plotStsHeatmap: Plot STS heatmap

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Plot STS heatmap

Description

Displays variable-expression values along a trajectory direction with a smoothed heatmap (from left to right).

Usage

plotStsHeatmap(
  object,
  variables,
  id = idST(object),
  width = getTrajectoryLength(object, id),
  arrange_rows = "none",
  unit = getDefaultUnit(object),
  smooth_span = 0.3,
  multiplier = 10,
  clrsp = NULL,
  .f = NULL,
  .cols = dplyr::everything(),
  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.
variables	Character vector. The names of the data variables of interest.
arrange_rows	Alter the way the rows of the heatmap are displayed in order to highlight patterns. Currently either 'maxima', 'minima' or 'input'. If 'input', variables are displayed in the same order as they are provided in the argument variables.
unit	Character value. Specifies the desired unit in which distance measures or area measures are provided. Run validUnitsOfLength() or validUnitsOfArea() for valid input options.
smooth_span	Numeric value. Controls the degree of smoothing. Given to argument span of stats::loess().
multiplier	Numeric value. For better visualization the transient pattern is smoothed with a loess fit. The total number of predicted values (via stats::predict()) is the number of bins multiplied with the input for this argument.
clrsp	Character value. Specifies the color spectrum to be used to represent continuous values of numeric variables. Run validColorSpectra() to obtain valid input options.
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

A ggplot.

Examples

library(SPATA2)

data("example_data")

object <- example_data$object_UKF269T_diet

object <- normalizeCounts(object, activate = TRUE)

genes <- c("EGFR", "MBP", "MAG", "SNAP25")

plotStsHeatmap(object, id = "horizontal_mid", variables = genes)

plotStsLineplot(object, id = "horizontal_mid", variables = genes)

plotStsRidgeplot(object, id = "horizontal_mid", variables = genes)

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