# Integrating SpatialExperiment with Simple Features in sf

## Documentation for package ‘SpatialFeatureExperiment’ version 1.3.0

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

## Help Pages

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

## -- A --

addImg-method | Images in SpatialFeatureExperiment object
addVisiumSpotPoly | Add Visium spot polygons to colGeometry
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-method | Spatial graph methods
annotGraphs<- | Spatial graph methods
annotGraphs<--method | 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

## -- C --

cbind-method | Concatenate SpatialFeatureExperiment objects
cellSeg | Dimension geometry methods
cellSeg<- | Dimension geometry methods
centroids | Dimension geometry methods
centroids<- | Dimension geometry methods
changeSampleIDs | Change sample IDs
colGeometries | Dimension geometry methods
colGeometries<- | Dimension geometry methods
colGeometry | Dimension geometry methods
colGeometry<- | Dimension geometry methods
colGeometryNames | Dimension geometry methods
colGeometryNames<- | Dimension geometry methods
colGraph | Spatial graph methods
colGraph<- | Spatial graph methods
colGraphNames | Spatial graph methods
colGraphNames<- | Spatial graph methods
colGraphs | Spatial graph methods
colGraphs-method | Spatial graph methods
colGraphs<- | Spatial graph methods
colGraphs<--method | Spatial graph methods
crop | Crop an SFE object with a geometry

## -- D --

df2sf | From ordinary data frame to sf to construct SFE object
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

## -- F --

findSpatialNeighbors | Find spatial neighborhood graph
findSpatialNeighbors-method | Find spatial neighborhood graph
findVisiumGraph | Find spatial neighborhood graphs for Visium spots

## -- I --

imgRaster-method | Images in SpatialFeatureExperiment object
imgSource-method | Images in SpatialFeatureExperiment object

## -- L --

localResult | Organize results from local spatial statistics
localResult-method | Organize results from local spatial statistics
localResult<- | Organize results from local spatial statistics
localResult<--method | Organize results from local spatial statistics
localResultAttrs | Organize results from local spatial statistics
localResultAttrs-method | Organize results from local spatial statistics
localResultFeatures | Organize results from local spatial statistics
localResultFeatures-method | Organize results from local spatial statistics
localResultNames | Organize results from local spatial statistics
localResultNames-method | Organize results from local spatial statistics
localResultNames<- | Organize results from local spatial statistics
localResultNames<--method | Organize results from local spatial statistics
localResults | Organize results from local spatial statistics
localResults-method | Organize results from local spatial statistics
localResults<- | Organize results from local spatial statistics
localResults<--method | Organize results from local spatial statistics

## -- M --

mirror | Transpose or mirror SFE object in histological space
mirrorImg-method | Images in SpatialFeatureExperiment object

## -- N --

nucSeg | Dimension geometry methods
nucSeg<- | Dimension geometry methods

## -- R --

read10xVisiumSFE | Read 10X Visium data as SpatialFeatureExperiment
readVizgen | Read Vizgen MERFISH output as SpatialFeatureExperiment
removeEmptySpace | Remove empty space
ROIPoly | Dimension geometry methods
ROIPoly<- | Dimension geometry methods
rowGeometries | Dimension geometry methods
rowGeometries<- | Dimension geometry methods
rowGeometry | Dimension geometry methods
rowGeometry<- | Dimension geometry methods
rowGeometryNames | Dimension geometry methods
rowGeometryNames<- | Dimension geometry methods
rowGraph | Spatial graph methods
rowGraph<- | Spatial graph methods
rowGraphNames | Spatial graph methods
rowGraphNames<- | Spatial graph methods
rowGraphs | Spatial graph methods
rowGraphs-method | Spatial graph methods
rowGraphs<- | Spatial graph methods
rowGraphs<--method | Spatial graph methods

## -- S --

sampleIDs | Get all unique sample IDs
SFE-image | Images in SpatialFeatureExperiment object
SFE-transform | Transpose or mirror SFE object in histological space
SFEVersion | Update a SpatialFeatureExperiment object
show-method | Print method for SpatialFeatureExperiment
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-class | Images in SpatialFeatureExperiment object
spotPoly | Dimension geometry methods
spotPoly<- | Dimension geometry methods
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
toSpatialFeatureExperiment | SpatialFeatureExperiment coercion methods
toSpatialFeatureExperiment-method | SpatialFeatureExperiment coercion methods
transpose | Transpose or mirror SFE object in histological space
transposeImg | Images in SpatialFeatureExperiment object
transposeImg-method | Images in SpatialFeatureExperiment object
txSpots | Dimension geometry methods
txSpots<- | Dimension geometry methods

## -- 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