gate_quadrant_draw: Draw Quadrant Gates Around Populations.

In DillonHammill/cytoSuite: Compensation, Gating & Visualisation Toolkit for Analysis of Flow Cytometry Data

Description

gate_quadrant_draw constructs an interactive plotting window for user to select the crosshair center of 4 populations which is used to construct 4 rectangleGate objects which are stored in afilters list. Populations are assigned in the following order: bottom left, bottom right, top right and top left.

Usage

gate_quadrant_draw(fr, alias = NULL, channels, plot = TRUE,
  label = TRUE, ...)

Arguments

fr	a flowFrame object containing the flow cytometry data for plotting and gating.
alias	the name(s) of the 4 populations to be gated. alias is NULL by default which will halt the gating routine.
channels	vector of channel names to use for plotting, can be of length 1 for 1-D density histogram or length 2 for 2-D scatter plot.
plot	logical indicating whether the data should be plotted. This feature allows for constructing gates of different types over existing plots which may already contain a different gate type.
label	logical indicating whether to include cyto_plot_label for the gated population(s), TRUE by default.
...	additional arguments for cyto_plot,flowFrame-method.

Value

afilters list containing the 4 constructed rectangleGate objects.

Author(s)

Dillon Hammill ([e-mail])

See Also

cyto_plot,flowFrame-method

gate_draw

Examples

## Not run: 

# Copy and paste into console to interactively draw gates

library(CytoRSuiteData)

# Load in samples to flowSet
fs <- Activation

# Transform fluorescent channels
fs <- transform(fs, estimateLogicle(fs[[4]], cyto_fluor_channels(fs)))

# Get quadrant gates using gate_quadrant_draw
qg <- gate_quadrant_draw(fs[[4]],
  alias = c("DN", "CD4", "DP", "CD8"),
  channels = c("Alexa Fluor 700-A", "Alexa Fluor 488-A")
)

# qg is a filters object - extract each rectangleGate using `[[`
qg[[4]]

## End(Not run)

DillonHammill/cytoSuite documentation built on March 7, 2019, 10:09 a.m.