Package index
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SpatialFeatureExperiment-class
- The SpatialFeatureExperiment class
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toSpatialFeatureExperiment(<SpatialExperiment>)
toSpatialFeatureExperiment(<SingleCellExperiment>)
toSpatialFeatureExperiment(<Seurat>)
- SpatialFeatureExperiment coercion methods
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SpatialFeatureExperiment()
- Constructor of SpatialFeatureExperiment object
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show(<SpatialFeatureExperiment>)
- Print method for SpatialFeatureExperiment
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unit(<SpatialFeatureExperiment>)
- Get unit of a SpatialFeatureExperiment
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updateObject(<SpatialFeatureExperiment>)
SFEVersion()
- Update a SpatialFeatureExperiment object
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read10xVisiumSFE()
- Read 10X Visium data as SpatialFeatureExperiment
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readCosMX()
- Read CosMX data into SFE
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readVizgen()
- Read Vizgen MERFISH output as SpatialFeatureExperiment
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readXenium()
- Read 10X Xenium output as SpatialFeatureExperiment
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annotGeometries(<SpatialFeatureExperiment>)
`annotGeometries<-`(<SpatialFeatureExperiment>)
annotGeometryNames(<SpatialFeatureExperiment>)
`annotGeometryNames<-`(<SpatialFeatureExperiment>,<character>)
annotGeometry(<SpatialFeatureExperiment>)
`annotGeometry<-`(<SpatialFeatureExperiment>)
tissueBoundary()
`tissueBoundary<-`()
- Annotation geometry methods
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colFeatureData()
rowFeatureData()
geometryFeatureData()
reducedDimFeatureData()
- Get global spatial analysis results and metadata of colData, rowData, and geometries
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colGeometry()
`colGeometry<-`()
colGeometries()
`colGeometries<-`()
colGeometryNames()
`colGeometryNames<-`()
spotPoly()
`spotPoly<-`()
centroids()
`centroids<-`()
ROIPoly()
`ROIPoly<-`()
cellSeg()
`cellSeg<-`()
nucSeg()
`nucSeg<-`()
- Column geometry getters and setters
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dimGeometries(<SpatialFeatureExperiment>)
`dimGeometries<-`(<SpatialFeatureExperiment>)
dimGeometryNames(<SpatialFeatureExperiment>)
`dimGeometryNames<-`(<SpatialFeatureExperiment>,<numeric>,<character>)
dimGeometry(<SpatialFeatureExperiment>)
`dimGeometry<-`(<SpatialFeatureExperiment>)
- Dimension geometry methods
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getParams()
- Get parameters used in spatial methods
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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
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rowGeometry()
`rowGeometry<-`()
rowGeometries()
`rowGeometries<-`()
rowGeometryNames()
`rowGeometryNames<-`()
txSpots()
`txSpots<-`()
- Row geometry getters and setters
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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
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findSpatialNeighbors(<SpatialFeatureExperiment>)
- Find spatial neighborhood graph
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findVisiumGraph()
- Find spatial neighborhood graphs for Visium spots
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formatTxSpots()
addTxSpots()
- Read and process transcript spots geometry for SFE
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formatTxTech()
addTxTech()
- Read and process transcript spots for specific commercial technologies
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readSelectTx()
addSelectTx()
- Read transcript spots of select genes
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transpose()
mirror()
rotate()
translate()
scale()
affine()
- Affine transfortaion of SFE object in histological space
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addVisiumSpotPoly()
- Add Visium spot polygons to colGeometry
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aggregate(<SpatialFeatureExperiment>)
- Aggregate data in SFE using geometry
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aggregateTx()
aggregateTxTech()
- Aggregate transcript spots from file
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annotOp()
- Binary operations for geometry of each cell/spot and annotation
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annotPred()
annotNPred()
- Binary predicates for geometry of each cell/spot and annotation
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annotSummary()
- Summarize attributes of an annotGeometry for each cell/spot
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bbox(<SpatialFeatureExperiment>)
- Find bounding box of SFE objects
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crop()
- Crop an SFE object with a geometry
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removeEmptySpace()
- Remove empty space
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splitByCol(<SpatialFeatureExperiment>,<sf>)
splitByCol(<SpatialFeatureExperiment>,<sfc>)
splitByCol(<SpatialFeatureExperiment>,<list>)
splitSamples()
splitContiguity()
- Split SFE object with categorical vector or geometry
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st_any_pred()
st_any_intersects()
st_n_pred()
st_n_intersects()
- Simple geometry predicates
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`[`(<SpatialFeatureExperiment>,<ANY>,<ANY>,<ANY>)
- Subsetting SpatialFeatureExperiment objects
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cbind(<SpatialFeatureExperiment>)
- Concatenate SpatialFeatureExperiment objects
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isFull(<BioFormatsImage>)
origin(<BioFormatsImage>)
transformation(<BioFormatsImage>)
- Other
BioFormatsImage
getters
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show(<BioFormatsImage>)
BioFormatsImage()
- On disk representation of BioFormats images in SFE object
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show(<ExtImage>)
ExtImage()
- Use the EBImage
Image
class in SFE objects
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SpatRasterImage()
show(<SpatRasterImage>)
- SpatRaster representation of images in SFE objects
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toExtImage(<BioFormatsImage>)
toExtImage(<SpatRasterImage>)
- Convert images to ExtImage
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toSpatRasterImage(<ExtImage>)
toSpatRasterImage(<BioFormatsImage>)
- Convert images to SpatRasterImage
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`Img<-`(<SpatialExperiment>)
- Image setter
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addImg(<SpatialFeatureExperiment>)
transposeImg(<SpatialFeatureExperiment>)
mirrorImg(<SpatialFeatureExperiment>)
rotateImg(<SpatialFeatureExperiment>)
translateImg(<SpatialFeatureExperiment>)
scaleImg(<SpatialFeatureExperiment>)
affineImg(<SpatialFeatureExperiment>)
- Methods for handling image-related data
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dim(<BioFormatsImage>)
- Find dimension of BioFormatsImage
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ext(<BioFormatsImage>)
ext(<ExtImage>)
ext(<SpatRasterImage>)
`ext<-`(<BioFormatsImage>,<numeric>)
`ext<-`(<ExtImage>,<numeric>)
`ext<-`(<SpatRasterImage>,<numeric>)
- Get and set extent of image objects
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imgRaster
imgRaster,SpatRasterImage-method
imgRaster,BioFormatsImage-method
imgRaster,ExtImage-method
- Get the image from *Image class
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imgSource(<SpatRasterImage>)
imgSource(<BioFormatsImage>)
imgSource(<ExtImage>)
- Source of images that are on disk
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affineImg(<SpatRasterImage>)
affineImg(<BioFormatsImage>)
affineImg(<ExtImage>)
- Affine transformation of images
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mirrorImg(<SpatRasterImage>)
mirrorImg(<BioFormatsImage>)
mirrorImg(<ExtImage>)
- Mirror/flip images
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scaleImg(<AlignedSpatialImage>)
- Scale image
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translateImg(<SpatRasterImage>)
translateImg(<BioFormatsImage>)
translateImg(<ExtImage>)
- Translate/shift image in space
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aggBboxes()
- Aggregate bounding boxes
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bbox_center()
- Find center of bounding box
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changeSampleIDs()
- Change sample IDs
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df2sf()
- From ordinary data frame to sf to construct SFE object
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gdalParquetAvailable()
- Check if Parquet GDAL driver is available
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getPixelSize()
- Get physical size of pixels
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getTechTxFields()
- Get relevant fields and file paths for transcript spots
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imageIDs()
- Show all image_ids in the SFE object
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sampleIDs()
- Get all unique sample IDs
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saveRDS(<SpatialFeatureExperiment>)
- Save SpatialFeatureExperiment as RDS file
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visium_row_col
- Row and columns of Visium barcodes on the slide
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colData()
rowData()
`colData<-`()
spatialCoords()
`spatialCoords<-`()
spatialCoordsNames()
getImg()
imgData()
rmvImg()
counts()
logcounts()
reducedDim()
- Functions re-exported from other packages