Draw Rectangle Gate(s) Around Populations.

Source: R/gating-functions.R

gate_rectangle_draw constructs an interactive plotting window to allow manual selection of the co-ordinates of a rectangle gate(s) (through mouse click) which are constructed into rectangleGate objects and stored in a filters list. Simply select 2 diagonal co-ordinates to construct the rectangleGate(s).

gate_rectangle_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. 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.
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 polygonGate using gate_rectangle_draw - add contour lines
rg <- gate_rectangle_draw(fs[[4]],
  alias = "Cells",
  channels = c("FSC-A", "SSC-A"),
  contour_lines = 15
)

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