plotSurfaceSAS: Plot screening area of SAS set up

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Plot screening area of SAS set up

Description

Plots the surface of the sample three times with different coloring to visualize how spatialAnnotationScreening() screens the sample depending on the input of arguments binwidth, n_bins_dist, n_bins_angle.

Usage

plotSurfaceSAS(object, ...)

## S4 method for signature 'SPATA2'
plotSurfaceSAS(
  object,
  ids,
  distance = distToEdge(object, id),
  resolution = recSgsRes(object),
  color_by = c("dist", "bins_dist", "angle", "bins_angle"),
  unit = getDefaultUnit(object),
  angle_span = c(0, 360),
  color_outside = ggplot2::alpha("lightgrey", 0.25),
  show_plots = TRUE,
  ggpLayers = list(),
  bcs_exclude = NULL,
  verbose = NULL,
  ...
)

## S4 method for signature 'SpatialAnnotationScreening'
plotSurfaceSAS(
  object,
  show_plots = TRUE,
  display_angle = FALSE,
  display_bins_angle = TRUE,
  display_bins_dist = TRUE,
  ggpLayers = list(),
  ...
)

Arguments

object	An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
...	Used to absorb deprecated arguments or functions.
ids	Character vector. Specifies the IDs of the spatial annotations of interest.
distance	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.)
resolution	Distance measure. The resolution with which the expression gradient is inferred. Defaults are platform specific. See more in detail section of recSgsRes().
color_by	Character value. The variables by which to color the data points.
unit	Character value. Specifies the desired unit in which distance measures or area measures are provided. Run validUnitsOfLength() or validUnitsOfArea() for valid input options.
angle_span	Numeric vector of length 2. Confines the area screened by an angle span relative to the center of its closest spatial annotation.
show_plots	Logical value. If TRUE, the plots are immediately plotted. If FALSE, only a list of plots is returned (invisibly).
ggpLayers	List of ggproto-objects that are added to each plot. Skim ggpLayer*()-functions for more options.
bcs_exclude	Character value containing the barcodes of observations to be excluded from the analysis.
verbose	Logical. If TRUE, informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)
display_angle, display_bins_angle, display_circle	Logical value. If TRUE, the plot is included. If FALSE, plotting is skipped.
color_core, color_outside	Character value. Denotes the colors with which the area of image annotation (color_core) and the area that is not included in the screening (color_outside) is displayed.

Details

The method for class SpatialAnnotationScreening (the output of the function spatialAnnotationScreening()) can be used to show the area on which the results are based on. Therefore, it does not have arguments binwidth, n_bins_circle and n_bins_angle.

Value

An invisible list of ggplots.

theMILOlab/SPATA2 documentation built on Feb. 8, 2025, 11:41 p.m.