Integrating SpatialExperiment with Simple Features in sf
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Documentation for package ‘SpatialFeatureExperiment’ version 1.11.1
Help Pages
A B C D E F G I L M N O R S T U V misc
-- A --
| addImg-method | Methods for handling image-related data |
| addSelectTx | Read transcript spots of select genes |
| addTxSpots | Read and process transcript spots geometry for SFE |
| addTxTech | Read and process transcript spots for specific commercial technologies |
| addVisiumSpotPoly | Add Visium spot polygons to colGeometry |
| affine | Affine transfortaion of SFE object in histological space |
| affineImg | Affine transformation of images |
| affineImg-method | Methods for handling image-related data |
| affineImg-method | Affine transformation of images |
| aggBboxes | Aggregate bounding boxes |
| aggregate-method | Aggregate data in SFE using geometry |
| aggregateTx | Aggregate transcript spots from file |
| aggregateTxTech | Aggregate transcript spots from file |
| 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<- | 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 |
| bbox_center | Find center of bounding box |
| BioFormatsImage | On disk representation of BioFormats images in SFE object |
| BioFormatsImage-class | On disk representation of BioFormats images in SFE object |
| BioFormatsImage-getters | Other 'BioFormatsImage' getters |
-- C --
| cbind-method | Concatenate SpatialFeatureExperiment objects |
| cellSeg | Column geometry getters and setters |
| cellSeg<- | Column geometry getters and setters |
| centroids | Column geometry getters and setters |
| centroids<- | Column geometry getters and setters |
| changeSampleIDs | Change sample IDs |
| colData | Functions re-exported from other packages |
| colData<- | Functions re-exported from other packages |
| colFeatureData | Get global spatial analysis results and metadata of colData, rowData, and geometries |
| colGeometries | Column geometry getters and setters |
| colGeometries<- | Column geometry getters and setters |
| colGeometry | Column geometry getters and setters |
| colGeometry<- | Column geometry getters and setters |
| colGeometryNames | Column geometry getters and setters |
| colGeometryNames<- | Column geometry getters and setters |
| colGraph | Spatial graph methods |
| colGraph<- | Spatial graph methods |
| colGraphNames | Spatial graph methods |
| colGraphNames<- | Spatial graph methods |
| colGraphs | Spatial graph methods |
| colGraphs<- | Spatial graph methods |
| containsOutOfMemoryData-method | Whether an SFE object contains out of memory data |
| counts | Functions re-exported from other packages |
| crop | Crop an SFE object with a geometry |
| cropImg | Crop images |
| cropImg-method | Crop images |
-- D --
| df2sf | From ordinary data frame to sf to construct SFE object |
| dim-method | Find dimension of BioFormatsImage |
| dim-method | Find dimensions of ExtImage |
| 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 |
-- E --
| ext | Get and set extent of image objects |
| ext-method | Get and set extent of image objects |
| ext<--method | Get and set extent of image objects |
| ExtImage | Use the EBImage 'Image' class in SFE objects |
| ExtImage-class | Use the EBImage 'Image' class in SFE objects |
-- F --
| findDebrisCells | Identify cells in small bits outside the main piece of tissue |
| findDebrisCells-method | Identify cells in small bits outside the main piece of tissue |
| findSpatialNeighbors | Find spatial neighborhood graph |
| findSpatialNeighbors-method | Find spatial neighborhood graph |
| findVisiumGraph | Find spatial neighborhood graphs for Visium spots |
| findVisiumHDGraph | Find Visium HD spatial neighborhood graph |
| formatTxSpots | Read and process transcript spots geometry for SFE |
| formatTxTech | Read and process transcript spots for specific commercial technologies |
-- G --
| gdalParquetAvailable | Check if Parquet GDAL driver is available |
| geometryFeatureData | Get global spatial analysis results and metadata of colData, rowData, and geometries |
| getImg | Functions re-exported from other packages |
| getParams | Get parameters used in spatial methods |
| getPixelSize | Get physical size of pixels |
| getTechTxFields | Get relevant fields and file paths for transcript spots |
| getTissueBoundaryConcave | Get tissue boundary from concave hull of cell geometries |
| getTissueBoundaryImg | Get tissue boundary from histology image |
-- I --
| imageIDs | Show all image_ids in the SFE object |
| Img<- | Image setter |
| Img<--method | Image setter |
| imgData | Functions re-exported from other packages |
| imgRaster | Get the image from *Image class |
| imgRaster-method | Get the image from *Image class |
| imgSource | Source of images that are on disk |
| imgSource-method | Source of images that are on disk |
| isFull | Other 'BioFormatsImage' getters |
| isFull-method | Other 'BioFormatsImage' getters |
-- L --
| localResult | Get and set results from local spatial statistics |
| localResult-method | Get and set results from local spatial statistics |
| localResult<- | Get and set results from local spatial statistics |
| localResult<--method | Get and set results from local spatial statistics |
| localResultAttrs | Get and set results from local spatial statistics |
| localResultAttrs-method | Get and set results from local spatial statistics |
| localResultFeatures | Get and set results from local spatial statistics |
| localResultFeatures-method | Get and set results from local spatial statistics |
| localResultNames | Get and set results from local spatial statistics |
| localResultNames-method | Get and set results from local spatial statistics |
| localResultNames<- | Get and set results from local spatial statistics |
| localResultNames<--method | Get and set results from local spatial statistics |
| localResults | Get and set results from local spatial statistics |
| localResults-method | Get and set results from local spatial statistics |
| localResults<- | Get and set results from local spatial statistics |
| localResults<--method | Get and set results from local spatial statistics |
| logcounts | Functions re-exported from other packages |
-- M --
| mirror | Affine transfortaion of SFE object in histological space |
| mirrorImg | Mirror/flip images |
| mirrorImg-method | Methods for handling image-related data |
| mirrorImg-method | Mirror/flip images |
| multi_listw2sparse | Convert multiple listw graphs into a single sparse adjacency matrix |
-- N --
| nucSeg | Column geometry getters and setters |
| nucSeg<- | Column geometry getters and setters |
-- O --
| origin | Other 'BioFormatsImage' getters |
| origin-method | Other 'BioFormatsImage' getters |
-- R --
| read10xVisiumSFE | Read 10X Visium data as SpatialFeatureExperiment |
| readCosMX | Read CosMX data into SFE |
| readSelectTx | Read transcript spots of select genes |
| readVisiumHD | Read Visium HD data |
| readVizgen | Read Vizgen MERFISH output as SpatialFeatureExperiment |
| readXenium | Read 10X Xenium output as SpatialFeatureExperiment |
| reducedDim | Functions re-exported from other packages |
| reducedDimFeatureData | Get global spatial analysis results and metadata of colData, rowData, and geometries |
| reexports | Functions re-exported from other packages |
| removeEmptySpace | Remove empty space |
| rmvImg | Functions re-exported from other packages |
| ROIPoly | Column geometry getters and setters |
| ROIPoly<- | Column geometry getters and setters |
| rotate | Affine transfortaion of SFE object in histological space |
| rotateImg | Rotate image |
| rotateImg-method | Methods for handling image-related data |
| rotateImg-method | Rotate image |
| rowData | Functions re-exported from other packages |
| rowFeatureData | Get global spatial analysis results and metadata of colData, rowData, and geometries |
| rowGeometries | Row geometry getters and setters |
| rowGeometries<- | Row geometry getters and setters |
| rowGeometry | Row geometry getters and setters |
| rowGeometry<- | Row geometry getters and setters |
| rowGeometryNames | Row geometry getters and setters |
| rowGeometryNames<- | Row geometry getters and setters |
| rowGraph | Spatial graph methods |
| rowGraph<- | Spatial graph methods |
| rowGraphNames | Spatial graph methods |
| rowGraphNames<- | Spatial graph methods |
| rowGraphs | Spatial graph methods |
| rowGraphs<- | Spatial graph methods |
-- S --
| sampleIDs | Get all unique sample IDs |
| saveRDS-method | Save SpatialFeatureExperiment as RDS file |
| scale | Affine transfortaion of SFE object in histological space |
| scaleImg | Scale image |
| scaleImg-method | Methods for handling image-related data |
| scaleImg-method | Scale image |
| SFE-image | Methods for handling image-related data |
| SFE-transform | Affine transfortaion of SFE object in histological space |
| SFEVersion | Update a SpatialFeatureExperiment object |
| show-method | On disk representation of BioFormats images in SFE object |
| show-method | Use the EBImage 'Image' class in SFE objects |
| show-method | SpatRaster representation of images in SFE objects |
| show-method | Print method for SpatialFeatureExperiment |
| spatialCoords | Functions re-exported from other packages |
| spatialCoords<- | Functions re-exported from other packages |
| spatialCoordsNames | Functions re-exported from other packages |
| 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 | SpatRaster representation of images in SFE objects |
| SpatRasterImage-class | SpatRaster representation of images in SFE objects |
| splitByCol | Split SFE object with categorical vector or geometry |
| splitByCol-method | Split SFE object with categorical vector or geometry |
| splitComponent | Split SFE object with categorical vector or geometry |
| splitContiguity | Split SFE object with categorical vector or geometry |
| splitSamples | Split SFE object with categorical vector or geometry |
| spotPoly | Column geometry getters and setters |
| spotPoly<- | Column geometry getters and setters |
| 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 |
| toExtImage | Convert images to ExtImage |
| toExtImage-method | Convert images to ExtImage |
| toSpatialFeatureExperiment | SpatialFeatureExperiment coercion methods |
| toSpatialFeatureExperiment-method | SpatialFeatureExperiment coercion methods |
| toSpatRasterImage | Convert images to SpatRasterImage |
| toSpatRasterImage-method | Convert images to SpatRasterImage |
| transformation | Other 'BioFormatsImage' getters |
| transformation-method | Other 'BioFormatsImage' getters |
| translate | Affine transfortaion of SFE object in histological space |
| translateImg | Translate/shift image in space |
| translateImg-method | Methods for handling image-related data |
| translateImg-method | Translate/shift image in space |
| transpose | Affine transfortaion of SFE object in histological space |
| transposeImg | Transpose images |
| transposeImg-method | Methods for handling image-related data |
| transposeImg-method | Transpose images |
| txSpots | Row geometry getters and setters |
| txSpots<- | Row geometry getters and setters |
-- 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 |