Crop SPATA2 object

Creates a subset of the original SPATA2 object based on x- and y-range. Data poitns that fall into the rectangle given by xrange and yrange are kept.

cropSpataObject(
  object,
  xrange,
  yrange,
  spatial_proc = TRUE,
  adjust_capture_area = TRUE,
  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.

xrange, yrange

Distance vector of length two or NULL. If not NULL, specifies the x- and y-range to which the spatial output is cropped. E.g. xrange = c(200, 500) results in the two dimensional space being cropped from x-coordinate 200px up to x-coordinate 500px. If NULL, the original range is used.

spatial_proc

Logical value. Indicates whether the new sub-object is processed spatially. If TRUE, a new tissue outline is identified based on the remaining observations via identifyTissueOutline(). Then, spatial annotations are tested on being located on either of the remaining tissue sections. If they are not, they are removed.

If FALSE, these processing steps are skipped. Generally speaking, this is not recommended. Only set to FALSE, if you know what you're doing.

Only relevant, if barcodes is not NULL.

adjust_capture_area

Logical. If TRUE, the capture area is adjusted to the input of xrange and yrange. If FALSE, it stays as is. Defaults to TRUE.

verbose

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

(Warning messages will always be printed.)

Value

The updated input object, containing the added, removed or computed results.

See also

ggpLayerRect() to visualize the rectangle based on which the subsetting is done. subsetSpataObject() is the working horse behind this function.

Examples

library(SPATA2)
library(tidyverse)
library(patchwork)

# ----- Example 1: subsetSpataObject()
object <- loadExampleObject("UKF313T", meta = TRUE)

barcodes_keep <-
 getMetaDf(object) %>%
 filter(bayes_space %in% c("B3", "B2", "B1")) %>%
 pull(barcodes)

object_sub <- subsetSpataObject(object, barcodes = barcodes_keep)

show(object)
show(object_sub)

plotSpatialAnnotations(object) # plots all annotations
plotSpatialAnnotations(object_sub) # subsetting affects everything by default

ids <- getSpatAnnIds(object)
ids_sub <- getSpatAnnIds(object_sub)

# use patchwork to compare plots
plot_orig <-
  plotSurface(object, color_by = "bayes_space", outline = T) +
  ggpLayerSpatAnnOutline(object, ids = ids)

plot_sub <-
  plotSurface(object_sub, color_by = "bayes_space", outline = T) +
  ggpLayerSpatAnnOutline(object_sub, ids = ids_sub)

plot_orig + plot_sub

# ----- Example 2: splitSpataObject()
# uses subsetSpataObject() in the background

object_mouse <- loadExampleObject("LMU_MCI", process = TRUE, meta = TRUE)

orig_frame <- ggpLayerFrameByCoords(object_mouse)

ids <- getSpatAnnIds(object_mouse)

plotSurface(object_mouse, color_by = "tissue_section", pt_clr = "lightgrey") +
  ggpLayerSpatAnnOutline(object_mouse, ids = ids) +
  ggpLayerSpatAnnPointer(object_mouse, ids = ids, ptr_lengths = "0.45mm", text_dist = 10, text_size = 7)

obj_list <- splitSpataObject(object_mouse, grouping = "tissue_section")

# present resulting sub-objects
purrr::map(obj_list, .f = ~ .x)

# present remaining ids
purrr::map(obj_list, .f = ~ getSpatAnnIds(.x))

# show surface plot with all remaining spatial annotations
purrr::map(obj_list, .f = ~ plotSurface(.x) + ggpLayerSpatAnnOutline(.x) + orig_frame) %>%
  patchwork::wrap_plots()

# repeat with spatial_proc = FALSE
obj_list <- splitSpataObject(object_mouse, grouping = "tissue_section", spatial_proc = FALSE)

# present remaining spatial annotation ids
purrr::map(obj_list, .f = ~ getSpatAnnIds(.x))

# show surface plot with all remaining spatial annotations
purrr::map(obj_list, .f = ~ plotSurface(.x) + ggpLayerSpatAnnOutline(.x) + orig_frame) %>%
  patchwork::wrap_plots()

# -----  Example 3: cropSpataObject()
# uses subsetSpataObject() in the background
object <- loadExampleObject("UKF275T", meta = TRUE)

orig_frame <- ggpLayerFrameByCoords(object)

xcrop <- c("2.5mm", "5.5mm")
ycrop <- c("5mm", "7mm")

plotSurface(object, color_by = "bayes_space") +
 ggpLayerAxesSI(object) +
 ggpLayerRect(object, xrange = xcrop, yrange = ycrop)

object_cropped <-
 cropSpataObject(object, xrange = xcrop, yrange = ycrop)

plotSurface(object_cropped, color_by = "bayes_space", pt_size = 0.75) + orig_frame