The `SpatialDataAttrs` class

Usage

SpatialDataAttrs(
  x,
  type = c("array", "frame"),
  label = FALSE,
  trans = NULL,
  ver = "0.4",
  nch = 3,
  ...
)

# S4 method for class 'SpatialDataAttrs'
x$name

# S4 method for class 'SpatialDataPoint'
feature_key(x)

# S4 method for class 'SpatialDataAttrs'
feature_key(x)

# S4 method for class 'SpatialDataAttrs,character'
feature_key(x) <- value

# S4 method for class 'SingleCellExperiment'
region_key(x)

# S4 method for class 'SingleCellExperiment'
region(x)

# S4 method for class 'SingleCellExperiment'
regions(x)

# S4 method for class 'SingleCellExperiment,character'
regions(x) <- value

# S4 method for class 'SingleCellExperiment,NULL'
regions(x) <- value

# S4 method for class 'list'
instance_key(x)

# S4 method for class 'SingleCellExperiment'
instance_key(x)

# S4 method for class 'SpatialDataFrame'
instance_key(x)

# S4 method for class 'SpatialDataLabel'
instance_key(x)

# S4 method for class 'SpatialDataAttrs,character'
instance_key(x) <- value

# S4 method for class 'SingleCellExperiment,character'
instance_key(x) <- value

# S4 method for class 'SpatialDataLabel'
instances(x)

# S4 method for class 'SpatialDataPoint'
instances(x)

# S4 method for class 'SpatialDataShape'
instances(x)

# S4 method for class 'SingleCellExperiment'
instances(x)

# S4 method for class 'SingleCellExperiment'
instances(x) <- value

Arguments

x: element or list extracted from a OME-NGFF compliant .zattrs file.
type: character string; either "array" (image/label) or "frame" (point/shape).
label: flag; when type="frame", should attributes be for a label?
trans: list of coordinate transformations; defaults to identity only.
ver: character string; specified the .zarr version to comply with.
nch: scalar integer; how many channels should there be? (ignored unless type="frame" and label=FALSE).
...: additional attributes (e.g., version, feature_key).
name: character string for extraction (see ?base::`$`).
value: character string (for one region and _keys), or vector (for many regions, instances and regions).

Value

character string

Details

When x is a spatial element, the following applies: SpatialDataFrame: feature/instance_key, SingleCellExperiment: region, region/instance_key.

When missing x, SpatialDataAttrs will generate a valid object with default axes (array: cyx, frame: xy) and transformations (identify) according to the specified type.

Examples

x <- file.path("extdata", "blobs.zarr")
x <- system.file(x, package="SpatialData")
x <- readSpatialData(x)

# tables
region(table(x))
#> [1] "blobs_labels"
region_key(table(x))
#> [1] "region"

# points
instance_key(point(x))
#> [1] "instance_id"
fk <- feature_key(point(x))
base::table(point(x)[[fk]])
#> 
#> gene_a gene_b 
#>     90    110 

# transformations
(z <- meta(label(x)))
#> class: SpatialDataAttrs
#> axes(2):
#> - name: y x 
#> - type: space space 
#> coordTrans(5):
#> - global: (identity)
#> - scale: (scale:[3,2])
#> - translation: (translation:[-50,10])
#> - affine: (affine:[[20,10,30],[50,40,60]])
#> - sequence: (scale:[3,2]), (translation:[-50,10])
#> datasets(1): 0
#> - 0: (scale:[1,1])
CTname(z)
#> [1] "global"      "scale"       "translation" "affine"      "sequence"   
CTtype(z)
#> [1] "identity"    "scale"       "translation" "affine"      "sequence"   
CTdata(z, "scale")
#> [[1]]
#> [1] 3
#> 
#> [[2]]
#> [1] 2
#> 

# constructor
SpatialDataAttrs(type="frame")
#> class: SpatialDataAttrs
#> axes(2):
#> - name: x y 
#> - type: space space 
#> coordTrans(1):
#> - global: (identity)
SpatialDataAttrs(type="array")
#> class: SpatialDataAttrs
#> axes(3):
#> - name: c y x 
#> - type: channel space space 
#> coordTrans(1):
#> - global: (identity)
#> datasets(1): 0
#> - 0: (scale:[1,1])
#> channels(3): a b c
SpatialDataAttrs(type="array", nch=7)
#> class: SpatialDataAttrs
#> axes(3):
#> - name: c y x 
#> - type: channel space space 
#> coordTrans(1):
#> - global: (identity)
#> datasets(1): 0
#> - 0: (scale:[1,1])
#> channels(7): a b ... f g
SpatialDataAttrs(type="array", label=TRUE)
#> class: SpatialDataAttrs
#> axes(2):
#> - name: y x 
#> - type: space space 
#> coordTrans(1):
#> - global: (identity)
#> datasets(1): 0
#> - 0: (scale:[1,1])
#> channels(3): a b c