plotGate {prada}R Documentation

Visualize Observations within defined Gates

Description

This functions visualize which observations are included in gates defined by the functions gate.cytoFrame, gate.cytoSet, and gate.matrix. The make use of the visualization function threePanelPlot .

Usage

plot.cytoFrameGate(x, y, x.panels = c(1, 4, 5), y.panels = c(2, 3, 6),
                   use.smoothScatter = TRUE, limits = c(0, 1023),
                   plotTitle = "Gated Data", gate.colour = "red",
                   new.device = TRUE, verbose = TRUE, ...)

Arguments

x gate resulting, e.g., from function gate.cytoFrame; thus x is of class cytoFrameGate or similar
y the original data used to derive gate x, thus either a cytoFrame, cytoSet or matrix
x.panels which variables (columns) are to be plotted at the x-axis of the three variables
y.panels which variables (columns) are to be plotted at the y-axis of the three variables
use.smoothScatter logical, should the function smoothScatter be employed for plotting the data (plots data densities rather than individual points)
limits minimum and maximum value (theoretically) observed in the data; e.g., with 10-channel digitized data it is c(0,1023)
plotTitle title for the plot
gate.colour which colour to use for observations within the gate x
new.device logical; should a new device be opened for the three plots; if FALSE the three plots will be plotted to the currently active device
verbose logical; do you want extended output to STDOUT
... further arguments passed on to plot.default

Value

No value is returned. These functions are called for producing the three plots.

Author(s)

Joern Toedling toedling@ebi.ac.uk

See Also

gate.cytoFrame,threePanelPlot

Examples

   # see the example in function 'gate.cytoFrame'

[Package prada version 1.6.3 Index]