gate_draw-GatingSet-method: gate_draw GatingSet Method

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

Description

Manually draw gates around populations for analysis of flow cytometry data.

Usage

## S4 method for signature 'GatingSet'
gate_draw(x, group_by = NULL, select = NULL,
  parent = "root", alias = NULL, channels = NULL, type = "polygon",
  gatingTemplate = NULL, display = NULL, axis = "x",
  density_smooth = 1.5, label = TRUE, plot = TRUE, ...)

Arguments

x	object of class GatingSet.
group_by	vector of pData column names (e.g. c("Treatment","Concentration") indicating how the samples should be grouped prior to gating, set to the length of x by default to construct a single gate for all samples. If group_by is supplied a different gate will be constructed for each group.
select	vector containing the indices of samples within each group to use for plotting.
parent	name of the parent population to extract for 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.
type	vector of gate type names used to construct the gates. Multiple gate 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 "interval" for 1D gates and "polygon" for 2D gates.
gatingTemplate	name of gatingTemplate csv file to be 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.
axis	indicates whether the "x" or "y" axis should be gated for 2-D interval gates.
density_smooth	smoothing factor passed to density for 1-D plots (defaults to 1.5).
label	logical indicating whether to include cyto_plot_label for the gated population(s), TRUE by default.
plot	logical indicating whether a plot should be drawn, set to TRUE by default.
...	additional arguments for cyto_plot,GatingSet-method.

Value

drawn gates are applied to the GatingSet and saved to a gatingTemplate.

Author(s)

Dillon Hammill, [e-mail]

See Also

cyto_plot,GatingSet-method

gate_draw,flowFrame-method

gate_draw,flowSet-method

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(fs))
gs <- transform(gs, trans)

# Gate using gate_draw
gating(Activation_gatingTemplate, gs)

# draw gates using gate_draw - add contour lines & overlay control
gate_draw(gs,
  parent = "Dendritic Cells",
  channels = c("Alexa Fluor 488-A", "Alexa Fluor 700-A"),
  alias = c("CD8+ DC", "CD4+ DC"),
  gatingTemplate = "Example-gatingTemplate.csv",
  type = "rectangle",
  contour_lines = 15
)

# Constructed gate applied directly to GatingSet
getNodes(gs)

## End(Not run)

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