gate_draw: DrawGate plugin for openCyto
In DillonHammill/CytoGate: openCyto Plugin Gating Functions

Description Usage Arguments Value Author(s) Examples

DrawGate allows the user to draw polygon gates directly onto plots of flow cytometry data. Simply left click to gate and right click to close the gate.

gate_draw(fr, pp_res, channels, filterId = "", gate_range = NULL,
  min = NULL, max = NULL, gate_type = c("polygon", "rectangle",
  "interval", "threshold", "ellipse", "quadrant"), N = 1, axis = c("x",
  "y"), adjust = 1.5, ...)

`fr`	a `flowFrame` object containing the flow cytometry data for gating.
`pp_res`	output of preprocessing function.
`channels`	a vector of length 2 indicating the channels used to construct the 2D plot.
`filterId`	gate name assigned by openCyto from the `gatingTemplate`.
`gate_range`	range in which gate should be constructed (only needed for autogating functions).
`min`	argument passed to `truncate_flowFrame` to restrict data to values > `min`.
`max`	argument passed to `truncate_flowFrame` to restrict data to values < `max`.
`gate_type`	type of gate to be constructed, supported types include `c("polygon", "rectangle", "interval", "threshold", "ellipse", "quadrant")`.
`N`	an integer indicating the number of gates to construct, set to 1 by default.
`axis`	indicates the axis to use for gating for `gate_type="interval"` when 2 fluorescent channel are supplied.
`adjust`	numeric smoothing factor used for 1D density plots.
`...`	additional arguments passsed to `DrawGate`.

a polygonGate constructed from coordinates supplied by DrawGate.

Dillon Hammill (Dillon.Hammill@anu.edu.au)

{
library(openCyto)

registerPlugins(fun = gate_draw, methodName = "DrawGate")
listgtMethods()   # check plugin has been registered with openCyto

fs <- read.flowSet(path = "Samples", pattern = ".fcs") # load in .fcs files

gs <- GatingSet(fs) # add flowSet to GatingSet

template <- add_pop(
gs, alias = "Lymphocytes", pop = "+", parent = "root", dims = "FSC-A,SSC-A", gating_method = "DrawGate", gaating_args = "gate_type='ellipse'",
gating_args = "subSample=10000", collapseDataForGating = TRUE, groupBy = 2
)

# gating window will open to construct gate left click vertices on plot and close gate by right click and selecting "stop".

ggcyto(gs[[1]], subset = "root", aes(x = "FSC-A",y = "SSC-A")) + geom_hex(bins = 100) + geom_stats()

}