plotSasDensityplot.Rd
Plots changes in grouping proportion against the distance to a spatial annotation. Similar to plotSasBarplot, but plots density instead of discrete bars.
plotSasDensityplot(
object,
grouping,
id = idSA(object),
distance = distToEdge(object, id),
resolution = getCCD(object) * 2,
unit = getDefaultUnit(object),
angle_span = c(0, 360),
core = FALSE,
clrp = NULL,
clrp_adjust = NULL,
position = "fill",
expand_x = c(0.025, 0),
expand_y = c(0.0125, 0),
verbose = NULL,
geom_density_bw = NULL,
geom_density_adjust = 1/5,
...
)
An object of class SPATA2
or, in case of S4 generics,
objects of classes for which a method has been defined.
Character value. The grouping variable of interest. Use
getGroupingOptions()
to obtain all valid input options.
Distance measure
. Specifies
the distance from the border of the spatial annotation to the horizon in
the periphery up to which the screening is conducted. Defaults to a distance
that covers the whole tissue section the spatial annotation is located
on using distToEdge()
. (This distance must not be exceeded.)
Distance measure. The resolution
with which the expression gradient is inferred. Defaults are platform specific.
See more in detail section of recSgsRes()
.
Character value. The unit in which the distance to the spatial annotation is displayed on the x-axis.
If FALSE
, plots the bin numbers instead.
Numeric vector of length 2. Confines the area screened by an angle span relative to the center of its closest spatial annotation.
Character value. Specifies the color palette to be used to represent
groups of discrete variables. Run validColorPalettes()
to obtain valid
input options.
Named character vector or NULL. If character, it adjusts the color palette that is used to represent the groups. Names of the input vector must refer to the group and the respective named element denotes the color with which to represent the group.
Given to argument expand
of ggplot2:scale_x/y_continuous()
.
Logical. If TRUE
, informative messages regarding
the computational progress will be printed.
(Warning messages will always be printed.)
Numeric value. Adjusts the smoothing bandwidth of the density plot. For example, adjust = 1/2 means use half of the default bandwidth.
Needed arguments that depend on the input/unit combination. If
one of both is 'px', argument object
must be specified.
A ggplot.
The vignette on distance measures in SPATA2 has been replaced. Click
here
to read it.