Save/load spatial omics data to/from file
Overview
The SpatialExperiment class (from the SpatialExperiment
package) provides a representation of spatial transcriptomics data that
is compatible with Bioconductor’s SummarizedExperiment
ecosystem. The alabaster.spatial
package contains methods to save and load SpatialExperiment
objects into and out of file. Check out the alabaster.base
for more details on the motivation and concepts of the
alabaster framework.
Quick start
To demonstrate, we’ll use the example dataset provided in the SpatialExperiment package:
library(SpatialExperiment)
# Copying the example from ?read10xVisium.
dir <- system.file("extdata", "10xVisium", package = "SpatialExperiment")
sample_ids <- c("section1", "section2")
samples <- file.path(dir, sample_ids, "outs")
spe <- read10xVisium(
samples,
sample_ids,
type = "sparse",
data = "raw",
images = "lowres",
load = FALSE
)
colnames(spe) <- make.unique(colnames(spe)) # Making the column names unique.
spe## class: SpatialExperiment
## dim: 50 99
## metadata(0):
## assays(1): counts
## rownames(50): ENSMUSG00000051951 ENSMUSG00000089699 ...
## ENSMUSG00000005886 ENSMUSG00000101476
## rowData names(1): symbol
## colnames(99): AAACAACGAATAGTTC-1 AAACAAGTATCTCCCA-1 ...
## AAAGTCGACCCTCAGT-1.1 AAAGTGCCATCAATTA-1.1
## colData names(4): in_tissue array_row array_col sample_id
## reducedDimNames(0):
## mainExpName: NULL
## altExpNames(0):
## spatialCoords names(2) : pxl_col_in_fullres pxl_row_in_fullres
## imgData names(4): sample_id image_id data scaleFactorWe call the usual saveObject() function to save its
contents to file:
## [1] "OBJECT" "assays/0/OBJECT"
## [3] "assays/0/matrix.h5" "assays/names.json"
## [5] "column_data/OBJECT" "column_data/basic_columns.h5"
## [7] "coordinates/OBJECT" "coordinates/array.h5"
## [9] "images/0.png" "images/1.png"
## [11] "images/mapping.h5" "row_data/OBJECT"
## [13] "row_data/basic_columns.h5"This goes through the usual saving process for
SingleCellExperiments, with an additional saving step for
the spatial data (see the coordinates/ and
images/ subdirectories). We can then load it back in using
the readObject() function:
More details on the metadata and on-disk layout are provided in the schema.
Session info
## R version 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] alabaster.spatial_1.7.1 alabaster.base_1.7.2
## [3] SpatialExperiment_1.17.0 SingleCellExperiment_1.29.1
## [5] SummarizedExperiment_1.37.0 Biobase_2.67.0
## [7] GenomicRanges_1.59.1 GenomeInfoDb_1.43.2
## [9] IRanges_2.41.2 S4Vectors_0.45.2
## [11] BiocGenerics_0.53.3 generics_0.1.3
## [13] MatrixGenerics_1.19.0 matrixStats_1.4.1
## [15] BiocStyle_2.35.0
##
## loaded via a namespace (and not attached):
## [1] rjson_0.2.23 xfun_0.49
## [3] bslib_0.8.0 rhdf5_2.51.1
## [5] lattice_0.22-6 rhdf5filters_1.19.0
## [7] tools_4.4.2 parallel_4.4.2
## [9] R.oo_1.27.0 Matrix_1.7-1
## [11] sparseMatrixStats_1.19.0 dqrng_0.4.1
## [13] lifecycle_1.0.4 GenomeInfoDbData_1.2.13
## [15] compiler_4.4.2 statmod_1.5.0
## [17] alabaster.se_1.7.0 codetools_0.2-20
## [19] htmltools_0.5.8.1 sys_3.4.3
## [21] buildtools_1.0.0 sass_0.4.9
## [23] alabaster.matrix_1.7.4 yaml_2.3.10
## [25] crayon_1.5.3 jquerylib_0.1.4
## [27] R.utils_2.12.3 BiocParallel_1.41.0
## [29] limma_3.63.2 DelayedArray_0.33.3
## [31] cachem_1.1.0 magick_2.8.5
## [33] abind_1.4-8 locfit_1.5-9.10
## [35] digest_0.6.37 maketools_1.3.1
## [37] fastmap_1.2.0 grid_4.4.2
## [39] cli_3.6.3 SparseArray_1.7.2
## [41] magrittr_2.0.3 S4Arrays_1.7.1
## [43] edgeR_4.5.1 DelayedMatrixStats_1.29.0
## [45] UCSC.utils_1.3.0 rmarkdown_2.29
## [47] XVector_0.47.0 httr_1.4.7
## [49] DropletUtils_1.27.1 R.methodsS3_1.8.2
## [51] beachmat_2.23.4 alabaster.sce_1.7.0
## [53] HDF5Array_1.35.2 evaluate_1.0.1
## [55] knitr_1.49 rlang_1.1.4
## [57] Rcpp_1.0.13-1 scuttle_1.17.0
## [59] BiocManager_1.30.25 alabaster.ranges_1.7.0
## [61] alabaster.schemas_1.7.0 jsonlite_1.8.9
## [63] R6_2.5.1 Rhdf5lib_1.29.0
## [65] zlibbioc_1.52.0