DrawGate: Interactive Gate Drawing for Flow Cytometry Data.

In DillonHammill/CytoGate: openCyto Plugin Gating Functions

Description

DrawGate implements an interactive manual gating routine for flow cytometry data. Users can easily select gate coordinates on plots of flow cytometry data using a mouse click. Based on the user input, DrawGate can construct many different types of gates, including polygon, rectangle, interval, threshold, ellipse, and quadrant. The type of gate to be constructed must be supplied as the gate_type argument which by default is set to a polygonGate. Each gate_type has specific gating instructions which are printed to the console during gating. The selection of multiple gates is supported for rectangle and interval gate types.

Usage

DrawGate(fr, channels, gate_type, N = 1, axis = "x", adjust = 1.5, ...)

Arguments

fr	a flowFrame object containing the flow cytometry data for plotting and gating.
channels	a vector indicating the fluorescent channel(s) to be used for gating. If a single channel is supplied, a histogram of of the kernel density will be constructed.
gate_type	a character string of length 1 indicating the type of gate to be constructed. Supported gates are "polygon", "rectangle", "interval", "threshold", "ellipse" and "quadrant".
N	an integer indicating the number of gates to construct.
axis	indicates which axis should be gated for gate_type="interval" with 2 fluorescent channel supplied.
adjust	numeric smoothing factor used for 1D density plots.
...	additional arguments for plotDens.

Value

a dataframe object containing the coordinates required to construct the gate.

Author(s)

Dillon Hammill ([e-mail])

DillonHammill/CytoGate documentation built on May 16, 2019, 7:20 a.m.