Package index • SpatialFeatureExperiment

SpatialFeatureExperiment class

SpatialFeatureExperiment-class: The SpatialFeatureExperiment class

toSpatialFeatureExperiment(<SpatialExperiment>) toSpatialFeatureExperiment(<SingleCellExperiment>) toSpatialFeatureExperiment(<Seurat>): SpatialFeatureExperiment coercion methods

SpatialFeatureExperiment(): Constructor of SpatialFeatureExperiment object

show(<SpatialFeatureExperiment>): Print method for SpatialFeatureExperiment

unit(<SpatialFeatureExperiment>): Get unit of a SpatialFeatureExperiment

updateObject(<SpatialFeatureExperiment>) SFEVersion(): Update a SpatialFeatureExperiment object

Read data into SFE

read10xVisiumSFE(): Read 10X Visium data as SpatialFeatureExperiment

readCosMX(): Read CosMX data into SFE

readVisiumHD(): Read Visium HD data

readVizgen(): Read Vizgen MERFISH output as SpatialFeatureExperiment

readXenium(): Read 10X Xenium output as SpatialFeatureExperiment

Getters and setters

annotGeometries(<SpatialFeatureExperiment>) `annotGeometries<-`(<SpatialFeatureExperiment>) annotGeometryNames(<SpatialFeatureExperiment>) `annotGeometryNames<-`(<SpatialFeatureExperiment>,<character>) annotGeometry(<SpatialFeatureExperiment>) `annotGeometry<-`(<SpatialFeatureExperiment>) tissueBoundary() `tissueBoundary<-`(): Annotation geometry methods

colFeatureData() rowFeatureData() geometryFeatureData() reducedDimFeatureData(): Get global spatial analysis results and metadata of colData, rowData, and geometries

colGeometry() `colGeometry<-`() colGeometries() `colGeometries<-`() colGeometryNames() `colGeometryNames<-`() spotPoly() `spotPoly<-`() centroids() `centroids<-`() ROIPoly() `ROIPoly<-`() cellSeg() `cellSeg<-`() nucSeg() `nucSeg<-`(): Column geometry getters and setters

dimGeometries(<SpatialFeatureExperiment>) `dimGeometries<-`(<SpatialFeatureExperiment>) dimGeometryNames(<SpatialFeatureExperiment>) `dimGeometryNames<-`(<SpatialFeatureExperiment>,<numeric>,<character>) dimGeometry(<SpatialFeatureExperiment>) `dimGeometry<-`(<SpatialFeatureExperiment>): Dimension geometry methods

getParams(): Get parameters used in spatial methods

localResults(<SpatialFeatureExperiment>) `localResults<-`(<SpatialFeatureExperiment>) localResultNames(<SpatialFeatureExperiment>) `localResultNames<-`(<SpatialFeatureExperiment>,<character>) localResultFeatures(<SpatialFeatureExperiment>) localResultAttrs(<SpatialFeatureExperiment>) localResult(<SpatialFeatureExperiment>) `localResult<-`(<SpatialFeatureExperiment>): Get and set results from local spatial statistics

rowGeometry() `rowGeometry<-`() rowGeometries() `rowGeometries<-`() rowGeometryNames() `rowGeometryNames<-`() txSpots() `txSpots<-`(): Row geometry getters and setters

spatialGraphs(<SpatialFeatureExperiment>) colGraphs() rowGraphs() annotGraphs() `spatialGraphs<-`(<SpatialFeatureExperiment>) `colGraphs<-`() `rowGraphs<-`() `annotGraphs<-`() spatialGraphNames(<SpatialFeatureExperiment>,<numeric>) `spatialGraphNames<-`(<SpatialFeatureExperiment>,<numeric>,<ANY>,<character>) colGraphNames() rowGraphNames() annotGraphNames() `colGraphNames<-`() `rowGraphNames<-`() `annotGraphNames<-`() spatialGraph(<SpatialFeatureExperiment>) colGraph() rowGraph() annotGraph() `spatialGraph<-`(<SpatialFeatureExperiment>) `colGraph<-`() `rowGraph<-`() `annotGraph<-`(): Spatial graph methods

Find spatial neighborhood graph

findSpatialNeighbors(<SpatialFeatureExperiment>): Find spatial neighborhood graph

findVisiumGraph(): Find spatial neighborhood graphs for Visium spots

findVisiumHDGraph(): Find Visium HD spatial neighborhood graph

listw2sparse(): Convert listw into sparse adjacency matrix

multi_listw2sparse(): Convert multiple listw graphs into a single sparse adjacency matrix

Transcript spots

formatTxSpots() addTxSpots(): Read and process transcript spots geometry for SFE

formatTxTech() addTxTech(): Read and process transcript spots for specific commercial technologies

readSelectTx() addSelectTx(): Read transcript spots of select genes

Geometric/spatial operations

transpose() mirror() rotate() translate() scale() affine(): Affine transfortaion of SFE object in histological space

addVisiumSpotPoly(): Add Visium spot polygons to colGeometry

aggregate(<SpatialFeatureExperiment>): Aggregate data in SFE using geometry

aggregateTx() aggregateTxTech(): Aggregate transcript spots from file

annotOp(): Binary operations for geometry of each cell/spot and annotation

annotPred() annotNPred(): Binary predicates for geometry of each cell/spot and annotation

annotSummary(): Summarize attributes of an annotGeometry for each cell/spot

bbox(<SpatialFeatureExperiment>): Find bounding box of SFE objects

crop(): Crop an SFE object with a geometry

removeEmptySpace(): Remove empty space

splitByCol(<SpatialFeatureExperiment>,<sf>) splitByCol(<SpatialFeatureExperiment>,<sfc>) splitByCol(<SpatialFeatureExperiment>,<list>) splitSamples() splitContiguity(): Split SFE object with categorical vector or geometry

st_any_pred() st_any_intersects() st_n_pred() st_n_intersects(): Simple geometry predicates

Non-spatial operations

`[`(<SpatialFeatureExperiment>,<ANY>,<ANY>,<ANY>): Subsetting SpatialFeatureExperiment objects

cbind(<SpatialFeatureExperiment>): Concatenate SpatialFeatureExperiment objects

Image classes

isFull(<BioFormatsImage>) origin(<BioFormatsImage>) transformation(<BioFormatsImage>): Other BioFormatsImage getters

show(<BioFormatsImage>) BioFormatsImage(): On disk representation of BioFormats images in SFE object

show(<ExtImage>) ExtImage(): Use the EBImage Image class in SFE objects

SpatRasterImage() show(<SpatRasterImage>): SpatRaster representation of images in SFE objects

toExtImage(<BioFormatsImage>) toExtImage(<SpatRasterImage>): Convert images to ExtImage

toSpatRasterImage(<ExtImage>) toSpatRasterImage(<BioFormatsImage>): Convert images to SpatRasterImage

Image methods

`Img<-`(<SpatialExperiment>): Image setter

addImg(<SpatialFeatureExperiment>) transposeImg(<SpatialFeatureExperiment>) mirrorImg(<SpatialFeatureExperiment>) rotateImg(<SpatialFeatureExperiment>) translateImg(<SpatialFeatureExperiment>) scaleImg(<SpatialFeatureExperiment>) affineImg(<SpatialFeatureExperiment>): Methods for handling image-related data

cropImg(<SpatRasterImage>) cropImg(<BioFormatsImage>) cropImg(<ExtImage>): Crop images

dim(<BioFormatsImage>): Find dimension of BioFormatsImage

ext(<BioFormatsImage>) ext(<ExtImage>) ext(<SpatRasterImage>) `ext<-`(<BioFormatsImage>,<numeric>) `ext<-`(<ExtImage>,<numeric>) `ext<-`(<SpatRasterImage>,<numeric>): Get and set extent of image objects

imgRaster imgRaster,SpatRasterImage-method imgRaster,BioFormatsImage-method imgRaster,ExtImage-method: Get the image from *Image class

imgSource(<SpatRasterImage>) imgSource(<BioFormatsImage>) imgSource(<ExtImage>): Source of images that are on disk

Image affine transformations

affineImg(<SpatRasterImage>) affineImg(<BioFormatsImage>) affineImg(<ExtImage>): Affine transformation of images

mirrorImg(<SpatRasterImage>) mirrorImg(<BioFormatsImage>) mirrorImg(<ExtImage>): Mirror/flip images

rotateImg(<SpatRasterImage>) rotateImg(<BioFormatsImage>) rotateImg(<ExtImage>): Rotate image

scaleImg(<AlignedSpatialImage>): Scale image

translateImg(<SpatRasterImage>) translateImg(<BioFormatsImage>) translateImg(<ExtImage>): Translate/shift image in space

transposeImg(<SpatRasterImage>) transposeImg(<BioFormatsImage>) transposeImg(<ExtImage>): Transpose images

Utilities

aggBboxes(): Aggregate bounding boxes

bbox_center(): Find center of bounding box

changeSampleIDs(): Change sample IDs

df2sf(): From ordinary data frame to sf to construct SFE object

gdalParquetAvailable(): Check if Parquet GDAL driver is available

getPixelSize(): Get physical size of pixels

getTechTxFields(): Get relevant fields and file paths for transcript spots

imageIDs(): Show all image_ids in the SFE object

sampleIDs(): Get all unique sample IDs

saveRDS(<SpatialFeatureExperiment>): Save SpatialFeatureExperiment as RDS file

visium_row_col: Row and columns of Visium barcodes on the slide

Re-exports

colData() rowData() `colData<-`() spatialCoords() `spatialCoords<-`() spatialCoordsNames() getImg() imgData() rmvImg() counts() logcounts() reducedDim(): Functions re-exported from other packages