SpaMTPData makes the experiment data used in SpaMTP
workflows discoverable through ExperimentHub. The package itself remains
small and users download only the resources required for a particular
workflow.
The submission API uses camelCase function names. Install SpaMTPData >= 0.99.4, SpaMTPdb >= 0.99.3 and SpaMTP >= 0.99.4 together to replace the historical API. Package versions and the version of a published dataset are independent.
library(SpaMTPData)
resources <- spaMTPDataResources(version = "latest")
resources[c("resource", "version", "category", "r_data_class", "requires_conversion")]## resource version category
## 1 mouse_brain_visium 1.1.0 mouse_brain
## 2 mouse_brain_fmp10 1.1.0 mouse_brain
## 3 mouse_brain_dhb_striatum 1.1.0 mouse_brain
## 4 mouse_bladder_raw 1.1.0 mouse_bladder
## 5 mouse_bladder_annotated 1.1.0 mouse_bladder
## 6 mouse_bladder_histology 1.1.0 mouse_bladder
## 7 mouse_bladder_intensity_csv 1.1.0 mouse_bladder
## 8 mouse_bladder_metadata_csv 1.1.0 mouse_bladder
## 9 simulated_xenium 1.1.0 simulated_multiomics
## 10 simulated_maldi 1.1.0 simulated_multiomics
## 11 annotation_refinement_input 1.1.0 annotation_refinement
## 12 annotation_refinement_scores 1.1.0 annotation_refinement
## 13 big_data_roi 1.1.0 big_data
## 14 human_brain_integrated 1.1.0 human_brain
## 15 human_brain_pathways 1.1.0 human_brain
## 16 pig_fetus_cardinal 1.1.0 import_examples
## 17 human_rcc_cardinal 1.1.0 import_examples
## 18 annotation_refinement_results_csv 1.1.0 annotation_refinement
## r_data_class requires_conversion
## 1 SpatialExperiment FALSE
## 2 SpatialExperiment FALSE
## 3 SpatialExperiment FALSE
## 4 MSImagingExperiment FALSE
## 5 SpatialExperiment FALSE
## 6 array FALSE
## 7 FilePath FALSE
## 8 FilePath FALSE
## 9 SpatialExperiment FALSE
## 10 SpatialExperiment FALSE
## 11 MSImagingExperiment FALSE
## 12 list FALSE
## 13 MSImagingExperiment FALSE
## 14 SpatialExperiment FALSE
## 15 data.frame FALSE
## 16 MSImagingExperiment FALSE
## 17 MSImagingExperiment FALSE
## 18 FilePath FALSE## [1] "1.1.0" "1.0.0"spaMTPExampleData() constructs a small, deterministic
synthetic SpatialExperiment. It is not a biological dataset and does not
load Seurat. Use it to check the container interface or run the
three-package workflow demonstrated in SpaMTP’s
SpaMTP_Companion_Workflow vignette.
## [1] "counts"## [1] 149.0444 171.0264 181.0707 203.0526 166.0863 500.0500## [1] edge edge edge edge edge edge core core core core core core
## Levels: core edge## x y
## [1,] 0 0
## [2,] 0 1
## [3,] 0 2
## [4,] 1 0
## [5,] 1 1
## [6,] 1 2
## [7,] 2 0
## [8,] 2 1
## [9,] 2 2
## [10,] 3 0
## [11,] 3 1
## [12,] 3 2## [1] "transcriptome"The maintainer recipe
inst/scripts/prepare-native-resources.R extracts the seven
archival Seurat datasets into native release 1.1.0, now
published in Zenodo record
22733262. It retains counts/data, feature and pixel annotations,
image-centroid coordinates and paired transcriptomes. The resulting
SpatialExperiment RDS can be read directly without Seurat or any further
conversion:
striatum <- spaMTPData("mouse_brain_dhb_striatum", version = "1.1.0")
SummarizedExperiment::assayNames(striatum)
SpatialExperiment::spatialCoords(striatum)
SingleCellExperiment::altExpNames(striatum) # SPTThis downloading example is not evaluated during a package build. The
accompanying native manifest records source and output hashes. Optical
rasters, polygons, graphs, reductions and Seurat-specific weight objects
are omitted; the retained data layer is not reinterpreted
as log-normalized expression. The simulated datasets retain their
explicit synthetic status.
The resource API selects 1.1.0 by default. Native files
have new filenames and checksums and are not substituted under an old
archive’s identity. Use version = "1.0.0" to request the
original immutable archives explicitly. Hub ingestion is separate from
publication and package metadata registration.
The native files are published in the same Zenodo version family as SpaMTPdb’s annotation resources. SpaMTPdb coordinates file publication; SpaMTPData retains experimental resource ownership, documentation and reading. There is no runtime dependency between the two data packages. Registration of a published native release preserves the 1.0.0 history and carries forward all 18 resources, including eleven unchanged files at their original locations.
Inspect the mouse brain/DHB record without downloading the object:
striatum_metadata <- spaMTPData(
"mouse_brain_dhb_striatum",
metadata = TRUE
)
striatum_metadata[c("resource", "version", "r_data_class", "bytes")]## resource version r_data_class bytes
## 21 mouse_brain_dhb_striatum 1.1.0 SpatialExperiment 47643252stopifnot(striatum_metadata$r_data_class == "SpatialExperiment",
!striatum_metadata$requires_conversion)Omit metadata = TRUE to retrieve and cache the native
object. ExperimentHub is preferred; an immutable source-URL fallback is
available before ingestion:
This default file is a SpatialExperiment and does not need Seurat. Historical metadata can be inspected without downloading the old Seurat object:
historical <- spaMTPData("mouse_brain_dhb_striatum",
version = "1.0.0", metadata = TRUE)
historical[c("resource", "version", "r_data_class", "requires_conversion")]## resource version r_data_class requires_conversion
## 3 mouse_brain_dhb_striatum 1.0.0 Seurat TRUEHistorical entries marked requires_conversion = TRUE
need explicit conversion at the SpaMTP workflow boundary. Downloading an
old file does not update its scientific processing. Its class and
checksum remain unchanged.
The same interface can use a previously downloaded local file:
options(SpaMTPData.resource_dir = "/path/to/SpaMTPData-files")
striatum <- spaMTPData("mouse_brain_dhb_striatum", offline = TRUE)Local files and caches are verified against the recorded size and
MD5. offline = TRUE also uses previously verified
download-cache entries; it never queries ExperimentHub or Zenodo. A
missing or invalid file is an error, not a reason to silently use
another version. verify = FALSE permits intentional local
development fixtures but does not bypass object-class validation.
The explicit resource accessor follows the same interface:
## resource version category
## 21 mouse_brain_dhb_striatum 1.1.0 mouse_brain
## title file_name
## 21 SpaMTPData_mouse_brain_dhb_striatum_1.1.0 mouse_brain_dhb_striatum_spe.rds
## location_prefix
## 21 https://zenodo.org/api/records/22733262/files/
## rdata_path source_url
## 21 mouse_brain_dhb_striatum_spe.rds/content https://zenodo.org/records/22733262
## r_data_class dispatch_class bytes md5
## 21 SpatialExperiment Rds 47643252 629a3f78651a512484550b4ba0e5d66c
## requires_conversion
## 21 FALSE## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 26.04.1 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-r0.3.32.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=en_US.UTF-8
## [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] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] SpaMTPData_0.99.5 BiocStyle_2.41.0
##
## loaded via a namespace (and not attached):
## [1] KEGGREST_1.53.6 SummarizedExperiment_1.43.0
## [3] rjson_0.2.23 xfun_0.61
## [5] bslib_0.12.0 httr2_1.3.0
## [7] lattice_0.23-1 Biobase_2.73.2
## [9] vctrs_0.7.3 tools_4.6.1
## [11] generics_0.1.4 stats4_4.6.1
## [13] curl_8.0.0 tibble_3.3.1
## [15] AnnotationDbi_1.75.2 RSQLite_3.53.3
## [17] blob_1.3.0 pkgconfig_2.0.3
## [19] BiocBaseUtils_1.15.1 Matrix_1.7-6
## [21] dbplyr_2.6.0 S4Vectors_0.51.10
## [23] lifecycle_1.0.5 compiler_4.6.1
## [25] Biostrings_2.81.9 Seqinfo_1.3.2
## [27] htmltools_0.5.9 sys_3.4.3
## [29] buildtools_1.0.0 sass_0.4.10
## [31] yaml_2.3.12 pillar_1.11.1
## [33] crayon_1.5.3 jquerylib_0.1.4
## [35] SingleCellExperiment_1.35.2 DelayedArray_0.39.8
## [37] cachem_1.1.0 magick_2.9.1
## [39] abind_1.4-8 ExperimentHub_3.3.2
## [41] AnnotationHub_4.3.2 tidyselect_1.2.1
## [43] digest_0.6.39 dplyr_1.2.1
## [45] BiocVersion_3.24.0 maketools_1.3.2
## [47] grid_4.6.1 fastmap_1.2.0
## [49] SparseArray_1.13.4 cli_3.6.6
## [51] magrittr_2.0.5 S4Arrays_1.13.2
## [53] filelock_1.0.3 rappdirs_0.3.4
## [55] bit64_4.8.6 rmarkdown_2.32
## [57] XVector_0.53.0 httr_1.4.9
## [59] matrixStats_1.5.0 bit_4.6.0
## [61] otel_0.2.0 png_0.1-9
## [63] SpatialExperiment_1.23.0 memoise_2.0.1
## [65] evaluate_1.0.5 knitr_1.52
## [67] GenomicRanges_1.65.4 IRanges_2.47.5
## [69] BiocFileCache_3.3.0 rlang_1.3.0
## [71] Rcpp_1.1.2 glue_1.8.1
## [73] DBI_1.3.0 BiocManager_1.30.27
## [75] BiocGenerics_0.59.12 jsonlite_2.0.0
## [77] R6_2.6.1 MatrixGenerics_1.25.0