Plot SAS heatmap

Plots gene expression changes against the distance to the spatial annotation using a heatmap.

plotSasHeatmap(
  object,
  variables,
  ids = idSA(object),
  distance = "dte",
  resolution = recSgsRes(object),
  core = FALSE,
  arrange_rows = "none",
  unit = getDefaultUnit(object),
  smooth_span = 0.3,
  multiplier = 10,
  clrsp = NULL,
  border_linealpha = 0.75,
  border_linecolor = "black",
  border_linesize = 1,
  border_linetype = "dashed",
  .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 numeric variables to be included in the screening process. Makre sure that the correct matrix is active in the respective assays.

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().

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.

border_linealpha, border_linecolor, border_linesize, border_linetype

Given to ggplot2::geom_vline(). Adjusts appearance of the vertical line that represents the border of the spatial annotation.

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.

Distance measures

The vignette on distance measures in SPATA2 has been replaced. Click here to read it.

Examples

library(SPATA2)
library(ggplot2)

data("example_data")

object <- example_data$object_UKF313T_diet

ids <- getSpatAnnIds(object, tags = c("necrotic", "compr"), test = "identical")

object <- normalizeCounts(object, activate = T)

# visualize with lines
plotSasLineplot(object, ids = ids, variables = c("VEGFA", "HM_HYPOXIA", "RCTM_TCR_SIGNALING", "CD74")) +
  labs(x = "Distance to Necrosis")

# visualize with ridgeplots
plotSasRidgeplot(object, ids = ids, variables = c("VEGFA", "HM_HYPOXIA", "RCTM_TCR_SIGNALING", "CD74")) +
  labs(x = "Distance to Necrosis")

# visualize with a heatmap
plotSasHeatmap(object, ids = ids, variables = c("VEGFA", "HM_HYPOXIA", "RCTM_TCR_SIGNALING", "CD74")) +
  labs(x = "Distance to Necrosis")