[,SpatialExperiment,ANY,ANY,ANY-method
                        Subset for grid level analysis
allocateCells           Annotate all cells with contour level of cell
                        type-specific density.
cellsInRegion           Check which cells are in which regions
computeDensity          Perform kernel density estimation on
                        SpatialExperiment
computeDensityHex       Perform kernel density estimation on
                        SpatialExperiment
contour2sf              Draw a contour region on some density level
coord_hash              Hash two 15-bytes signed integers into one
                        32-bytes integer.
corDensity              Test for density correlation between two cell
                        types.
findNbrsGrid            Construct a neighbour list from grid
                        coordinates.
findNbrsSNN             Construct a SNN neighbour list from assay.
findNbrsSpatial         Construct a distance-based neighbour list from
                        cell coordinates.
findROI                 Find ROIs based on cell type-specific densities
                        via graph-based method.
getClusters             Cluster cells in spe using graph methods.
getContour              Get contour from density
getContourRegions       Calculate areas between every two density
                        levels
getNiche                Build a niche assay based on the profile of
                        neighbouring cells
globalMoran             Calculate global Moran for 1 to 2 variables.
grid2df                 Convert x,y nodes to data.frame of polygons
grid2sf                 Convert x,y nodes to sf polygons
gridDensity             Perform kernel density estimation on
                        SpatialExperiment for cell types of interest
gridSPE                 Summarize a SpatialExperiment object at
                        grid-level
localMoran              Calculate local Moran for 1 to 2 variables.
mergeROI                Manually merge ROIs
normalizeAssay          Perform log normalization for counts
plotCellCompo           Plot cell type composition in each density
                        level of cell of interest.
plotContour             Plot contour lines.
plotContourRegion       Visualising an sf object (for internal use only
                        at the moment)
plotCorHeatmap          Plot model statistics using heatmap.
plotDR                  Plot reduced dimensions.
plotDensCor             Plot density correlation between two cell types
plotDensity             Plot grid-based density.
plotGrid                Plot grid from metadata.
plotImage               Plot background image of spe
plotLISA                Plotting LISA (e.g. moran)
plotROI                 Plot ROIs on spatial.
plotSpatial             Plot cells based on spatial coordinates.
postSelRegion           Merge sel_region from the selectRegion function
                        to SpatialExperiment.
realignVisium           Scale and straighten out Visium coordinates
realignVisiumHD         Scale and straighten out VisiumHD coordinates
runPCA                  Fast PCA using irlba.
runUMAP                 UMAP using uwot. Parameters are set to be
                        similar to Seurat's
selectRegion            Select region of interest from plot
spe2PB                  Given a 'SpatialExperiment' data object, create
                        pseudo-bulk samples using the colData
                        information and return a DGEList object
update_bound            Update the x,y limits of a plot
