Summary of the MultiAssaySpatialExperiment API

A one-page reference. MultiAssaySpatialExperiment (MASE) extends MultiAssayExperiment (MAE), so the whole MAE API applies as well; see the MultiAssayExperiment cheatsheet for that half. Listed below is what MASE adds, plus the inherited functions used most often alongside it.

Worked examples are in Introduction to MultiAssaySpatialExperiment; the slots and mapping tables are documented in Design of MultiAssaySpatialExperiment.

Constructors

Function	Description	Returns
`MultiAssaySpatialExperiment()`	Create a MASE from experiments, maps and spatial layers	`MultiAssaySpatialExperiment`
`prepMASE()`	Wrap `prepMultiAssay()`, harmonizing names and spatial keys	`list` of constructor arguments
`buildSpatialMap()`	Assemble a `spatialMap` from a `sampleMap`	`DataFrame`
`PointsLayerList()`	Named list of point layers	`PointsLayerList`
`ShapesLayerList()`	Named list of geometry layers	`ShapesLayerList`
`RasterLayerList()`	Named list of image or label layers	`RasterLayerList`

Platform readers

Function	Platform
`readXeniumMASE()`	10x Xenium
`readVisiumMASE()`	10x Visium
`readVisiumHDMASE()`	10x Visium HD
`readCosMxMASE()`	NanoString CosMx
`readMERSCOPEMASE()`	Vizgen MERSCOPE

Spatial accessors

Function	Description	Returns
`spatialPoints()`	Get or set the point layers	`PointsLayerList`
`spatialShapes()`	Get or set the geometry layers	`ShapesLayerList`
`spatialImages()`	Get or set the image layers	`RasterLayerList`
`spatialLabels()`	Get or set the segmentation-mask layers	`RasterLayerList`
`spatialMap()`	Get or set the observation-to-element map	`DataFrame`
`imgData()`	Get or set the specimen-to-image map	`DataFrame`

Inherited accessors used most often

Function	Description	Returns
`experiments()`	Get or set the assays	`ExperimentList`
`colData()`	Get or set specimen metadata	`DataFrame`
`sampleMap()`	Get or set the observation-to-specimen map	`DataFrame`
`metadata()`	Get or set experiment-level metadata	`list`

Subsetting

Expression	Cuts on	Effect on spatial layers
`mase[i, j, k]`	features, specimens, assays	links updated
`mase[, "P1"]`	one specimen, across every assay	links updated
`mase[, list(rna = ...)]`	columns of one named assay	that assay’s links updated
`subsetByColData()`	specimens	updates `spatialMap` and `imgData`
`subsetByRow()`	assay features	unchanged
`subsetByColumn()`	assay columns	trims linked points, shapes, images, labels
`subsetByAssay()`	assay name	keeps layers still referenced
`subsetByBoundingBox()`	a rectangle in space	selects elements, then the columns mapped to them
`subsetByPolygon()`	an arbitrary region	as above

Spatial operations

Function	Description	Returns
`annotateWithRegions()`	Point-in-polygon join; adds a new `spatialMap` column named for the shapes layer	`MultiAssaySpatialExperiment`
`aggregateByRegion()`	Summarise assay values per annotated region	`list` of matrices
`spatialJoin()`	Join two layer `DataFrame` objects directly	`DataFrame`

The join predicate defaults to sf::st_intersects; pass join = to change it, for example sf::st_nearest_feature.

Coercion

Expression	Requires
`as(spe, "MultiAssaySpatialExperiment")`	a `SpatialExperiment`
`as(mase, "SpatialExperiment")`	exactly one compatible assay
`as(sfe, "MultiAssaySpatialExperiment")`	`SpatialFeatureExperiment` installed
`as(mase, "SpatialFeatureExperiment")`	exactly one compatible assay

Combining

Function	Description
`c()`	Merge two objects, unioning assays and spatial layers
`cbind()`	Bind objects that share assay names, along observations

Session info

sessionInfo()

## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 26.04 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] BiocStyle_2.41.0
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.39       R6_2.6.1            fastmap_1.2.0      
##  [4] xfun_0.60           maketools_1.3.2     cachem_1.1.0       
##  [7] knitr_1.51          htmltools_0.5.9     rmarkdown_2.32     
## [10] buildtools_1.0.0    lifecycle_1.0.5     cli_3.6.6          
## [13] sass_0.4.10         jquerylib_0.1.4     compiler_4.6.1     
## [16] sys_3.4.3           tools_4.6.1         bslib_0.12.0       
## [19] evaluate_1.0.5      yaml_2.3.12         otel_0.2.0         
## [22] BiocManager_1.30.27 jsonlite_2.0.0      rlang_1.3.0

- Summary of the MultiAssaySpatialExperiment API
- Session info

MultiAssaySpatialExperiment Cheatsheet