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The `SpatialData` class

Source: R/AllClasses.R, R/SpatialData.R, R/methods.R
SpatialData.Rd

SpatialData provides an R interface to Python's spatialdata, which enables the representation of diverse spatial omics datasets using the OME-NGFF (Next Generation File Format) standard. In R,

  • images and labels are ZarrArrays (Rarr package).

  • points and shapes are managed using duckspatial tables.

  • tables are SingleCellExperiments (read with anndataR).

Usage

SpatialData(
  images = list(),
  labels = list(),
  points = list(),
  shapes = list(),
  tables = list()
)

# S4 method for class 'SpatialData'
x$name

# S4 method for class 'SpatialData'
x$name <- value

# S4 method for class 'SpatialData,numeric,ANY'
x[[i, j, ...]]

# S4 method for class 'SpatialData,character,ANY'
x[[i, j, ...]]

# S4 method for class 'SpatialDataElement'
data(x, k = 1, ...)

# S4 method for class 'SpatialDataElement'
meta(x)

# S4 method for class 'SpatialData,ANY,ANY,ANY'
x[i, j, ..., drop = FALSE]

# S4 method for class 'SpatialData'
rownames(x)

# S4 method for class 'SpatialData'
colnames(x)

# S4 method for class 'SpatialData,character'
layer(x, i)

# S4 method for class 'SpatialData,ANY'
layer(x, i)

# S4 method for class 'SpatialData,character'
element(x, i)

# S4 method for class 'SpatialData,numeric'
element(x, i)

# S4 method for class 'SpatialData,missing'
element(x, i)

# S4 method for class 'SpatialData,ANY'
element(x, i)

# S4 method for class 'SpatialData,character'
element(x, i) <- value

# S4 method for class 'SpatialData'
images(x)

# S4 method for class 'SpatialData'
labels(object)

# S4 method for class 'SpatialData'
points(x)

# S4 method for class 'SpatialData'
shapes(x)

# S4 method for class 'SpatialData'
tables(x)

# S4 method for class 'SpatialData,character,ANY'
x[[i]] <- value

# S4 method for class 'SpatialData,numeric,ANY'
x[[i]] <- value

# S4 method for class 'SpatialData,ANY,ANY'
x[[i]] <- value

Arguments

images

list of SpatialDataImages

labels

list of SpatialDataLabels

points

list of SpatialDataPoints

shapes

list of SpatialDataShapes

tables

list of SingleCellExperiments

x, object

SpatialData object.

name

character string for extraction (see ?base::`$`).

value

(list of) element(s) with layer-compliant object(s), or NULL/list() to remove an element/layer completely; for element<-, a single SpatialDataElement of the same class as element(x, i).

i, j

character string, scalar or vector of indices specifying the element to extract from a given layer.

...

optional arguments passed to and from other methods.

k

scalar index specifying which scale to use; Inf to use lowest available resolution.

drop

ignored.

Value

SpatialData

Examples

x <- file.path("extdata", "blobs.zarr")
x <- system.file(x, package="spatialdataR")
(x <- readSpatialData(x))
#> class: SpatialData
#> - images(2):
#>   - blobs_image (3,64,64)
#>   - blobs_multiscale_image (3,64,64)
#> - labels(2):
#>   - blobs_labels (64,64)
#>   - blobs_multiscale_labels (64,64)
#> - points(1):
#>   - blobs_points (200)
#> - shapes(3):
#>   - blobs_circles (5,circle)
#>   - blobs_multipolygons (2,polygon)
#>   - blobs_polygons (5,polygon)
#> - tables(1):
#>   - table (3,10) [blobs_labels]
#> coordinate systems(5):
#> - global(8): blobs_image blobs_multiscale_image ... blobs_polygons
#>   blobs_points
#> - scale(1): blobs_labels
#> - translation(1): blobs_labels
#> - affine(1): blobs_labels
#> - sequence(1): blobs_labels

# subsetting
# layers are taken in order of appearance
# (images, labels, points, shapes, tables)
x[-4] # drop layer
#> class: SpatialData
#> - images(2):
#>   - blobs_image (3,64,64)
#>   - blobs_multiscale_image (3,64,64)
#> - labels(2):
#>   - blobs_labels (64,64)
#>   - blobs_multiscale_labels (64,64)
#> - points(1):
#>   - blobs_points (200)
#> - shapes(0):
#> - tables(1):
#>   - table (3,10) [blobs_labels]
#> coordinate systems(5):
#> - global(5): blobs_image blobs_multiscale_image blobs_labels
#>   blobs_multiscale_labels blobs_points
#> - scale(1): blobs_labels
#> - translation(1): blobs_labels
#> - affine(1): blobs_labels
#> - sequence(1): blobs_labels
x[4, -2] # drop element
#> dropping table 'table' because all its annotated regions were removed
#> class: SpatialData
#> - images(0):
#> - labels(0):
#> - points(0):
#> - shapes(2):
#>   - blobs_circles (5,circle)
#>   - blobs_polygons (5,polygon)
#> - tables(0):
#> coordinate systems(1):
#> - global(2): blobs_circles blobs_polygons
x["shapes", c(1, 3)] # subset layer
#> dropping table 'table' because all its annotated regions were removed
#> class: SpatialData
#> - images(0):
#> - labels(0):
#> - points(0):
#> - shapes(2):
#>   - blobs_circles (5,circle)
#>   - blobs_polygons (5,polygon)
#> - tables(0):
#> coordinate systems(1):
#> - global(2): blobs_circles blobs_polygons
x[c(1, 2), list(1, c(1, 2))] # multiple
#> class: SpatialData
#> - images(1):
#>   - blobs_image (3,64,64)
#> - labels(2):
#>   - blobs_labels (64,64)
#>   - blobs_multiscale_labels (64,64)
#> - points(0):
#> - shapes(0):
#> - tables(0):
#> coordinate systems(5):
#> - global(3): blobs_image blobs_labels blobs_multiscale_labels
#> - scale(1): blobs_labels
#> - translation(1): blobs_labels
#> - affine(1): blobs_labels
#> - sequence(1): blobs_labels