gate_edit: Edit Existing Gate(s).

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

Description

Edit Existing Gate(s).

Usage

gate_edit(x, select = NULL, parent = NULL, alias = NULL,
  overlay = NULL, type = NULL, gatingTemplate = NULL,
  display = NULL, ...)

Arguments

x	an object of class GatingSet.
select	vector containing the indicies of samples within gs to use for plotting.
parent	name of the parental population.
alias	name(s) of the gate to edit (e.g. "Single Cells").
overlay	name(s) of the population(s) to overlay onto the plot.
type	vector of gate type names used to construct the gates. Multiple types are supported but should be accompanied with an alias argument of the same length (i.e. one type per alias). Supported gate_types are polygon, rectangle, ellipse, threshold, boundary, interval, quadrant and web which can be abbreviated as upper or lower case first letters as well. Default type is "polygon".
gatingTemplate	name of the gatingTemplate csv file (e.g. "gatingTemplate.csv") where the gate is saved.
display	numeric [0,1] to control the percentage of events to be plotted. Specifying a value for display can substantial improve plotting speed for less powerful machines.
...	additional arguments passed to cyto_plot, see ?cyto_plot for details.

Value

an object of class GatingSet with edited gate applied, as well as gatingTemplate file with edited gate saved.

Author(s)

Dillon Hammill, [e-mail]

Examples

## Not run: 
library(CytoRSuiteData)

# Load in samples
fs <- Activation
gs <- GatingSet(fs)

# Apply compensation
gs <- compensate(gs, fs[[1]]@description$SPILL)

# Transform fluorescent channels
trans <- estimateLogicle(gs[[4]], cyto_fluor_channels(gs))
gs <- transform(gs, trans)

# Gate using gate_draw
gt <- Activation_gatingTemplate
gating(gt, gs)

# Edit CD4 T Cells Gate - replace gatingTemplate name
gate_edit(gs,
  parent = "T Cells",
  alias = "CD4 T Cells",
  gatingTemplate = "gatingTemplate.csv"
)

## End(Not run)

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