Package: SpatialFeatureExperiment 1.9.4
Lambda Moses
SpatialFeatureExperiment: Integrating SpatialExperiment with Simple Features in sf
A new S4 class integrating Simple Features with the R package sf to bring geospatial data analysis methods based on vector data to spatial transcriptomics. Also implements management of spatial neighborhood graphs and geometric operations. This pakage builds upon SpatialExperiment and SingleCellExperiment, hence methods for these parent classes can still be used.
Authors:
SpatialFeatureExperiment_1.9.4.tar.gz
SpatialFeatureExperiment_1.9.4.zip(r-4.5)SpatialFeatureExperiment_1.9.4.zip(r-4.4)SpatialFeatureExperiment_1.9.4.zip(r-4.3)
SpatialFeatureExperiment_1.9.4.tgz(r-4.4-any)SpatialFeatureExperiment_1.9.4.tgz(r-4.3-any)
SpatialFeatureExperiment_1.9.4.tar.gz(r-4.5-noble)SpatialFeatureExperiment_1.9.4.tar.gz(r-4.4-noble)
SpatialFeatureExperiment_1.9.4.tgz(r-4.4-emscripten)SpatialFeatureExperiment_1.9.4.tgz(r-4.3-emscripten)
SpatialFeatureExperiment.pdf |SpatialFeatureExperiment.html✨
SpatialFeatureExperiment/json (API)
NEWS
| # Install 'SpatialFeatureExperiment' in R: |
| install.packages('SpatialFeatureExperiment', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/pachterlab/spatialfeatureexperiment/issues
- visium_row_col - Row and columns of Visium barcodes on the slide
On BioConductor:SpatialFeatureExperiment-1.9.0(bioc 3.21)SpatialFeatureExperiment-1.8.2(bioc 3.20)
datarepresentationtranscriptomicsspatial
Last updated 2 days agofrom:6e4508db40. Checks:OK: 1 NOTE: 3 ERROR: 3. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 23 2024 |
| R-4.5-win | NOTE | Nov 23 2024 |
| R-4.5-linux | NOTE | Nov 23 2024 |
| R-4.4-win | NOTE | Nov 23 2024 |
| R-4.4-mac | ERROR | Nov 23 2024 |
| R-4.3-win | ERROR | Nov 23 2024 |
| R-4.3-mac | ERROR | Nov 23 2024 |
Exports:.check_features.check_rg.check_sample_id.ext_.rm_empty_geometries.symbol2id.value2df.warn_symbol_duplicateaddImgaddSelectTxaddTxSpotsaddTxTechaddVisiumSpotPolyaffineaffineImgaggBboxesaggregateaggregateTxaggregateTxTechannotGeometriesannotGeometries<-annotGeometryannotGeometry<-annotGeometryNamesannotGeometryNames<-annotGraphannotGraph<-annotGraphNamesannotGraphNames<-annotGraphsannotGraphs<-annotNPredannotOpannotPredannotSummarybboxbbox_centerBioFormatsImagecbindcellSegcellSeg<-centroidscentroids<-changeSampleIDscolDatacolData<-colFeatureDatacolGeometriescolGeometries<-colGeometrycolGeometry<-colGeometryNamescolGeometryNames<-colGraphcolGraph<-colGraphNamescolGraphNames<-colGraphscolGraphs<-countscropcropImgdf2sfdimGeometriesdimGeometries<-dimGeometrydimGeometry<-dimGeometryNamesdimGeometryNames<-extext<-ExtImagefindSpatialNeighborsfindVisiumGraphfindVisiumHDGraphformatTxSpotsformatTxTechgdalParquetAvailablegeometryFeatureDatagetImggetParamsgetPixelSizegetTechTxFieldsimageIDsImg<-imgDataimgRasterimgSourceisFulllistw2sparselocalResultlocalResult<-localResultAttrslocalResultFeatureslocalResultNameslocalResultNames<-localResultslocalResults<-logcountsmirrormirrorImgmulti_listw2sparsenucSegnucSeg<-originread10xVisiumSFEreadCosMXreadSelectTxreadVisiumHDreadVizgenreadXeniumreducedDimreducedDimFeatureDataremoveEmptySpacermvImgROIPolyROIPoly<-rotaterotateImgrowDatarowFeatureDatarowGeometriesrowGeometries<-rowGeometryrowGeometry<-rowGeometryNamesrowGeometryNames<-rowGraphrowGraph<-rowGraphNamesrowGraphNames<-rowGraphsrowGraphs<-sampleIDssaveRDSscalescaleImgSFEVersionshowspatialCoordsspatialCoords<-spatialCoordsNamesSpatialFeatureExperimentspatialGraphspatialGraph<-spatialGraphNamesspatialGraphNames<-spatialGraphsspatialGraphs<-SpatRasterImagesplitByColsplitContiguitysplitSamplesspotPolyspotPoly<-st_any_intersectsst_any_predst_n_intersectsst_n_predtissueBoundarytissueBoundary<-toExtImagetoSpatialFeatureExperimenttoSpatRasterImagetransformationtranslatetranslateImgtransposetransposeImgtxSpotstxSpots<-unitupdateObject
Dependencies:abindaskpassassortheadbase64encbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocNeighborsBiocParallelbitbit64bitopsblobbootbslibcachemclassclassIntclicodacodetoolscpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdeldirdigestdplyrdqrngDropletUtilse1071EBImageedgeRevaluatefansifastmapfftwtoolsfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgeometriesglueHDF5ArrayhighrhtmltoolshtmlwidgetshttrIRangesjpegjquerylibjsonliteKernSmoothknitrlambda.rlatticeLearnBayeslifecyclelimmalocfitmagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimemultcompmvtnormnlmeopensslpillarpkgconfigplogrpngproxypurrrR.methodsS3R.ooR.utilsR6rappdirsRcppRCurlrhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownRSQLites2S4ArraysS4VectorssandwichsassscuttlesfsfheadersSingleCellExperimentsitmosnowspSparseArraysparseMatrixStatsSpatialExperimentspatialregspDataspdepstatmodstringistringrSummarizedExperimentsurvivalsysterraTH.datatibbletidyrtidyselecttifftinytexUCSC.utilsunitsutf8vctrswithrwkxfunXVectoryamlzeallotzlibbioczoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add Visium spot polygons to colGeometry | addVisiumSpotPoly |
| Affine transformation of images | affineImg affineImg,BioFormatsImage-method affineImg,ExtImage-method affineImg,SpatRasterImage-method |
| Aggregate bounding boxes | aggBboxes |
| Aggregate data in SFE using geometry | aggregate,SpatialFeatureExperiment-method |
| Aggregate transcript spots from file | aggregateTx aggregateTxTech |
| Annotation geometry methods | annotGeometries annotGeometries,SpatialFeatureExperiment-method annotGeometries<- annotGeometries<-,SpatialFeatureExperiment-method annotGeometry annotGeometry,SpatialFeatureExperiment-method annotGeometry<- annotGeometry<-,SpatialFeatureExperiment-method annotGeometryNames annotGeometryNames,SpatialFeatureExperiment-method annotGeometryNames<- annotGeometryNames<-,SpatialFeatureExperiment,character-method tissueBoundary tissueBoundary<- |
| Binary operations for geometry of each cell/spot and annotation | annotOp |
| Binary predicates for geometry of each cell/spot and annotation | annotNPred annotPred |
| Summarize attributes of an annotGeometry for each cell/spot | annotSummary |
| Find center of bounding box | bbox_center |
| Find bounding box of SFE objects | bbox bbox,SpatialFeatureExperiment-method |
| On disk representation of BioFormats images in SFE object | BioFormatsImage BioFormatsImage-class show,BioFormatsImage-method |
| Other 'BioFormatsImage' getters | BioFormatsImage-getters isFull isFull,BioFormatsImage-method origin origin,BioFormatsImage-method transformation transformation,BioFormatsImage-method |
| Concatenate SpatialFeatureExperiment objects | cbind,SpatialFeatureExperiment-method |
| Change sample IDs | changeSampleIDs |
| Get global spatial analysis results and metadata of colData, rowData, and geometries | colFeatureData geometryFeatureData reducedDimFeatureData rowFeatureData |
| Column geometry getters and setters | cellSeg cellSeg<- centroids centroids<- colGeometries colGeometries<- colGeometry colGeometry<- colGeometryNames colGeometryNames<- nucSeg nucSeg<- ROIPoly ROIPoly<- spotPoly spotPoly<- |
| Crop an SFE object with a geometry | crop |
| Crop images | cropImg cropImg,BioFormatsImage-method cropImg,ExtImage-method cropImg,SpatRasterImage-method |
| From ordinary data frame to sf to construct SFE object | df2sf |
| Find dimension of BioFormatsImage | dim,BioFormatsImage-method |
| Dimension geometry methods | dimGeometries dimGeometries,SpatialFeatureExperiment-method dimGeometries<- dimGeometries<-,SpatialFeatureExperiment-method dimGeometry dimGeometry,SpatialFeatureExperiment-method dimGeometry<- dimGeometry<-,SpatialFeatureExperiment-method dimGeometryNames dimGeometryNames,SpatialFeatureExperiment-method dimGeometryNames<- dimGeometryNames<-,SpatialFeatureExperiment,numeric,character-method |
| Get and set extent of image objects | ext ext,BioFormatsImage-method ext,ExtImage-method ext,SpatRasterImage-method ext<-,BioFormatsImage,numeric-method ext<-,ExtImage,numeric-method ext<-,SpatRasterImage,numeric-method |
| Use the EBImage 'Image' class in SFE objects | ExtImage ExtImage-class show,ExtImage-method |
| Find spatial neighborhood graph | findSpatialNeighbors findSpatialNeighbors,SpatialFeatureExperiment-method |
| Find spatial neighborhood graphs for Visium spots | findVisiumGraph |
| Find Visium HD spatial neighborhood graph | findVisiumHDGraph |
| Read and process transcript spots geometry for SFE | addTxSpots formatTxSpots |
| Read and process transcript spots for specific commercial technologies | addTxTech formatTxTech |
| Check if Parquet GDAL driver is available | gdalParquetAvailable |
| Get parameters used in spatial methods | getParams |
| Get physical size of pixels | getPixelSize |
| Get relevant fields and file paths for transcript spots | getTechTxFields |
| Show all image_ids in the SFE object | imageIDs |
| Image setter | Img<- Img<-,SpatialExperiment-method |
| Get the image from *Image class | imgRaster imgRaster,BioFormatsImage-method imgRaster,ExtImage-method imgRaster,SpatRasterImage-method |
| Source of images that are on disk | imgSource imgSource,BioFormatsImage-method imgSource,ExtImage-method imgSource,SpatRasterImage-method |
| Convert listw into sparse adjacency matrix | listw2sparse |
| Get and set results from local spatial statistics | localResult localResult,SpatialFeatureExperiment-method localResult<- localResult<-,SpatialFeatureExperiment-method localResultAttrs localResultAttrs,SpatialFeatureExperiment-method localResultFeatures localResultFeatures,SpatialFeatureExperiment-method localResultNames localResultNames,SpatialFeatureExperiment-method localResultNames<- localResultNames<-,SpatialFeatureExperiment,character-method localResults localResults,SpatialFeatureExperiment-method localResults<- localResults<-,SpatialFeatureExperiment-method |
| Mirror/flip images | mirrorImg mirrorImg,BioFormatsImage-method mirrorImg,ExtImage-method mirrorImg,SpatRasterImage-method |
| Convert multiple listw graphs into a single sparse adjacency matrix | multi_listw2sparse |
| Read 10X Visium data as SpatialFeatureExperiment | read10xVisiumSFE |
| Read CosMX data into SFE | readCosMX |
| Read transcript spots of select genes | addSelectTx readSelectTx |
| Read Visium HD data | readVisiumHD |
| Read Vizgen MERFISH output as SpatialFeatureExperiment | readVizgen |
| Read 10X Xenium output as SpatialFeatureExperiment | readXenium |
| Functions re-exported from other packages | colData colData<- counts getImg imgData logcounts reducedDim reexports rmvImg rowData spatialCoords spatialCoords<- spatialCoordsNames |
| Remove empty space | removeEmptySpace |
| Rotate image | rotateImg rotateImg,BioFormatsImage-method rotateImg,ExtImage-method rotateImg,SpatRasterImage-method |
| Row geometry getters and setters | rowGeometries rowGeometries<- rowGeometry rowGeometry<- rowGeometryNames rowGeometryNames<- txSpots txSpots<- |
| Get all unique sample IDs | sampleIDs |
| Save SpatialFeatureExperiment as RDS file | saveRDS,SpatialFeatureExperiment-method |
| Scale image | scaleImg scaleImg,AlignedSpatialImage-method |
| Methods for handling image-related data | addImg,SpatialFeatureExperiment-method affineImg,SpatialFeatureExperiment-method mirrorImg,SpatialFeatureExperiment-method rotateImg,SpatialFeatureExperiment-method scaleImg,SpatialFeatureExperiment-method SFE-image translateImg,SpatialFeatureExperiment-method transposeImg,SpatialFeatureExperiment-method |
| Affine transfortaion of SFE object in histological space | affine mirror rotate scale SFE-transform translate transpose |
| Print method for SpatialFeatureExperiment | show,SpatialFeatureExperiment-method |
| Constructor of SpatialFeatureExperiment object | SpatialFeatureExperiment |
| The SpatialFeatureExperiment class | SpatialFeatureExperiment-class |
| SpatialFeatureExperiment coercion methods | SpatialFeatureExperiment-coercion toSpatialFeatureExperiment toSpatialFeatureExperiment,Seurat-method toSpatialFeatureExperiment,SingleCellExperiment-method toSpatialFeatureExperiment,SpatialExperiment-method |
| Subsetting SpatialFeatureExperiment objects | SpatialFeatureExperiment-subset [,SpatialFeatureExperiment,ANY,ANY,ANY-method |
| Spatial graph methods | annotGraph annotGraph<- annotGraphNames annotGraphNames<- annotGraphs annotGraphs<- colGraph colGraph<- colGraphNames colGraphNames<- colGraphs colGraphs<- rowGraph rowGraph<- rowGraphNames rowGraphNames<- rowGraphs rowGraphs<- spatialGraph spatialGraph,SpatialFeatureExperiment-method spatialGraph<- spatialGraph<-,SpatialFeatureExperiment-method spatialGraphNames spatialGraphNames,SpatialFeatureExperiment,numeric-method spatialGraphNames<- spatialGraphNames<-,SpatialFeatureExperiment,numeric,ANY,character-method spatialGraphs spatialGraphs,SpatialFeatureExperiment-method spatialGraphs<- spatialGraphs<-,SpatialFeatureExperiment-method |
| SpatRaster representation of images in SFE objects | show,SpatRasterImage-method SpatRasterImage SpatRasterImage-class |
| Split SFE object with categorical vector or geometry | splitByCol splitByCol,SpatialFeatureExperiment,list-method splitByCol,SpatialFeatureExperiment,sf-method splitByCol,SpatialFeatureExperiment,sfc-method splitContiguity splitSamples |
| Simple geometry predicates | st_any_intersects st_any_pred st_n_intersects st_n_pred |
| Convert images to ExtImage | toExtImage toExtImage,BioFormatsImage-method toExtImage,SpatRasterImage-method |
| Convert images to SpatRasterImage | toSpatRasterImage toSpatRasterImage,BioFormatsImage-method toSpatRasterImage,ExtImage-method |
| Translate/shift image in space | translateImg translateImg,BioFormatsImage-method translateImg,ExtImage-method translateImg,SpatRasterImage-method |
| Transpose images | transposeImg transposeImg,BioFormatsImage-method transposeImg,ExtImage-method transposeImg,SpatRasterImage-method |
| Get unit of a SpatialFeatureExperiment | unit unit,SpatialFeatureExperiment-method |
| Update a SpatialFeatureExperiment object | SFEVersion updateObject updateObject,SpatialFeatureExperiment-method |
| Row and columns of Visium barcodes on the slide | visium_row_col |
