plotExprVsDistSA: Plot expression as a function of distance to a spatial...

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Plot expression as a function of distance to a spatial references

Description

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.

Usage

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)

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