Package: SpatialFeatureExperiment 1.15.0

Lambda Moses

SpatialFeatureExperiment: Integrating SpatialExperiment with Simple Features in sf

A new S4 class integrating Simple Features with the R package sf to bring geospatial data analysis methods based on vector data to spatial transcriptomics. Also implements management of spatial neighborhood graphs and geometric operations. This pakage builds upon SpatialExperiment and SingleCellExperiment, hence methods for these parent classes can still be used.

Authors:Lambda Moses [aut, cre], Alik Huseynov [aut], Lior Pachter [aut, ths]

# Install 'SpatialFeatureExperiment' in R:

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

Bug tracker:https://github.com/pachterlab/spatialfeatureexperiment/issues

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

Datasets:

visium_row_col - Row and columns of Visium barcodes on the slide

On BioConductor:SpatialFeatureExperiment-1.15.0(bioc 3.24)SpatialFeatureExperiment-1.14.0(bioc 3.23)

datarepresentation transcriptomics spatial

10.18 score 57 stars 2 packages 804 scripts 756 downloads 180 exports 149 dependencies

Last updated from:df605bf0b0. Checks:2 ERROR, 6 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	300
linux-devel-x86_64	WARNING	1590
source / vignettes	OK	477
linux-release-x86_64	ERROR	1540
macos-release-arm64	WARNING	1062
macos-oldrel-arm64	WARNING	924
windows-devel	WARNING	1564
windows-release	WARNING	1665
windows-oldrel	WARNING	1822
wasm-release	OK	246

Exports:.check_features .check_rg .check_sample_id .check_tx_file .check_tx_file_mem .ext_.rm_empty_geometries .symbol2id .value2df .warn_symbol_duplicate addImg addSelectTx addTxSpots addTxTech addVisiumSpotPoly affine affineImg aggBboxes aggregate aggregateTx aggregateTxTech annotGeometries annotGeometries<-annotGeometry annotGeometry<-annotGeometryNames annotGeometryNames<-annotGraph annotGraph<-annotGraphNames annotGraphNames<-annotGraphs annotGraphs<-annotNPred annotOp annotPred annotSummary bbox bbox_center BioFormatsImage cbind cellSeg cellSeg<-centroids centroids<-changeSampleIDs colData colData<-colFeatureData colGeometries colGeometries<-colGeometry colGeometry<-colGeometryNames colGeometryNames<-colGraph colGraph<-colGraphNames colGraphNames<-colGraphs colGraphs<-containsOutOfMemoryData counts crop cropImg df2sf dimGeometries dimGeometries<-dimGeometry dimGeometry<-dimGeometryNames dimGeometryNames<-ext ext<-ExtImage findDebrisCells findSpatialNeighbors findVisiumGraph findVisiumHDGraph formatTxSpots formatTxTech gdalParquetAvailable geometryFeatureData getImg getParams getPixelSize getTechTxFields getTissueBoundaryConcave getTissueBoundaryImg imageIDs Img<-imgData imgRaster imgSource isFull localResult localResult<-localResultAttrs localResultFeatures localResultNames localResultNames<-localResults localResults<-logcounts mirror mirrorImg multi_listw2sparse nucSeg nucSeg<-origin read10xVisiumSFE readCosMX readSelectTx readVisiumHD readVizgen readXenium reducedDim reducedDimFeatureData removeEmptySpace rmvImg ROIPoly ROIPoly<-rotate rotateImg rotateMinRect rowData rowFeatureData rowGeometries rowGeometries<-rowGeometry rowGeometry<-rowGeometryNames rowGeometryNames<-rowGraph rowGraph<-rowGraphNames rowGraphNames<-rowGraphs rowGraphs<-sampleIDs saveRDS scale scaleImg SFEVersion show spatialCoords spatialCoords<-spatialCoordsNames SpatialFeatureExperiment spatialGraph spatialGraph<-spatialGraphNames spatialGraphNames<-spatialGraphs spatialGraphs<-SpatRasterImage splitByCol splitComponent splitContiguity splitSamples spotPoly spotPoly<-st_any_intersects st_any_pred st_n_intersects st_n_pred tissueBoundary tissueBoundary<-toExtImage toSpatialFeatureExperiment toSpatRasterImage transformation translate translateImg transpose transposeImg txSpots txSpots<-unit updateObject

Dependencies:abind askpass assorthead backports base64enc beachmat BH Biobase BiocFileCache BiocGenerics biocmake BiocNeighbors BiocParallel bit bit64 bitops blob boot bslib cachem checkmate class classInt cli coda codetools cpp11 curl data.table DBI dbplyr DelayedArray DelayedMatrixStats deldir digest dir.expiry dplyr dqrng DropletUtils e1071 EBImage edgeR evaluate fastmap fftwtools filelock fontawesome formatR Formula fs futile.logger futile.options generics GenomicRanges geometries glue h5mread HDF5Array highr htmltools htmlwidgets httr2 insight IRanges jpeg jquerylib jsonlite KernSmooth knitr lambda.r lattice LearnBayes lifecycle limma locfit magick magrittr marginaleffects MASS Matrix MatrixGenerics matrixStats memoise mime multcomp mvtnorm nlme openssl pillar pkgconfig png proxy purrr R.methodsS3 R.oo R.utils R6 rappdirs Rcpp RCurl rhdf5 rhdf5filters Rhdf5lib rjson rlang rmarkdown RSQLite s2 S4Arrays S4Vectors sandwich sass scuttle Seqinfo sf sfheaders SingleCellExperiment sitmo snow sp SparseArray sparseMatrixStats SpatialExperiment spatialreg spData spdep statmod stringi stringr SummarizedExperiment survival sys terra TH.data tibble tidyr tidyselect tiff tinytex units utf8 vctrs withr wk xfun XVector yaml zeallot zoo

Introduction to the SpatialFeatureExperiment class

Rendered fromSFE.Rmdusingknitr::rmarkdown

Last update: 2026-04-10
Started: 2022-03-30

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add Visium spot polygons to colGeometry	addVisiumSpotPoly
Affine transformation of images	affineImg affineImg,BioFormatsImage-method affineImg,ExtImage-method affineImg,SpatRasterImage-method
Aggregate bounding boxes	aggBboxes
Aggregate data in SFE using geometry	aggregate,SpatialFeatureExperiment-method
Aggregate transcript spots from file	aggregateTx aggregateTxTech
Annotation geometry methods	annotGeometries annotGeometries,SpatialFeatureExperiment-method annotGeometries<- annotGeometries<-,SpatialFeatureExperiment-method annotGeometry annotGeometry,SpatialFeatureExperiment-method annotGeometry<- annotGeometry<-,SpatialFeatureExperiment-method annotGeometryNames annotGeometryNames,SpatialFeatureExperiment-method annotGeometryNames<- annotGeometryNames<-,SpatialFeatureExperiment,character-method tissueBoundary tissueBoundary<-
Binary operations for geometry of each cell/spot and annotation	annotOp
Binary predicates for geometry of each cell/spot and annotation	annotNPred annotPred
Summarize attributes of an annotGeometry for each cell/spot	annotSummary
Find center of bounding box	bbox_center
Find bounding box of SFE objects	bbox bbox,SpatialFeatureExperiment-method
On disk representation of BioFormats images in SFE object	BioFormatsImage BioFormatsImage-class show,BioFormatsImage-method
Other 'BioFormatsImage' getters	BioFormatsImage-getters isFull isFull,BioFormatsImage-method origin origin,BioFormatsImage-method transformation transformation,BioFormatsImage-method
Concatenate SpatialFeatureExperiment objects	cbind,SpatialFeatureExperiment-method
Change sample IDs	changeSampleIDs
Get global spatial analysis results and metadata of colData, rowData, and geometries	colFeatureData geometryFeatureData reducedDimFeatureData rowFeatureData
Column geometry getters and setters	cellSeg cellSeg<- centroids centroids<- colGeometries colGeometries<- colGeometry colGeometry<- colGeometryNames colGeometryNames<- nucSeg nucSeg<- ROIPoly ROIPoly<- spotPoly spotPoly<-
Whether an SFE object contains out of memory data	containsOutOfMemoryData,SpatialFeatureExperiment-method
Crop an SFE object with a geometry	crop
Crop images	cropImg cropImg,BioFormatsImage-method cropImg,ExtImage-method cropImg,SpatRasterImage-method
From ordinary data frame to sf to construct SFE object	df2sf
Find dimension of BioFormatsImage	dim,BioFormatsImage-method
Find dimensions of ExtImage	dim,ExtImage-method
Dimension geometry methods	dimGeometries dimGeometries,SpatialFeatureExperiment-method dimGeometries<- dimGeometries<-,SpatialFeatureExperiment-method dimGeometry dimGeometry,SpatialFeatureExperiment-method dimGeometry<- dimGeometry<-,SpatialFeatureExperiment-method dimGeometryNames dimGeometryNames,SpatialFeatureExperiment-method dimGeometryNames<- dimGeometryNames<-,SpatialFeatureExperiment,numeric,character-method
Get and set extent of image objects	ext ext,BioFormatsImage-method ext,ExtImage-method ext,SpatRasterImage-method ext<-,BioFormatsImage,numeric-method ext<-,ExtImage,numeric-method ext<-,SpatRasterImage,numeric-method
Use the EBImage 'Image' class in SFE objects	ExtImage ExtImage-class show,ExtImage-method
Identify cells in small bits outside the main piece of tissue	findDebrisCells findDebrisCells,matrix-method findDebrisCells,sf-method findDebrisCells,sfc-method findDebrisCells,SpatialExperiment-method
Find spatial neighborhood graph	findSpatialNeighbors findSpatialNeighbors,SpatialFeatureExperiment-method
Find spatial neighborhood graphs for Visium spots	findVisiumGraph
Find Visium HD spatial neighborhood graph	findVisiumHDGraph
Read and process transcript spots geometry for SFE	addTxSpots formatTxSpots
Read and process transcript spots for specific commercial technologies	addTxTech formatTxTech
Check if Parquet GDAL driver is available	gdalParquetAvailable
Get parameters used in spatial methods	getParams
Get physical size of pixels	getPixelSize
Get relevant fields and file paths for transcript spots	getTechTxFields
Get tissue boundary from concave hull of cell geometries	getTissueBoundaryConcave getTissueBoundaryConcave,sf-method getTissueBoundaryConcave,sfc-method getTissueBoundaryConcave,SpatialFeatureExperiment-method
Get tissue boundary from histology image	getTissueBoundaryImg
Show all image_ids in the SFE object	imageIDs
Image setter	Img<- Img<-,SpatialExperiment-method
Get the image from *Image class	imgRaster imgRaster,BioFormatsImage-method imgRaster,ExtImage-method imgRaster,SpatRasterImage-method
Source of images that are on disk	imgSource imgSource,BioFormatsImage-method imgSource,ExtImage-method imgSource,SpatRasterImage-method
Get and set results from local spatial statistics	localResult localResult,SpatialFeatureExperiment-method localResult<- localResult<-,SpatialFeatureExperiment-method localResultAttrs localResultAttrs,SpatialFeatureExperiment-method localResultFeatures localResultFeatures,SpatialFeatureExperiment-method localResultNames localResultNames,SpatialFeatureExperiment-method localResultNames<- localResultNames<-,SpatialFeatureExperiment,character-method localResults localResults,SpatialFeatureExperiment-method localResults<- localResults<-,SpatialFeatureExperiment-method
Mirror/flip images	mirrorImg mirrorImg,BioFormatsImage-method mirrorImg,ExtImage-method mirrorImg,SpatRasterImage-method
Convert multiple listw graphs into a single sparse adjacency matrix	multi_listw2sparse
Read 10X Visium data as SpatialFeatureExperiment	read10xVisiumSFE
Read CosMX data into SFE	readCosMX
Read transcript spots of select genes	addSelectTx readSelectTx
Read Visium HD data	readVisiumHD
Read Vizgen MERFISH output as SpatialFeatureExperiment	readVizgen
Read 10X Xenium output as SpatialFeatureExperiment	readXenium
Functions re-exported from other packages	colData colData<- counts getImg imgData logcounts reducedDim reexports rmvImg rowData spatialCoords spatialCoords<- spatialCoordsNames
Remove empty space	removeEmptySpace
Rotate image	rotateImg rotateImg,BioFormatsImage-method rotateImg,ExtImage-method rotateImg,SpatRasterImage-method
Rotate the tissue to reduce empty space in plots	rotateMinRect rotateMinRect,matrix-method rotateMinRect,sf-method rotateMinRect,sfc-method rotateMinRect,SpatialFeatureExperiment-method
Row geometry getters and setters	rowGeometries rowGeometries<- rowGeometry rowGeometry<- rowGeometryNames rowGeometryNames<- txSpots txSpots<-
Get all unique sample IDs	sampleIDs
Save SpatialFeatureExperiment as RDS file	saveRDS,SpatialFeatureExperiment-method
Scale image	scaleImg scaleImg,AlignedSpatialImage-method scaleImg,BioFormatsImage-method
Methods for handling image-related data	addImg,SpatialFeatureExperiment-method affineImg,SpatialFeatureExperiment-method mirrorImg,SpatialFeatureExperiment-method rotateImg,SpatialFeatureExperiment-method scaleImg,SpatialFeatureExperiment-method SFE-image translateImg,SpatialFeatureExperiment-method transposeImg,SpatialFeatureExperiment-method
Affine transfortaion of SFE object in histological space	affine mirror rotate scale SFE-transform translate transpose
Print method for SpatialFeatureExperiment	show,SpatialFeatureExperiment-method
Constructor of SpatialFeatureExperiment object	SpatialFeatureExperiment
The SpatialFeatureExperiment class	SpatialFeatureExperiment-class
SpatialFeatureExperiment coercion methods	SpatialFeatureExperiment-coercion toSpatialFeatureExperiment toSpatialFeatureExperiment,Seurat-method toSpatialFeatureExperiment,SingleCellExperiment-method toSpatialFeatureExperiment,SpatialExperiment-method
Subsetting SpatialFeatureExperiment objects	SpatialFeatureExperiment-subset [,SpatialFeatureExperiment,ANY,ANY,ANY-method
Spatial graph methods	annotGraph annotGraph<- annotGraphNames annotGraphNames<- annotGraphs annotGraphs<- colGraph colGraph<- colGraphNames colGraphNames<- colGraphs colGraphs<- rowGraph rowGraph<- rowGraphNames rowGraphNames<- rowGraphs rowGraphs<- spatialGraph spatialGraph,SpatialFeatureExperiment-method spatialGraph<- spatialGraph<-,SpatialFeatureExperiment-method spatialGraphNames spatialGraphNames,SpatialFeatureExperiment,numeric-method spatialGraphNames<- spatialGraphNames<-,SpatialFeatureExperiment,numeric,ANY,character-method spatialGraphs spatialGraphs,SpatialFeatureExperiment-method spatialGraphs<- spatialGraphs<-,SpatialFeatureExperiment-method
SpatRaster representation of images in SFE objects	show,SpatRasterImage-method SpatRasterImage SpatRasterImage-class
Split SFE object with categorical vector or geometry	splitByCol splitByCol,SpatialFeatureExperiment,list-method splitByCol,SpatialFeatureExperiment,sf-method splitByCol,SpatialFeatureExperiment,sfc-method splitContiguity splitSamples
Split by graph component	splitComponent splitComponent,sf-method splitComponent,sfc-method splitComponent,SpatialFeatureExperiment-method
Simple geometry predicates	st_any_intersects st_any_pred st_n_intersects st_n_pred
Convert images to ExtImage	toExtImage toExtImage,BioFormatsImage-method toExtImage,SpatRasterImage-method
Convert images to SpatRasterImage	toSpatRasterImage toSpatRasterImage,BioFormatsImage-method toSpatRasterImage,ExtImage-method
Translate/shift image in space	translateImg translateImg,BioFormatsImage-method translateImg,ExtImage-method translateImg,SpatRasterImage-method
Transpose images	transposeImg transposeImg,BioFormatsImage-method transposeImg,ExtImage-method transposeImg,SpatRasterImage-method
Get unit of a SpatialFeatureExperiment	unit unit,SpatialFeatureExperiment-method
Update a SpatialFeatureExperiment object	SFEVersion updateObject updateObject,SpatialFeatureExperiment-method
Row and columns of Visium barcodes on the slide	visium_row_col