ggpLayerExprEstimatesSAS: Add SAS expression estimates

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Add SAS expression estimates

Description

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

Usage

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,
  ...
)

Arguments

object	An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
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().
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. The size with which to display lines of the expression estimates.
line_size_core	Numeric. The size with which to display the core outline of the spatial annotation.
incl_edge	Logical. If TRUE, makes use of SPATA2 automatic tissue outline algorithm.
verbose	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.

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")

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"))

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