ggpLayerHorizonSAS.Rd
Visualizes the border between screened tissue (environment) and everything beyond that is not included in the screening (periphery).
ggpLayerHorizonSAS(
object,
id,
distance = distToEdge(object, id),
line_alpha = 0.9,
line_color = "black",
line_size = 1.5,
line_type = "solid",
incl_edge = TRUE,
incr_vert = FALSE,
verbose = NULL,
...
)
An object of class SPATA2
or, in case of S4 generics,
objects of classes for which a method has been defined.
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.)
Numeric. Affects alpha of main lines of the plot.
Character. Affects color of the main lines of the plot.
Numeric. The size with which to display lines of the expression estimates.
Character. The line type. One of 'blank', 'solid', 'dashed', 'dotted', 'dotdash', 'longdash' and 'twodash'.
Logical. If TRUE
, makes use of SPATA2
automatic tissue outline algorithm.
Logical value. If TRUE
, the number of vertices of the polygon
to be plotted is increased by linear interpolation. This can lead to smoother
visualization but also to increased runtime.
Logical. If TRUE
, informative messages regarding
the computational progress will be printed.
(Warning messages will always be printed.)
Used to absorb deprecated arguments or functions.
ggpLayer*()
-functions return lists of ggproto
objects
that can be added to ggplots via the +
operator. In most of the cases
they are supposed to be added to plots created with the plotSurface*()
family.
library(SPATA2)
library(tidyverse)
object <- loadExampleObject("UKF275T")
object <-
createNumericAnnotations(
object = object,
variable = "HM_HYPOXIA",
threshold = "kmeans_high",
id = "hypoxia_ann",
force1 = TRUE
)
plotSurface(object, color_by = "HM_HYPOXIA", outline = T, pt_clrsp = "Reds 3") +
ggpLayerHorizonSAS(object, id = "hypoxia_ann", distance = "3mm") +
ggpLayerScaleBarSI(object, sb_pos = c("3mm", "2mm"))