Plot SAS rideplot

Plots gene expression changes against the distance to to the spatial annotation using the design of ridgeplots.

plotSasRidgeplot(
  object,
  variables,
  ids = idSA(object),
  distance = distToEdge(object, id),
  resolution = recSgsRes(object),
  angle_span = c(0, 360),
  core = FALSE,
  smooth_span = 0.3,
  unit = getSpatialMethod(object)@unit,
  bcs_exclude = character(0),
  alpha = 1,
  fill = NULL,
  clrp = NULL,
  clrp_adjust = NULL,
  line_color = "black",
  line_size = 1.5,
  border_linealpha = 0.75,
  border_linecolor = "black",
  border_linesize = 1,
  border_linetype = "dashed",
  overlap = 0.5,
  strip_pos = "right",
  free_y = FALSE,
  ggpLayers = NULL,
  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().

angle_span

Numeric vector of length 2. Confines the area screened by an angle span relative to the center of its closest spatial annotation.

smooth_span

Numeric value. Controls the degree of smoothing. Given to argument span of stats::loess().

unit

Character value. Specifies the desired unit.

bcs_exclude

Character value containing the barcodes of observations to be excluded from the analysis.

clrp

Character value. Specifies the color palette to be used to represent groups of discrete variables. Run validColorPalettes() to obtain valid input options.

clrp_adjust

Named character vector or NULL. If character, it adjusts the color palette that is used to represent the groups. Names of the input vector must refer to the group and the respective named element denotes the color with which to represent the group.

line_color

Character. Affects color of the main lines of the plot.

line_size

Numeric. Affects size of the main lines of the plot.

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.

ggpLayers

List of ggproto-objects that are added to each plot. Skim ggpLayer*()-functions for more options.

verbose

Logical. If TRUE, informative messages regarding the computational progress will be printed.

(Warning messages will always be printed.)

...

Needed arguments that depend on the input/unit combination. If one of both is 'px', argument object must be specified.

scale

Logical value. If TRUE, density of cell types is scaled to make them comparable. Else, the absolute values defined by count/unit^2 is plotted.

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")