. Default is plasma. 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.

Value

A set of points describing the gate boundary.

See also

get.scatter.occupancy()