SpatialData annotations

SpatialData annotations

Usage

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

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

# S4 method for class 'SpatialData,character'
hasTable(x, i, name = FALSE)

# S4 method for class 'SpatialData,ANY'
getTable(x, i, j, assay = 1, drop = TRUE)

# S4 method for class 'SpatialData,character'
getTable(x, i, j, assay = 1, drop = TRUE)

# S4 method for class 'SpatialData,ANY'
setTable(x, i, ..., name = NULL, rk = "rk", ik = "ik")

# S4 method for class 'SpatialData,character'
setTable(x, i, y, name = NULL, rk = "region", ik = "instance_id")

Arguments

x

SpatialData object.

i

character string; name of the element for which to get/set a table.

name

logical; should the table name be returned instead of TRUE/FALSE?

j

character string; colData column, or row name to retrieve assay data.

assay

character string or scalar integer; specifies which assay to use when j is a row name.

drop

logical; should observations (columns) that don't belong to i be filtered out?

...

option arguments passed to and from other methods.

rk, ik

character string; region and instance key (the latter will be ignored if an instance key is already specified within element i).

y

SingleCellExperiment containing annotations for i.

Value

• hasTable: logical scalar (or character string, if name=TRUE); whether or not a table annotating i exists in x

• getTable: SingleCellExperiment; the table annotating i with optional filtering of matching observations

• valTable: vector of values (according to j) from the table annotating i

Examples

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

# check if element has a 'table'
hasTable(x, "blobs_points")
#> [1] FALSE
hasTable(x, "blobs_labels")
#> [1] TRUE

# retrieve 'table' for element 'i'
sce <- getTable(x, i="blobs_labels")
head(colData(sce))
#> DataFrame with 6 rows and 0 columns
meta(sce)
#> $instance_key
#> [1] "instance_id"
#> 
#> $region
#> [1] "blobs_labels"
#> 
#> $region_key
#> [1] "region"
#> 

# get values from 'table'
getTable(x,
  i="blobs_labels",
  j="channel_0_sum")
#>          3          4          5          8         10         11         12 
#> 25.0537079 10.6787960  3.2422082  3.4709382  7.7414086  0.9912003 40.3020305 
#>         13         15         16 
#>  0.2252217  1.2125781  7.0430209 

# add 'table' annotating an element 'i'

# labels
y <- x; tables(y) <- list()
mtx <- matrix(0, 1, length(instances(label(y))))
sce <- SingleCellExperiment(list(counts=mtx))
y <- setTable(y, i <- "blobs_labels", sce)
getTable(y, i)
#> class: SingleCellExperiment 
#> dim: 1 10 
#> metadata(0):
#> assays(1): counts
#> rownames: NULL
#> rowData names(0):
#> colnames: NULL
#> colData names(0):
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):

# shapes
i <- "blobs_circles"
mtx <- matrix(0, 1, nrow(shape(x, i)))
sce <- SingleCellExperiment(list(counts=mtx))
y <- setTable(x, i, sce)
getTable(y, i)
#> class: SingleCellExperiment 
#> dim: 1 5 
#> metadata(0):
#> assays(1): counts
#> rownames: NULL
#> rowData names(0):
#> colnames: NULL
#> colData names(0):
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):