Retrieve SpatialData on-disk paths
Usage
# S4 method for class 'SpatialDataArray'
path(object, ...)
# S4 method for class 'SpatialDataFrame'
path(object, ...)
# S4 method for class 'SingleCellExperiment'
path(object, ...)
# S4 method for class 'SpatialData'
path(object, simplify = TRUE, ...)Arguments
- object
SpatialDataobject or one of its elements.- ...
ignored.
- simplify
logical scalar; whether to flatten paths into a tibble.
Value
for single elements, a character string;
for SpatialData objects, if simplify=TRUE (default),
a tibble where rows=elements and columns=layers/elements/paths.
if simplify=FALSE, a depth-3 list where levels=layers/elements/paths.
Examples
zs <- file.path("extdata", "blobs.zarr")
zs <- system.file(zs, package="spatialdataR")
sd <- readSpatialData(zs)
# element-wise
path(shape(sd))
#> [1] "/home/runner/work/_temp/Library/spatialdataR/extdata/blobs.zarr/shapes/blobs_circles/shapes.parquet"
# object-wide
path(sd)
#> # A tibble: 9 × 3
#> layer element path
#> <chr> <chr> <chr>
#> 1 images blobs_image /home/runner/work/_temp/Library/spatialdataR/e…
#> 2 images blobs_multiscale_image /home/runner/work/_temp/Library/spatialdataR/e…
#> 3 labels blobs_labels /home/runner/work/_temp/Library/spatialdataR/e…
#> 4 labels blobs_multiscale_labels /home/runner/work/_temp/Library/spatialdataR/e…
#> 5 points blobs_points /home/runner/work/_temp/Library/spatialdataR/e…
#> 6 shapes blobs_circles /home/runner/work/_temp/Library/spatialdataR/e…
#> 7 shapes blobs_multipolygons /home/runner/work/_temp/Library/spatialdataR/e…
#> 8 shapes blobs_polygons /home/runner/work/_temp/Library/spatialdataR/e…
#> 9 tables table /home/runner/work/_temp/Library/spatialdataR/e…
path(sd, FALSE)$labels
#> $blobs_labels
#> [1] "/home/runner/work/_temp/Library/spatialdataR/extdata/blobs.zarr/labels/blobs_labels"
#>
#> $blobs_multiscale_labels
#> [1] "/home/runner/work/_temp/Library/spatialdataR/extdata/blobs.zarr/labels/blobs_multiscale_labels"
#>