ggpLayerExprEstimatesSAS.Rd
Visualizes the distances at which expression of a numeric feature is estimated with a certain SAS set up. Plotted as concentric circles around the annotation
ggpLayerExprEstimatesSAS(
object,
ids,
distance = "dte",
resolution = recSgsRes(object),
core = FALSE,
alpha_core = 0,
fill_core = NA,
line_alpha = 1,
line_color = "black",
line_size = (line_size_core * 0.75),
line_size_core = 1,
incl_edge = TRUE,
method = "normal",
verbose = NULL,
...
)
An object of class SPATA2
or, in case of S4 generics,
objects of classes for which a method has been defined.
Character vector. Specifies the IDs of the spatial annotations of interest.
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()
.
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.
Numeric. The size with which to display the core outline of the spatial annotation.
Logical. If TRUE
, makes use of SPATA2
automatic tissue outline algorithm.
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)
data("example_data")
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") +
ggpLayerExprEstimatesSAS(object, ids = "hypoxia_ann", distance = "3mm") +
ggpLayerScaleBarSI(object, sb_pos = c("3mm", "2mm"))