Man pages for pachterlab/SpatialFeatureExperiment
Integrating SpatialExperiment with Simple Features in sf
| addVisiumSpotPoly | Add Visium spot polygons to colGeometry |
| affineImg | Affine transformation of images |
| aggBboxes | Aggregate bounding boxes |
| aggregate-SpatialFeatureExperiment-method | Aggregate data in SFE using geometry |
| aggregateTx | Aggregate transcript spots from file |
| annotGeometries | Annotation geometry methods |
| annotOp | Binary operations for geometry of each cell/spot and... |
| annotPred | Binary predicates for geometry of each cell/spot and... |
| annotSummary | Summarize attributes of an annotGeometry for each cell/spot |
| bbox_center | Find center of bounding box |
| bbox-SpatialFeatureExperiment-method | Find bounding box of SFE objects |
| BioFormatsImage | On disk representation of BioFormats images in SFE object |
| BioFormatsImage-getters | Other 'BioFormatsImage' getters |
| cbind-SpatialFeatureExperiment-method | Concatenate SpatialFeatureExperiment objects |
| changeSampleIDs | Change sample IDs |
| colFeatureData | Get global spatial analysis results and metadata of colData,... |
| colGeometries | Column geometry getters and setters |
| crop | Crop an SFE object with a geometry |
| cropImg | Crop images |
| df2sf | From ordinary data frame to sf to construct SFE object |
| dim-BioFormatsImage-method | Find dimension of BioFormatsImage |
| dimGeometries | Dimension geometry methods |
| ext | Get and set extent of image objects |
| ExtImage | Use the EBImage 'Image' class in SFE objects |
| findSpatialNeighbors-SpatialFeatureExperiment-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... |
| gdalParquetAvailable | Check if Parquet GDAL driver is available |
| getParams | Get parameters used in spatial methods |
| 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 |
| imgRaster | Get the image from *Image class |
| Img-set-SpatialExperiment-method | Image setter |
| imgSource | Source of images that are on disk |
| internal-Voyager | Internal functions also used in Voyager |
| listw2sparse | Convert listw into sparse adjacency matrix |
| localResults | Get and set results from local spatial statistics |
| mirrorImg | Mirror/flip images |
| multi_listw2sparse | Convert multiple listw graphs into a single sparse adjacency... |
| 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 |
| reexports | Functions re-exported from other packages |
| removeEmptySpace | Remove empty space |
| rotateImg | Rotate image |
| rowGeometries | Row geometry getters and setters |
| sampleIDs | Get all unique sample IDs |
| saveRDS-SpatialFeatureExperiment-method | Save SpatialFeatureExperiment as RDS file |
| scaleImg | Scale image |
| SFE-image | Methods for handling image-related data |
| SFE-transform | Affine transfortaion of SFE object in histological space |
| show-SpatialFeatureExperiment-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 |
| spatialGraphs | Spatial graph methods |
| SpatRasterImage | SpatRaster representation of images in SFE objects |
| splitByCol | Split SFE object with categorical vector or geometry |
| st_any_pred | Simple geometry predicates |
| toExtImage | Convert images to ExtImage |
| toSpatRasterImage | Convert images to SpatRasterImage |
| translateImg | Translate/shift image in space |
| transposeImg | Transpose images |
| unit-SpatialFeatureExperiment-method | Get unit of a SpatialFeatureExperiment |
| updateObject | Update a SpatialFeatureExperiment object |
| visium_row_col | Row and columns of Visium barcodes on the slide |
