gs_gate_interactive: Interactive Manual Gating

In NKInstinct/flowGate: Interactive Cytometry Gating in R

Interactive Manual Gating

Description

gs_gate_interactive opens a new graphical window where you can draw rectangle, polygon, 1-D span, or 2-D quadrant gates that will be applied to an entire GateSet (see the flowWorkspace package for complete information about GateSets).

Usage

gs_gate_interactive(
  gs,
  filterId,
  sample = 1,
  dims = list("FSC-A", "SSC-A"),
  subset = "root",
  regate = FALSE,
  overlayGates = NULL
)

Arguments

gs	The GateSet that will be gated on.
filterId	String that gives the name of the new gate. Must be unique (can specify parent gates to aid in this).
sample	Numeric specifying which of the GatingHierarchy objects (i.e. which FCS file/flow sample) that make up the GateSet do you want to use to draw the gate? Note that the gate you draw will be applied to all GatingHierarchy objects in the GateSet. Defaults to the first GatingHierarchy object in the GateSet.
dims	A list of strings, length-1 or length-2, that specifies the x- and y- parameters that you will be gating on. Giving a length-1 list will result in a histogram, while a length-2 list will result in a dot-plot. Giving a length-3 or longer list will result in only the first two dimensions being used, and will generate a warning to say as much. Defaults to forward scatter ("FSC-A") and side scatter ("SSC-A").
subset	String that gives the name of the parent gate that you want to sample from. For example, if you wanted to gate all live cells out of a previously drawn "lymphocytes" gate, you would specify "lymphocytes" here. Defaults to "root" (ungated).
regate	A boolean specifying whether all gates with a name matching filterId should first be deleted before being re-drawn. Attempting to draw a gate with a non-unique filterId without specifying regate = TRUE will result in an error. Defaults to FALSE
overlayGates	List of strings giving the filterIds of other gates to draw on the example plot when gating. Useful for drawing multiple gates on the same population (for example, after specifying a marker-low population, you can overlay the marker-low gate to aid in drawing a marker-high gate). Defaults to NULL (no overlaid gates).

Value

A list of the interactively-specified parameters, including the drawn gate's coordinates, plot bins, and any flowjo biex coefs used to calculate those transforms.

Examples

path_to_fcs <- system.file("extdata", package = "flowGate")
fs <- read.flowSet(path = path_to_fcs,
                   pattern = ".FCS$",
                   full.names = TRUE)
gs <- GatingSet(fs)

if(interactive()) { # only run in interactive sessions
gs_gate_interactive(gs,
                    filterId = "Lymphocytes",
                    dims = list("FSC-H", "SSC-H"))
}

# returns gs with the same "Lymphocytes" gate on FSC-H and SSC-H applied to
# the root node (all events) of each sample in the GateSet.

if(interactive()) {
gs_gate_interactive(gs,
                    filterId = "Live cells",
                    dims = "Viability",
                    subset = "Lymphocytes")
}

# returns gs with a "Live cells" gate drawn on all cells included in the
# parent "Lymphocytes" gate. This gate would be based on a histogram of a
# marker called Viability, using the first GatingHierarchy sample as an
# example.

if(interactive()){
gs_gate_interactive(gs,
                    filterId = "Live cells",
                    dims = list("Viability", "SSC-A"),
                    subset = "Lymphocytes",
                    regate = TRUE)
}

# first deletes the "Live cells" gate drawn above, then adds a new "Live
# cells" gate to the set, this time based on a dot plot of Viability by
# side-scatter.

if(interactive()){
gs_gate_interactive(gs,
                    filterId = "Dead cells",
                    dims = list("Viability", "SSC-A"),
                    subset = "Lymphocytes",
                    overlayGates = "Live cells")
}

# returns gs with a "Dead cells" gate drawn on the same example graph that
# was used to draw the "Live cells" gate above. Overlays the "Live cells"
# gate on top of this graph to aid in drawing the "Dead cells" gate.

NKInstinct/flowGate documentation built on March 17, 2023, 7:29 a.m.