Integrating SpatialExperiment with Simple Features in sf

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Documentation for package ‘SpatialFeatureExperiment’ version 1.2.3

• 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
saveRDS-method	Save SpatialFeatureExperiment as RDS file
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