Plot expression as a function of distance to a spatial references

Generates a scatterplot to visualize the relationship between gene expression and the distance of data points to a spatial reference. Set line_alpha > 0 to visualize the inferred expression pattern used for spatial gradient screening.

plotExprVsDistSA(
  object,
  variables,
  ids = idSA(object),
  distance = "dte",
  resolution = recSgsRes(object),
  core = FALSE,
  pt_alpha = 0.1,
  pt_color = "black",
  pt_clrp = NULL,
  pt_size = 1.5,
  line_alpha = 0,
  line_color = "forestgreen",
  line_size = 1.75,
  border_linealpha = 1,
  border_linecolor = "black",
  border_linesize = 1,
  border_linetype = "solid",
  ee_linealpha = 0,
  ee_linecolor = "black",
  ee_lineend = "point",
  ee_linesize = 1,
  ee_linetype = "solid",
  se_fill = ggplot2::alpha("lightgrey", 0.5),
  unit = getDefaultUnit(object),
  ggpLayers = NULL,
  ncol = NULL,
  nrow = NULL,
  ...
)

plotExprVsDistST(
  object,
  variables,
  id = idST(object),
  resolution = recSgsRes(object),
  width = NULL,
  pt_alpha = 0.5,
  pt_color = "black",
  pt_clrp = NULL,
  pt_size = 1.5,
  line_alpha = 0.9,
  line_color = "forestgreen",
  line_size = 1,
  unit = getDefaultUnit(object),
  ggpLayers = NULL,
  ncol = NULL,
  nrow = NULL,
  ...
)

Arguments

object: An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
variables: Character vector. All numeric variables hat are supposed to be plotted.
ids: Character vector. Specifies the IDs of the spatial annotations of interest.
distance: A numeric vector of distances to the annotation's edge.
resolution: Distance measure. The resolution with which the expression gradient is inferred. Defaults are platform specific. See more in detail section of recSgsRes().
pt_alpha: Numeric value. Specifies the degree of transparency of all points.
pt_clrp: The color palette to be used if the specified variable displayed by color is categorical/discrete. Run validColorPalettes() to see valid input.
pt_size: Numeric value. Specifies the size of all points.
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.
se_fill: The fill color for the smoothing line's standard error area (default: "lightgrey").
unit: Character value. Specifies the desired unit in which distance measures or area measures are provided. Run validUnitsOfLength() or validUnitsOfArea() for valid input options.
ggpLayers: List of ggproto-objects that are added to each plot. Skim ggpLayer*()-functions for more options.
nrow, ncol: Numeric values or NULL. Used to arrange multiple plots.
...: Used to absorb deprecated arguments or functions.
id: Character value. The ID of the spatial trajectory.

Value

A ggplot.

Examples


library(SPATA2)
library(tidyverse)

data("example_data")

object <- example_data$object_UKF275T_diet

object <- normalizeCounts(object, activate = TRUE)

object <-
 createNumericAnnotations(
   object = object,
   variable = "HM_HYPOXIA",
   threshold = "kmeans_high",
   id = "hypoxia_ann",
   inner_borders = FALSE,
   force1 = TRUE
   )

 plotExprVsDistSA(object, variables = c("HM_HYPOXIA", "METRN"), ids = "hypoxia_ann", core = T)