gate_threshold_draw: Draw Threshold Gate(s) Around Populations.

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

Description

gate_threshold_draw constructs an interactive plotting window for user to select the lower bound of a population which is constructed into a rectangleGate object and stored in a filters list. Both 1-D and 2-D threshold gates are supported, for 2-D threshold gates all events above the select x and y coordinates are included in the gate. Multiple threshold gates are not currently supported.

Usage

gate_threshold_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 populations to be gated. Multiple threshold gates are not currently supported. 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 constructed rectangleGate object.

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 1-D threshold gate using gate_threshold_draw
tg <- gate_threshold_draw(fs[[4]],
  alias = "Cells",
  channels = c("PE-A")
)

# tg is a filters object - extract rectangleGate using `[[`
tg[[1]]

#' # Get 2-D threshold gate using gate_threshold_draw - overlay control
tg <- gate_threshold_draw(fs[[4]],
  alias = "Cells",
  channels = c("Alexa Fluor 647-A", "7-AAD-A"),
  overlay = fs[[1]]
)

# tg is a filters object - extract rectangleGate using `[[`
tg[[1]]

## End(Not run)

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