ggpLayerScreeningDirectionSAS.Rd
Visualizes the screenining direction of an SAS set up on top of a surface plots. See examples.
ggpLayerScreeningDirectionSAS(
object,
ids,
distance = "dte",
line_alpha = 1,
line_color = "black",
line_size = 1,
line_type = "solid",
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.)
Numeric. Affects alpha of main lines of the plot.
Character. Affects color of the main lines of the plot.
Numeric. Affects size of the main lines of the plot.
Character. The line type. One of 'blank', 'solid', 'dashed', 'dotted', 'dotdash', 'longdash' and 'twodash'.
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.
In contrast to ggpLayerExprEstimates()
, which visualizes
the precise positions of the expression estimates, ggpLayerScreeningDiretionSAS()
visualizes
only the concept, the idea, of the screening direction. This is particularly useful, if the screening
set up includes multiple annotations in one tissue section, where ggpLayerExprEstimates()
fails
to visualize the combined expression estimates.
library(SPATA2)
data("example_data")
object <- example_data$object_UKF313T_diet
ids <- getSpatAnnIds(object, tags = c("necrotic", "compr"))
plotImage(object) +
ggpLayerSpatAnnOutline(object, ids = ids, fill = "lightgrey") +
ggpLayerScreeningDirectionSAS(object, ids = ids, line_size = 0.5)