data were retrieved on Nov. 11th, 2024, from here.
Examples
x <- file.path("extdata", "blobs.zarr")
x <- system.file(x, package="SpatialData")
(x <- readSpatialData(x))
#>
#> Attaching package: ‘BiocGenerics’
#> The following object is masked from ‘package:SpatialData’:
#>
#> table
#> The following objects are masked from ‘package:stats’:
#>
#> IQR, mad, sd, var, xtabs
#> The following objects are masked from ‘package:base’:
#>
#> Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
#> as.data.frame, basename, cbind, colnames, dirname, do.call,
#> duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
#> lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
#> pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
#> tapply, union, unique, unsplit, which.max, which.min
#>
#> Attaching package: ‘MatrixGenerics’
#> The following objects are masked from ‘package:matrixStats’:
#>
#> colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
#> colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
#> colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
#> colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
#> colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
#> colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
#> colWeightedMeans, colWeightedMedians, colWeightedSds,
#> colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
#> rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
#> rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
#> rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
#> rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
#> rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
#> rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
#> rowWeightedSds, rowWeightedVars
#>
#> Attaching package: ‘S4Vectors’
#> The following objects are masked from ‘package:Matrix’:
#>
#> expand, unname
#> The following object is masked from ‘package:utils’:
#>
#> findMatches
#> The following objects are masked from ‘package:base’:
#>
#> I, expand.grid, unname
#>
#> Attaching package: ‘S4Arrays’
#> The following object is masked from ‘package:abind’:
#>
#> abind
#> The following object is masked from ‘package:base’:
#>
#> rowsum
#>
#> Attaching package: ‘DelayedArray’
#> The following objects are masked from ‘package:base’:
#>
#> apply, scale, sweep
#> 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)
#> 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