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Usage
SpatialData(images, labels, points, shapes, tables)
# S4 method for class 'SpatialData'
x$name
# S4 method for class 'SpatialDataElement'
data(x)
# S4 method for class 'SpatialDataElement'
meta(x)
# S4 method for class 'SpatialData'
images(x)
# S4 method for class 'SpatialData'
labels(x)
# S4 method for class 'SpatialData'
shapes(x)
# S4 method for class 'SpatialData'
points(x)
# S4 method for class 'SpatialData'
tables(x)
# S4 method for class 'SpatialData'
imageNames(x)
# S4 method for class 'SpatialData'
labelNames(x)
# S4 method for class 'SpatialData'
shapeNames(x)
# S4 method for class 'SpatialData'
pointNames(x)
# S4 method for class 'SpatialData'
tableNames(x)
# S4 method for class 'SpatialData'
image(x, i = 1)
# S4 method for class 'SpatialData'
label(x, i = 1)
# S4 method for class 'SpatialData'
shape(x, i = 1)
# S4 method for class 'SpatialData'
point(x, i = 1)
# S4 method for class 'SpatialData'
table(x, i = 1)
# S4 method for class 'SpatialData,numeric,ANY,ANY'
x[[i]] <- value
# S4 method for class 'SpatialData,character,ANY,ANY'
x[[i]] <- value
# S4 method for class 'SpatialData,list'
images(x) <- value
# S4 method for class 'SpatialData,list'
labels(x) <- value
# S4 method for class 'SpatialData,list'
shapes(x) <- value
# S4 method for class 'SpatialData,list'
points(x) <- value
# S4 method for class 'SpatialData,list'
tables(x) <- value
# S4 method for class 'SpatialData,character,ImageArray'
image(x, i) <- value
# S4 method for class 'SpatialData,character,LabelArray'
label(x, i) <- value
# S4 method for class 'SpatialData,character,PointFrame'
point(x, i) <- value
# S4 method for class 'SpatialData,character,ShapeFrame'
shape(x, i) <- value
# S4 method for class 'SpatialData,character,SingleCellExperiment'
table(x, i) <- value
# S4 method for class 'SpatialData,numeric,ImageArray'
image(x, i = 1) <- value
# S4 method for class 'SpatialData,numeric,LabelArray'
label(x, i = 1) <- value
# S4 method for class 'SpatialData,numeric,PointFrame'
point(x, i = 1) <- value
# S4 method for class 'SpatialData,numeric,ShapeFrame'
shape(x, i = 1) <- value
# S4 method for class 'SpatialData,numeric,SingleCellExperiment'
table(x, i = 1) <- value
# S4 method for class 'SpatialData,missing,ImageArray'
image(x, i) <- value
# S4 method for class 'SpatialData,missing,LabelArray'
label(x, i) <- value
# S4 method for class 'SpatialData,missing,PointFrame'
point(x, i) <- value
# S4 method for class 'SpatialData,missing,ShapeFrame'
shape(x, i) <- value
# S4 method for class 'SpatialData,missing,SingleCellExperiment'
table(x, i) <- value
# S4 method for class 'SpatialData,ANY,NULL'
image(x, i) <- value
# S4 method for class 'SpatialData,ANY,NULL'
label(x, i) <- value
# S4 method for class 'SpatialData,ANY,NULL'
shape(x, i) <- value
# S4 method for class 'SpatialData,ANY,NULL'
point(x, i) <- value
# S4 method for class 'SpatialData,ANY,NULL'
table(x, i) <- value
# S4 method for class 'SpatialData,ANY,ANY'
image(x, i) <- value
# S4 method for class 'SpatialData,ANY,ANY'
label(x, i) <- value
# S4 method for class 'SpatialData,ANY,ANY'
shape(x, i) <- value
# S4 method for class 'SpatialData,ANY,ANY'
point(x, i) <- value
# S4 method for class 'SpatialData,ANY,ANY'
table(x, i) <- valueArguments
- images
list of
ImageArrays- labels
list of
LabelArrays- points
list of
PointFrames- shapes
list of
ShapeFrames- tables
list of
SingleCellExperiments- x
SpatialData- name
character string for extraction (see
?base::`$`).- i
character string, scalar or vector of indices specifying the element to extract from a given layer.
- value
(list of) element(s) with layer-compliant object(s), or NULL/
list()to remove an element/layer completely.- j
ignored.
- ...
optional arguments passed to and from other methods.
Examples
x <- file.path("extdata", "blobs.zarr")
x <- system.file(x, package="SpatialData")
(x <- readSpatialData(x, tables=FALSE))
#> 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(0):
#> coordinate systems:
#> - 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(0):
#> coordinate systems:
#> - 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
#> class: SpatialData
#> - images(0):
#> - labels(0):
#> - points(0):
#> - shapes(2):
#> - blobs_circles (5,circle)
#> - blobs_polygons (5,polygon)
#> - tables(0):
#> coordinate systems:
#> - global(2): blobs_circles blobs_polygons
x["shapes", c(1, 3)] # subset layer
#> class: SpatialData
#> - images(0):
#> - labels(0):
#> - points(0):
#> - shapes(2):
#> - blobs_circles (5,circle)
#> - blobs_polygons (5,polygon)
#> - tables(0):
#> coordinate systems:
#> - 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:
#> - 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