Draw Interval Gate(s) Around Populations.

gate_interval_draw constructs an interactive plotting window for user to select the lower and upper bounds of a population (through mouse click) which is constructed into a rectangleGate object and stored in a filters list. Both 1-D and 2-D interval gates are supported, for 2-D interval gates an additional argument axis must be supplied to indicate which axis should be gated.

gate_interval_draw(fr, alias = NULL, channels, plot = TRUE,
  axis = "x", 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. If multiple population names are supplied (e.g. c("CD3,"CD4)) multiple gates will be returned. 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.
axis	indicates whether the "x" or "y" axis should be gated for 2-D interval gates.
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(s).

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 interval gate using gate_interval_draw - overlay control
ig <- gate_interval_draw(fs[[4]],
  alias = "Cells",
  channels = "PE-A",
  overlay = fs[[1]],
  density_stack = 0.5
)

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

# Get 2-D interval gate on y axis using gate_interval_draw
ig <- gate_interval_draw(fs[[4]],
  alias = "Cells",
  channels = c("PE-A", "Alexa Fluor 488-A"),
  axis = "y"
)

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