Add group outline — ggpLayerGroupOutline • SPATA2

Highlights groups of barcode-spots by encircling them. Depending on the plot_type this can be added to a surface plot or a dimensional reduction plot.

ggpLayerGroupOutline(
  object,
  grouping,
  group_subset = NULL,
  plot_type = "surface",
  line_alpha = 1,
  line_color = "black",
  line_size = 1,
  line_type = "solid",
  alpha = 0,
  fill = NA,
  incl_edge = FALSE,
  merdge_edge = FALSE,
  incr_vert = FALSE,
  bcsp_rm = character(0),
  outlier_rm = TRUE,
  eps = recDbscanEps(object),
  minPts = recDbscanMinPts(object),
  concavity = NULL,
  expand_outline = getCCD(object, "px") * 1.1,
  ...
)

Arguments

object: An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
grouping: Character value. The grouping variable of interest. Use getGroupingOptions() to obtain all valid input options.
group_subset: Character value or NULL. If character, specifies the exact groups that are outlined. If NULL, all groups are encircled.
plot_type: Character value. Either 'surface' or the name of a conducted dimensional reduction.
line_alpha: Numeric. Affects alpha of main lines of the plot.
line_color: Character. Affects color of the main lines of the plot.
line_size: Numeric. Affects size of the main lines of the plot.
line_type: Character. The line type. One of 'blank', 'solid', 'dashed', 'dotted', 'dotdash', 'longdash' and 'twodash'.
incl_edge: Logical. If TRUE, include tissue section outline. See examples of getTissueOutlineDf().
incr_vert: 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.
bcsp_rm: Character vector or NULL. If character, specifies barcode-spots that are removed before analysis or plotting. (Deprecated in favor of bcs_rm).
outlier_rm, minPts: Logical. If TRUE, spatial outlier of the group to outline are removed from the outline via dbscan::dbscan(..., minPts = minPts). Ignored if plot_type is not 'surface'.
eps: Distance measure. Given to eps of dbscan::dbscan(). Determines the size (radius) of the epsilon neighborhood.
concavity: Numeric value. Given to argument concavity of concaveman::concaveman(). Determines the relative measure of concavity. 1 results in a relatively detailed shape, Infinity results in a convex hull. You can use values lower than 1, but they can produce pretty crazy shapes.
expand_outline: Distance measure with which to expand the outline. Must be provided in pixel units!
...: Additional arguments given to ggforce::geom_polygon(). Affects the encircling.

Value

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.

Examples


library(SPATA2)
library(tidyverse)

data("example_data")

object <- loadExampleObject("UKF275T", meta = TRUE)

plotSurface(object, color_by = "bayes_space") +
 ggpLayerGroupOutline(object, grouping = "bayes_space", group_subset = c("B1", "B2"))