logical specifying whether to plot boolean gates.
character The title of the main page of the plot. Default is the sample name. Only valid when
x is GatingHierarchy
logical indicating whether to arrange different populations/nodes on the same page via
logical indicating whether to draw multiple gates on the same plot if these gates share the same parent population and same x,y dimensions/parameters;
list of character vectors used to customize x,y axis. By default, the x,y axis are determined by the respective gate parameters.
The elements of the list are named by the population name or path (see
y). Each element is a pair of named character specifying the channel name(or marker name) for x, y axis.
Short form of channel or marker names (e.g. "APC" or "CD3") can be used as long as they can be uniquely matched to the dimentions of flow data.
For example, projections = list("lymph" = c(x = "SSC-A", y = "FSC-A"), "CD3" = c(x = "CD3", y = "SSC-A"))
list of graphical parameters passed to
list of grid parameters passed to
formula a formula passed to
xyplot function of
flowViz, by default it is NULL, which means the formula is generated according to the x,y parameters associated with gate.
character the conditioning variable to be passed to lattice plot.
overlayNode names. These populations are plotted on top of the existing gates(defined by
y argument) as the overlaid dots.
overlay.symbolA named (lattice graphic parameter) list that defines the symbol color and size for each overlaid population.
If not given, we automatically assign the colors.
keyLattice legend paraemter for overlay symbols.
character specifiying y channel for xyplot when plotting a 1d gate. Default is "SSC-A" and session-wise setting can be stored by 'flowWorkspace.par.set("plotGate", list(default.y = "FSC-A"))'
character either "xyplot" or "densityplot". Default is "xyplot" and session-wise setting can be stored by 'flowWorkspace.par.set("plotGate", list(type = "xyplot"))'
fitGate used to disable behavior of plotting the gate region in 1d densityplot. Default is FALSE and session-wise setting can be stored by 'flowWorkspace.par.set("plotGate", list(fitGate = FALSE))'
ligcal specifies whether to show pop name in strip box,only valid when x is
logical whether to show the axis in raw(untransformed) scale. Default is TRUE and can be stored as session-wise setting by 'flowWorkspace.par.set("plotGate", list(raw.scale = TRUE))'
character can be either "instrument" or "data" which determines the x, y axis scale
either by instrument measurement range or the actual data range.
numeric which specifies customized range.
They can be stored as session-wise setting by 'flowWorkspace.par.set("plotGate", list(xlim = "instrument"))'
numeric scalar passed to getNodes method (used to control how the gating/node path is displayed)
... The other additional arguments to be passed to xyplot.