# Integrating SpatialExperiment with Simple Features in sf

## Documentation for package ‘SpatialFeatureExperiment’ version 1.12.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G I L M N O R S T U V misc

## -- A --

addImg-method | Methods for handling image-related data
addSelectTx | Read transcript spots of select genes
addTxSpots | Read and process transcript spots geometry for SFE
addTxTech | Read and process transcript spots for specific commercial technologies
addVisiumSpotPoly | Add Visium spot polygons to colGeometry
affine | Affine transfortaion of SFE object in histological space
affineImg | Affine transformation of images
affineImg-method | Methods for handling image-related data
affineImg-method | Affine transformation of images
aggBboxes | Aggregate bounding boxes
aggregate-method | Aggregate data in SFE using geometry
aggregateTx | Aggregate transcript spots from file
aggregateTxTech | Aggregate transcript spots from file
annotGeometries | Annotation geometry methods
annotGeometries-method | Annotation geometry methods
annotGeometries<- | Annotation geometry methods
annotGeometries<--method | Annotation geometry methods
annotGeometry | Annotation geometry methods
annotGeometry-method | Annotation geometry methods
annotGeometry<- | Annotation geometry methods
annotGeometry<--method | Annotation geometry methods
annotGeometryNames | Annotation geometry methods
annotGeometryNames-method | Annotation geometry methods
annotGeometryNames<- | Annotation geometry methods
annotGeometryNames<--method | Annotation geometry methods
annotGraph | Spatial graph methods
annotGraph<- | Spatial graph methods
annotGraphNames | Spatial graph methods
annotGraphNames<- | Spatial graph methods
annotGraphs | Spatial graph methods
annotGraphs<- | Spatial graph methods
annotNPred | Binary predicates for geometry of each cell/spot and annotation
annotOp | Binary operations for geometry of each cell/spot and annotation
annotPred | Binary predicates for geometry of each cell/spot and annotation
annotSummary | Summarize attributes of an annotGeometry for each cell/spot

## -- B --

bbox | Find bounding box of SFE objects
bbox-method | Find bounding box of SFE objects
bbox_center | Find center of bounding box
BioFormatsImage | On disk representation of BioFormats images in SFE object
BioFormatsImage-class | On disk representation of BioFormats images in SFE object
BioFormatsImage-getters | Other 'BioFormatsImage' getters

## -- C --

cbind-method | Concatenate SpatialFeatureExperiment objects
cellSeg | Column geometry getters and setters
cellSeg<- | Column geometry getters and setters
centroids | Column geometry getters and setters
centroids<- | Column geometry getters and setters
changeSampleIDs | Change sample IDs
colData | Functions re-exported from other packages
colData<- | Functions re-exported from other packages
colFeatureData | Get global spatial analysis results and metadata of colData, rowData, and geometries
colGeometries | Column geometry getters and setters
colGeometries<- | Column geometry getters and setters
colGeometry | Column geometry getters and setters
colGeometry<- | Column geometry getters and setters
colGeometryNames | Column geometry getters and setters
colGeometryNames<- | Column geometry getters and setters
colGraph | Spatial graph methods
colGraph<- | Spatial graph methods
colGraphNames | Spatial graph methods
colGraphNames<- | Spatial graph methods
colGraphs | Spatial graph methods
colGraphs<- | Spatial graph methods
containsOutOfMemoryData-method | Whether an SFE object contains out of memory data
counts | Functions re-exported from other packages
crop | Crop an SFE object with a geometry
cropImg | Crop images
cropImg-method | Crop images

## -- D --

df2sf | From ordinary data frame to sf to construct SFE object
dim-method | Find dimension of BioFormatsImage
dim-method | Find dimensions of ExtImage
dimGeometries | Dimension geometry methods
dimGeometries-method | Dimension geometry methods
dimGeometries<- | Dimension geometry methods
dimGeometries<--method | Dimension geometry methods
dimGeometry | Dimension geometry methods
dimGeometry-method | Dimension geometry methods
dimGeometry<- | Dimension geometry methods
dimGeometry<--method | Dimension geometry methods
dimGeometryNames | Dimension geometry methods
dimGeometryNames-method | Dimension geometry methods
dimGeometryNames<- | Dimension geometry methods
dimGeometryNames<--method | Dimension geometry methods

## -- E --

ext | Get and set extent of image objects
ext-method | Get and set extent of image objects
ext<--method | Get and set extent of image objects
ExtImage | Use the EBImage 'Image' class in SFE objects
ExtImage-class | Use the EBImage 'Image' class in SFE objects

## -- F --

findDebrisCells | Identify cells in small bits outside the main piece of tissue
findDebrisCells-method | Identify cells in small bits outside the main piece of tissue
findSpatialNeighbors | Find spatial neighborhood graph
findSpatialNeighbors-method | Find spatial neighborhood graph
findVisiumGraph | Find spatial neighborhood graphs for Visium spots
findVisiumHDGraph | Find Visium HD spatial neighborhood graph
formatTxSpots | Read and process transcript spots geometry for SFE
formatTxTech | Read and process transcript spots for specific commercial technologies

## -- G --

gdalParquetAvailable | Check if Parquet GDAL driver is available
geometryFeatureData | Get global spatial analysis results and metadata of colData, rowData, and geometries
getImg | Functions re-exported from other packages
getParams | Get parameters used in spatial methods
getPixelSize | Get physical size of pixels
getTechTxFields | Get relevant fields and file paths for transcript spots
getTissueBoundaryConcave | Get tissue boundary from concave hull of cell geometries
getTissueBoundaryImg | Get tissue boundary from histology image

## -- I --

imageIDs | Show all image_ids in the SFE object
Img<- | Image setter
Img<--method | Image setter
imgData | Functions re-exported from other packages
imgRaster | Get the image from *Image class
imgRaster-method | Get the image from *Image class
imgSource | Source of images that are on disk
imgSource-method | Source of images that are on disk
isFull | Other 'BioFormatsImage' getters
isFull-method | Other 'BioFormatsImage' getters

## -- L --

localResult | Get and set results from local spatial statistics
localResult-method | Get and set results from local spatial statistics
localResult<- | Get and set results from local spatial statistics
localResult<--method | Get and set results from local spatial statistics
localResultAttrs | Get and set results from local spatial statistics
localResultAttrs-method | Get and set results from local spatial statistics
localResultFeatures | Get and set results from local spatial statistics
localResultFeatures-method | Get and set results from local spatial statistics
localResultNames | Get and set results from local spatial statistics
localResultNames-method | Get and set results from local spatial statistics
localResultNames<- | Get and set results from local spatial statistics
localResultNames<--method | Get and set results from local spatial statistics
localResults | Get and set results from local spatial statistics
localResults-method | Get and set results from local spatial statistics
localResults<- | Get and set results from local spatial statistics
localResults<--method | Get and set results from local spatial statistics
logcounts | Functions re-exported from other packages

## -- M --

mirror | Affine transfortaion of SFE object in histological space
mirrorImg | Mirror/flip images
mirrorImg-method | Methods for handling image-related data
mirrorImg-method | Mirror/flip images
multi_listw2sparse | Convert multiple listw graphs into a single sparse adjacency matrix

## -- N --

nucSeg | Column geometry getters and setters
nucSeg<- | Column geometry getters and setters

## -- O --

origin | Other 'BioFormatsImage' getters
origin-method | Other 'BioFormatsImage' getters

## -- R --

read10xVisiumSFE | Read 10X Visium data as SpatialFeatureExperiment
readCosMX | Read CosMX data into SFE
readSelectTx | Read transcript spots of select genes
readVisiumHD | Read Visium HD data
readVizgen | Read Vizgen MERFISH output as SpatialFeatureExperiment
readXenium | Read 10X Xenium output as SpatialFeatureExperiment
reducedDim | Functions re-exported from other packages
reducedDimFeatureData | Get global spatial analysis results and metadata of colData, rowData, and geometries
reexports | Functions re-exported from other packages
removeEmptySpace | Remove empty space
rmvImg | Functions re-exported from other packages
ROIPoly | Column geometry getters and setters
ROIPoly<- | Column geometry getters and setters
rotate | Affine transfortaion of SFE object in histological space
rotateImg | Rotate image
rotateImg-method | Methods for handling image-related data
rotateImg-method | Rotate image
rowData | Functions re-exported from other packages
rowFeatureData | Get global spatial analysis results and metadata of colData, rowData, and geometries
rowGeometries | Row geometry getters and setters
rowGeometries<- | Row geometry getters and setters
rowGeometry | Row geometry getters and setters
rowGeometry<- | Row geometry getters and setters
rowGeometryNames | Row geometry getters and setters
rowGeometryNames<- | Row geometry getters and setters
rowGraph | Spatial graph methods
rowGraph<- | Spatial graph methods
rowGraphNames | Spatial graph methods
rowGraphNames<- | Spatial graph methods
rowGraphs | Spatial graph methods
rowGraphs<- | Spatial graph methods

## -- S --

sampleIDs | Get all unique sample IDs
saveRDS-method | Save SpatialFeatureExperiment as RDS file
scale | Affine transfortaion of SFE object in histological space
scaleImg | Scale image
scaleImg-method | Methods for handling image-related data
scaleImg-method | Scale image
SFE-image | Methods for handling image-related data
SFE-transform | Affine transfortaion of SFE object in histological space
SFEVersion | Update a SpatialFeatureExperiment object
show-method | On disk representation of BioFormats images in SFE object
show-method | Use the EBImage 'Image' class in SFE objects
show-method | SpatRaster representation of images in SFE objects
show-method | Print method for SpatialFeatureExperiment
spatialCoords | Functions re-exported from other packages
spatialCoords<- | Functions re-exported from other packages
spatialCoordsNames | Functions re-exported from other packages
SpatialFeatureExperiment | Constructor of SpatialFeatureExperiment object
SpatialFeatureExperiment-class | The SpatialFeatureExperiment class
SpatialFeatureExperiment-coercion | SpatialFeatureExperiment coercion methods
SpatialFeatureExperiment-subset | Subsetting SpatialFeatureExperiment objects
spatialGraph | Spatial graph methods
spatialGraph-method | Spatial graph methods
spatialGraph<- | Spatial graph methods
spatialGraph<--method | Spatial graph methods
spatialGraphNames | Spatial graph methods
spatialGraphNames-method | Spatial graph methods
spatialGraphNames<- | Spatial graph methods
spatialGraphNames<--method | Spatial graph methods
spatialGraphs | Spatial graph methods
spatialGraphs-method | Spatial graph methods
spatialGraphs<- | Spatial graph methods
spatialGraphs<--method | Spatial graph methods
SpatRasterImage | SpatRaster representation of images in SFE objects
SpatRasterImage-class | SpatRaster representation of images in SFE objects
splitByCol | Split SFE object with categorical vector or geometry
splitByCol-method | Split SFE object with categorical vector or geometry
splitComponent | Split SFE object with categorical vector or geometry
splitContiguity | Split SFE object with categorical vector or geometry
splitSamples | Split SFE object with categorical vector or geometry
spotPoly | Column geometry getters and setters
spotPoly<- | Column geometry getters and setters
st_any_intersects | Simple geometry predicates
st_any_pred | Simple geometry predicates
st_n_intersects | Simple geometry predicates
st_n_pred | Simple geometry predicates

## -- T --

tissueBoundary | Annotation geometry methods
tissueBoundary<- | Annotation geometry methods
toExtImage | Convert images to ExtImage
toExtImage-method | Convert images to ExtImage
toSpatialFeatureExperiment | SpatialFeatureExperiment coercion methods
toSpatialFeatureExperiment-method | SpatialFeatureExperiment coercion methods
toSpatRasterImage | Convert images to SpatRasterImage
toSpatRasterImage-method | Convert images to SpatRasterImage
transformation | Other 'BioFormatsImage' getters
transformation-method | Other 'BioFormatsImage' getters
translate | Affine transfortaion of SFE object in histological space
translateImg | Translate/shift image in space
translateImg-method | Methods for handling image-related data
translateImg-method | Translate/shift image in space
transpose | Affine transfortaion of SFE object in histological space
transposeImg | Transpose images
transposeImg-method | Methods for handling image-related data
transposeImg-method | Transpose images
txSpots | Row geometry getters and setters
txSpots<- | Row geometry getters and setters

## -- U --

unit | Get unit of a SpatialFeatureExperiment
unit-method | Get unit of a SpatialFeatureExperiment
updateObject | Update a SpatialFeatureExperiment object
updateObject-method | Update a SpatialFeatureExperiment object

## -- V --

visium_row_col | Row and columns of Visium barcodes on the slide

## -- misc --

[-method | Subsetting SpatialFeatureExperiment objects