Integrating SpatialExperiment with Simple Features in sf


[Up] [Top]

Documentation for package ‘SpatialFeatureExperiment’ version 1.2.3

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