Package: spatialdataR 0.99.44

Helena L. Crowell

spatialdataR: Representation of Python's spatialdata in R

R interface to Python/scverse's 'spatialdata' framework for unified spatial omics data handling. Adheres to OME-NGFF standards, providing lazy, on-disk representations for multiscale images and labels (ZarrArray), as well as points and shapes (DuckDB-backed tables). Includes handling of coordinate transformation systems and spatial utilities for cropping, masking, and querying. Integrates tabular annotations as 'SingleCellExperiment's (via 'anndataR'), enabling interoperable spatial omics workflows across R and Python.

Authors:Helena L. Crowell [aut, cre], Artür Manukyan [aut], Hugo Gruson [aut], Vince Carey [aut]

spatialdataR_0.99.44.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
spatialdataR/json (API)

# Install 'spatialdataR' in R:

install.packages('spatialdataR', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/helenalc/spatialdatar/issues

Pkgdown/docs site:https://helenalc.github.io

On CRAN:

dataimport datarepresentation infrastructure immunooncology geneexpression transcriptomics singlecell spatial

4.93 score 12 scripts 95 exports 87 dependencies

Last updated from:fe24cf05b2. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	212
linux-devel-x86_64	NOTE	406
source / vignettes	OK	300
linux-release-x86_64	NOTE	390
macos-release-arm64	NOTE	236
macos-oldrel-arm64	NOTE	258
windows-devel	NOTE	343
windows-release	NOTE	394
windows-oldrel	NOTE	402
wasm-release	OK	227

Exports:addCT as.data.frame axes centroids channels colnames combine crop CTdata CTgraph CTlist CTname CTpath CTplot CTtype data data_type element element<-extent feature_key feature_key<-filter flip flop geom_type getTable hasTable image image<-imageNames imageNames<-images images<-instance_key instance_key<-instances instances<-label label<-labelNames labelNames<-labels labels<-layer mask meta mirror mutate path point point<-pointNames pointNames<-points points<-pull query readImage readLabel readPoint readShape readSpatialData readTable region region_key regions regions<-rmvCT rotate rownames scale select sequence setTable shape shape<-shapeNames shapeNames<-shapes shapes<-SpatialData SpatialDataAttrs SpatialDataImage SpatialDataLabel SpatialDataPoint SpatialDataShape table table<-tableNames tableNames<-tables tables<-transform translation

Dependencies:abind anndataR arrow askpass assertthat base64enc BH Biobase BiocGenerics bit bit64 blob class classInt cli cpp11 curl DBI dbplyr DelayedArray digest dplyr duckdb duckspatial e1071 generics GenomicRanges geoarrow glue graph grumpy here httr2 IRanges jsonlite KernSmooth lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats nanoarrow openssl paws.common paws.storage pillar pkgconfig png proxy purrr R.methodsS3 R.oo R.utils R6 rappdirs Rarr RBGL Rcpp RcppTOML reticulate rlang rprojroot s2 S4Arrays S4Vectors Seqinfo sf SingleCellExperiment SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect units utf8 uuid vctrs withr wk xml2 XVector ZarrArray

spatialdataR

Rendered fromSpatialData.Rmdusingknitr::rmarkdown

Last update: 2026-07-05
Started: 2023-04-27

Help page	Topics
`SpatialData` .zarr toy datasets	blobs
Spatial element centroids	centroids centroids,ANY-method centroids,SpatialDataLabel-method centroids,SpatialDataPoint-method centroids,SpatialDataShape-method
Combine two 'SpatialData' objects	combine combine,list,missing-method combine,SpatialData,SpatialData-method
spatial cropping	crop crop,SpatialData-method crop,SpatialDataArray-method crop,SpatialDataFrame-method
Coord. trans. graph	CTgraph CTgraph,ANY-method CTgraph,SpatialData-method CTgraph,SpatialDataElement-method CTpath CTpath,ANY-method CTpath,SpatialData-method CTpath,SpatialDataElement-method CTplot
Coord. trans. utilities	addCT addCT,SpatialDataAttrs-method addCT,SpatialDataElement-method axes axes,SpatialDataAttrs-method axes,SpatialDataElement-method CTdata CTdata,SpatialDataAttrs-method CTdata,SpatialDataElement-method CTlist CTlist,SpatialDataAttrs-method CTlist,SpatialDataElement-method CTname CTname,SpatialData-method CTname,SpatialDataAttrs-method CTname,SpatialDataElement-method CTtype CTtype,SpatialDataAttrs-method CTtype,SpatialDataElement-method CTutils rmvCT rmvCT,SpatialDataAttrs-method rmvCT,SpatialDataElement-method
Spatial element extent	extent extent,SpatialData-method extent,SpatialDataArray-method extent,SpatialDataFrame-method
Aggregate data across layers	mask mask,SpatialData-method
Miscellaneous `SpatialData` methods	misc show,SpatialData-method show,SpatialDataArray-method show,SpatialDataPoint-method show,SpatialDataShape-method
Retrieve 'SpatialData' on-disk paths	path path,SingleCellExperiment-method path,SpatialData-method path,SpatialDataArray-method path,SpatialDataFrame-method
queries	query query,SpatialData-method
Reading `SpatialData`	readImage readLabel readPoint readShape readSpatialData readTable
The `SpatialData` class	$,SpatialData-method $<-,SpatialData-method .SpatialData colnames,SpatialData-method data data,SpatialDataElement-method element element,SpatialData,ANY-method element,SpatialData,character-method element,SpatialData,missing-method element,SpatialData,numeric-method element<- element<-,SpatialData,character-method image image<- imageNames imageNames<- images images,SpatialData-method images<- label label<- labelNames labelNames<- labels labels,SpatialData-method labels<- layer layer,SpatialData,ANY-method layer,SpatialData,character-method meta meta,SpatialDataElement-method point point<- pointNames pointNames<- points points,SpatialData-method points<- rownames,SpatialData-method shape shape<- shapeNames shapeNames<- shapes shapes,SpatialData-method shapes<- SpatialData SpatialData-class table table<- tableNames tableNames<- tables tables,SpatialData-method tables<- [,SpatialData,ANY,ANY,ANY-method [[,SpatialData,character,ANY-method [[,SpatialData,numeric,ANY-method [[<-,SpatialData,ANY,ANY-method [[<-,SpatialData,character,ANY-method [[<-,SpatialData,numeric,ANY-method
'SpatialDataArray'	channels channels,SpatialDataAttrs-method channels,SpatialDataElement-method channels,SpatialDataImage-method data_type data_type,DelayedArray-method data_type,SpatialDataArray-method dim,SpatialDataArray-method length,SpatialDataArray-method SpatialDataArray SpatialDataImage SpatialDataLabel [,SpatialDataImage,ANY,ANY,ANY-method [,SpatialDataLabel,ANY,ANY,ANY-method
The `SpatialDataAttrs` class	$,SpatialDataAttrs-method feature_key feature_key,SpatialDataAttrs-method feature_key,SpatialDataPoint-method feature_key<- feature_key<-,SpatialDataAttrs,character-method instances instances,SingleCellExperiment-method instances,SpatialDataLabel-method instances,SpatialDataPoint-method instances,SpatialDataShape-method instances<- instances<-,SingleCellExperiment-method instance_key instance_key,list-method instance_key,SingleCellExperiment-method instance_key,SpatialDataFrame-method instance_key,SpatialDataLabel-method instance_key<- instance_key<-,SingleCellExperiment,character-method instance_key<-,SpatialDataAttrs,character-method region region,SingleCellExperiment-method region<- regions regions,SingleCellExperiment-method regions<- regions<-,SingleCellExperiment,character-method regions<-,SingleCellExperiment,NULL-method region_key region_key,SingleCellExperiment-method region_key<- SpatialDataAttrs
'SpatialDataFrame'	$,SpatialDataPoint-method $,SpatialDataShape-method .DollarNames.SpatialDataShape as.data.frame,SpatialDataFrame-method dim,SpatialDataFrame-method filter.SpatialDataFrame geom_type geom_type,SpatialDataShape-method length,SpatialDataFrame-method mutate.SpatialDataFrame names,SpatialDataFrame-method pull.SpatialDataFrame select.SpatialDataFrame SpatialDataFrame SpatialDataPoint SpatialDataShape [,SpatialDataFrame,ANY,ANY,ANY-method [[,SpatialDataFrame,ANY,ANY-method
'SpatialData' annotations	getTable getTable,SpatialData,ANY-method getTable,SpatialData,character-method hasTable hasTable,SpatialData,ANY-method hasTable,SpatialData,character-method meta,SingleCellExperiment-method setTable setTable,SpatialData,ANY-method setTable,SpatialData,character-method table-utils
Transformations	flip flip,SpatialDataArray-method flop flop,SpatialDataArray-method mirror mirror,SpatialDataArray-method rotate rotate,SpatialDataArray-method rotate,SpatialDataFrame-method scale scale,SpatialDataArray-method scale,SpatialDataFrame-method sequence sequence,SpatialDataElement-method trans transform transform,SpatialDataElement-method translation translation,SpatialDataArray,numeric-method translation,SpatialDataFrame,numeric-method

Package: spatialdataR 0.99.44

spatialdataR: Representation of Python's spatialdata in R

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