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"annotGeometry", "annotGeometry,SpatialFeatureExperiment-method", "annotGeometry<-", "annotGeometry<-,SpatialFeatureExperiment-method", "annotGeometryNames", "annotGeometryNames,SpatialFeatureExperiment-method", "annotGeometryNames<-", "annotGeometryNames<-,SpatialFeatureExperiment,character-method", "tissueBoundary", "tissueBoundary<-" ] }, { "page": "annotOp", "title": "Binary operations for geometry of each cell/spot and annotation", "concept": [ "Geometric operations" ], "topics": [ "annotOp" ] }, { "page": "annotPred", "title": "Binary predicates for geometry of each cell/spot and annotation", "concept": [ "Geometric operations" ], "topics": [ "annotNPred", "annotPred" ] }, { "page": "annotSummary", "title": "Summarize attributes of an annotGeometry for each cell/spot", "concept": [ "Geometric operations" ], "topics": [ "annotSummary" ] }, { "page": "bbox_center", "title": "Find center of bounding box", "concept": [ "Utilities" ], "topics": [ "bbox_center" ] }, { "page": "bbox-SpatialFeatureExperiment-method", "title": "Find bounding box of SFE objects", "concept": [ "Geometric operations" ], "topics": [ "bbox", "bbox,SpatialFeatureExperiment-method" ] }, { "page": "BioFormatsImage", "title": "On disk representation of BioFormats images in SFE object", "concept": [ "Image classes" ], "topics": [ "BioFormatsImage", "BioFormatsImage-class", "show,BioFormatsImage-method" ] }, { "page": "BioFormatsImage-getters", "title": "Other 'BioFormatsImage' getters", "concept": [ "Image classes" ], "topics": [ "BioFormatsImage-getters", "isFull", "isFull,BioFormatsImage-method", "origin", "origin,BioFormatsImage-method", "transformation", "transformation,BioFormatsImage-method" ] }, { "page": "cbind-SpatialFeatureExperiment-method", "title": "Concatenate SpatialFeatureExperiment objects", "concept": [ "Non-spatial operations" ], "topics": [ "cbind,SpatialFeatureExperiment-method" ] }, { "page": "changeSampleIDs", "title": "Change sample IDs", "concept": [ "Utilities" ], "topics": [ "changeSampleIDs" ] }, { "page": "colFeatureData", "title": "Get global spatial analysis results and metadata of colData, rowData, and geometries", "concept": [ "Getters and setters" ], "topics": [ "colFeatureData", "geometryFeatureData", "reducedDimFeatureData", "rowFeatureData" ] }, { "page": "colGeometries", "title": "Column geometry getters and setters", "concept": [ "Getters and setters" ], "topics": [ "cellSeg", "cellSeg<-", "centroids", "centroids<-", "colGeometries", "colGeometries<-", "colGeometry", "colGeometry<-", "colGeometryNames", "colGeometryNames<-", "nucSeg", "nucSeg<-", "ROIPoly", "ROIPoly<-", "spotPoly", "spotPoly<-" ] }, { "page": "crop", "title": "Crop an SFE object with a geometry", "concept": [ "Geometric operations" ], "topics": [ "crop" ] }, { "page": "cropImg", "title": "Crop images", "concept": [ "Image methods", "image methods" ], "topics": [ "cropImg", "cropImg,BioFormatsImage-method", "cropImg,ExtImage-method", "cropImg,SpatRasterImage-method" ] }, { "page": "df2sf", "title": "From ordinary data frame to sf to construct SFE object", "concept": [ "Utilities" ], "topics": [ "df2sf" ] }, { "page": "dim-BioFormatsImage-method", "title": "Find dimension of BioFormatsImage", "concept": [ "Image methods", "image methods" ], "topics": [ "dim,BioFormatsImage-method" ] }, { "page": "dim-ExtImage-method", "title": "Find dimensions of ExtImage", "concept": [ "Image methods", "image methods" ], "topics": [ "dim,ExtImage-method" ] }, { "page": "dimGeometries", "title": "Dimension geometry methods", "concept": [ "Getters and setters" ], "topics": [ "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" ] }, { "page": "ext", "title": "Get and set extent of image objects", "concept": [ "Image methods", "image methods" ], "topics": [ "ext", "ext,BioFormatsImage-method", "ext,ExtImage-method", "ext,SpatRasterImage-method", "ext<-,BioFormatsImage,numeric-method", "ext<-,ExtImage,numeric-method", "ext<-,SpatRasterImage,numeric-method" ] }, { "page": "ExtImage", "title": "Use the EBImage 'Image' class in SFE objects", "concept": [ "Image classes" ], "topics": [ "ExtImage", "ExtImage-class", "show,ExtImage-method" ] }, { "page": "findDebrisCells", "title": "Identify cells in small bits outside the main piece of tissue", "concept": [ "Preprocessing and QC" ], "topics": [ "findDebrisCells", "findDebrisCells,matrix-method", "findDebrisCells,sf-method", "findDebrisCells,sfc-method", "findDebrisCells,SpatialExperiment-method" ] }, { "page": "findSpatialNeighbors", "title": "Find spatial neighborhood graph", "concept": [ "Spatial neighborhood graph" ], "topics": [ "findSpatialNeighbors", "findSpatialNeighbors,SpatialFeatureExperiment-method" ] }, { "page": "findVisiumGraph", "title": "Find spatial neighborhood graphs for Visium spots", "concept": [ "Spatial neighborhood graph" ], "topics": [ "findVisiumGraph" ] }, { "page": "findVisiumHDGraph", "title": "Find Visium HD spatial neighborhood graph", "concept": [ "Spatial neighborhood graph" ], "topics": [ "findVisiumHDGraph" ] }, { "page": "formatTxSpots", "title": "Read and process transcript spots geometry for SFE", "concept": [ "Transcript spots" ], "topics": [ "addTxSpots", "formatTxSpots" ] }, { "page": "formatTxTech", "title": "Read and process transcript spots for specific commercial technologies", "concept": [ "Transcript spots" ], "topics": [ "addTxTech", "formatTxTech" ] }, { "page": "gdalParquetAvailable", "title": "Check if Parquet GDAL driver is available", "concept": [ "Utilities" ], "topics": [ "gdalParquetAvailable" ] }, { "page": "getParams", "title": "Get parameters used in spatial methods", "concept": [ "Getters and setters" ], "topics": [ "getParams" ] }, { "page": "getPixelSize", "title": "Get physical size of pixels", "concept": [ "Utilities" ], "topics": [ "getPixelSize" ] }, { "page": "getTechTxFields", "title": "Get relevant fields and file paths for transcript spots", "concept": [ "Utilities" ], "topics": [ "getTechTxFields" ] }, { "page": "getTissueBoundaryConcave", "title": "Get tissue boundary from concave hull of cell geometries", "concept": [ "Preprocessing and QC" ], "topics": [ "getTissueBoundaryConcave", "getTissueBoundaryConcave,sf-method", "getTissueBoundaryConcave,sfc-method", "getTissueBoundaryConcave,SpatialFeatureExperiment-method" ] }, { "page": "getTissueBoundaryImg", "title": "Get tissue boundary from histology image", "concept": [ "Preprocessing and QC" ], "topics": [ "getTissueBoundaryImg" ] }, { "page": "imageIDs", "title": "Show all image_ids in the SFE object", "concept": [ "Utilities" ], "topics": [ "imageIDs" ] }, { "page": "Img-set-SpatialExperiment-method", "title": "Image setter", "concept": [ "Image methods" ], "topics": [ "Img<-", "Img<-,SpatialExperiment-method" ] }, { "page": "imgRaster", "title": "Get the image from *Image class", "concept": [ "Image methods", "image methods" ], "topics": [ "imgRaster", "imgRaster,BioFormatsImage-method", "imgRaster,ExtImage-method", "imgRaster,SpatRasterImage-method" ] }, { "page": "imgSource", "title": "Source of images that are on disk", "concept": [ "Image methods", "image methods" ], "topics": [ "imgSource", "imgSource,BioFormatsImage-method", "imgSource,ExtImage-method", "imgSource,SpatRasterImage-method" ] }, { "page": "localResults", "title": "Get and set results from local spatial statistics", "concept": [ "Getters and setters" ], "topics": [ "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" ] }, { "page": "mirrorImg", "title": "Mirror/flip images", "concept": [ "Image affine transformation", "image methods" ], "topics": [ "mirrorImg", "mirrorImg,BioFormatsImage-method", "mirrorImg,ExtImage-method", "mirrorImg,SpatRasterImage-method" ] }, { "page": "multi_listw2sparse", "title": "Convert multiple listw graphs into a single sparse adjacency matrix", "concept": [ "Utilities" ], "topics": [ "multi_listw2sparse" ] }, { "page": "read10xVisiumSFE", "title": "Read 10X Visium data as SpatialFeatureExperiment", "concept": [ "Read data into SFE" ], "topics": [ "read10xVisiumSFE" ] }, { "page": "readCosMX", "title": "Read CosMX data into SFE", "concept": [ "Read data into SFE" ], "topics": [ "readCosMX" ] }, { "page": "readSelectTx", "title": "Read transcript spots of select genes", "concept": [ "Transcript spots" ], "topics": [ "addSelectTx", "readSelectTx" ] }, { "page": "readVisiumHD", "title": "Read Visium HD data", "concept": [ "Read data into SFE" ], "topics": [ "readVisiumHD" ] }, { "page": "readVizgen", "title": "Read Vizgen MERFISH output as SpatialFeatureExperiment", "concept": [ "Read data into SFE" ], "topics": [ "readVizgen" ] }, { "page": "readXenium", "title": "Read 10X Xenium output as SpatialFeatureExperiment", "concept": [ "Read data into SFE" ], "topics": [ "readXenium" ] }, { "page": "reexports", "title": "Functions re-exported from other packages", "topics": [ "colData", "colData<-", "counts", "getImg", "imgData", "logcounts", "reducedDim", "reexports", "rmvImg", "rowData", "spatialCoords", "spatialCoords<-", "spatialCoordsNames" ] }, { "page": "removeEmptySpace", "title": "Remove empty space", "concept": [ "Geometric operations" ], "topics": [ "removeEmptySpace" ] }, { "page": "rotateImg", "title": "Rotate image", "concept": [ "Image affine transformation", "image methods" ], "topics": [ "rotateImg", "rotateImg,BioFormatsImage-method", "rotateImg,ExtImage-method", "rotateImg,SpatRasterImage-method" ] }, { "page": "rotateMinRect", "title": "Rotate the tissue to reduce empty space in plots", "concept": [ "Geometric operations" ], "topics": [ "rotateMinRect", "rotateMinRect,matrix-method", "rotateMinRect,sf-method", "rotateMinRect,sfc-method", "rotateMinRect,SpatialFeatureExperiment-method" ] }, { "page": "rowGeometries", "title": "Row geometry getters and setters", "concept": [ "Getters and setters" ], "topics": [ "rowGeometries", "rowGeometries<-", "rowGeometry", "rowGeometry<-", "rowGeometryNames", "rowGeometryNames<-", "txSpots", "txSpots<-" ] }, { "page": "sampleIDs", "title": "Get all unique sample IDs", "concept": [ "Utilities" ], "topics": [ "sampleIDs" ] }, { "page": "saveRDS-SpatialFeatureExperiment-method", "title": "Save SpatialFeatureExperiment as RDS file", "concept": [ "Utilities" ], "topics": [ "saveRDS,SpatialFeatureExperiment-method" ] }, { "page": "scaleImg", "title": "Scale image", "concept": [ "Image affine transformation", "image methods" ], "topics": [ "scaleImg", "scaleImg,AlignedSpatialImage-method", "scaleImg,BioFormatsImage-method" ] }, { "page": "SFE-image", "title": "Methods for handling image-related data", "concept": [ "Image methods", "image methods" ], "topics": [ "addImg,SpatialFeatureExperiment-method", "affineImg,SpatialFeatureExperiment-method", "mirrorImg,SpatialFeatureExperiment-method", "rotateImg,SpatialFeatureExperiment-method", "scaleImg,SpatialFeatureExperiment-method", "SFE-image", "translateImg,SpatialFeatureExperiment-method", "transposeImg,SpatialFeatureExperiment-method" ] }, { "page": "SFE-transform", "title": "Affine transfortaion of SFE object in histological space", "concept": [ "Geometric operations" ], "topics": [ "affine", "mirror", "rotate", "scale", "SFE-transform", "translate", "transpose" ] }, { "page": "show-SpatialFeatureExperiment-method", "title": "Print method for SpatialFeatureExperiment", "concept": [ "SpatialFeatureExperiment class" ], "topics": [ "show,SpatialFeatureExperiment-method" ] }, { "page": "SpatialFeatureExperiment", "title": "Constructor of SpatialFeatureExperiment object", "concept": [ "SpatialFeatureExperiment class" ], "topics": [ "SpatialFeatureExperiment" ] }, { "page": "SpatialFeatureExperiment-class", "title": "The SpatialFeatureExperiment class", "concept": [ "SpatialFeatureExperiment class" ], "topics": [ "SpatialFeatureExperiment-class" ] }, { "page": "SpatialFeatureExperiment-coercion", "title": "SpatialFeatureExperiment coercion methods", "concept": [ "SpatialFeatureExperiment class" ], "topics": [ "SpatialFeatureExperiment-coercion", "toSpatialFeatureExperiment", "toSpatialFeatureExperiment,Seurat-method", "toSpatialFeatureExperiment,SingleCellExperiment-method", "toSpatialFeatureExperiment,SpatialExperiment-method" ] }, { "page": "SpatialFeatureExperiment-subset", "title": "Subsetting SpatialFeatureExperiment objects", "concept": [ "Non-spatial operations" ], "topics": [ "SpatialFeatureExperiment-subset", "[,SpatialFeatureExperiment,ANY,ANY,ANY-method" ] }, { "page": "spatialGraphs", "title": "Spatial graph methods", "concept": [ "Getters and setters" ], "topics": [ "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", 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"splitComponent,sf-method", "splitComponent,sfc-method", "splitComponent,SpatialFeatureExperiment-method" ] }, { "page": "st_any_pred", "title": "Simple geometry predicates", "concept": [ "Geometric operations" ], "topics": [ "st_any_intersects", "st_any_pred", "st_n_intersects", "st_n_pred" ] }, { "page": "toExtImage", "title": "Convert images to ExtImage", "concept": [ "Image classes" ], "topics": [ "toExtImage", "toExtImage,BioFormatsImage-method", "toExtImage,SpatRasterImage-method" ] }, { "page": "toSpatRasterImage", "title": "Convert images to SpatRasterImage", "concept": [ "Image classes" ], "topics": [ "toSpatRasterImage", "toSpatRasterImage,BioFormatsImage-method", "toSpatRasterImage,ExtImage-method" ] }, { "page": "translateImg", "title": "Translate/shift image in space", "concept": [ "Image affine transformation", "image methods" ], "topics": [ "translateImg", "translateImg,BioFormatsImage-method", "translateImg,ExtImage-method", "translateImg,SpatRasterImage-method" ] }, { 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