| 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 |
| contour2sf | Draw a contour region on some density level |
| corDensity | Test for density correlation between two cell types. |
| findROI | Find ROIs based on cell type-specific densities via graph-based method. |
| getContour | Get contour from density |
| getContourRegions | Calculate areas between every two density levels |
| grid2sf | Combine grids in each ROI to a sf region |
| gridDensity | Perform kernel density estimation on SpatialExperiment for cell types of interest |
| mergeROI | Manually merge ROIs |
| 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. |
| plotDensCor | Plot density correlation between two cell types |
| plotDensity | Plot grid-based density. |
| plotROI | Plot ROIs on spatial. |
| plotSpatial | Plot cells based on spatial coordinates. |
| postSelRegion | Merge sel_region from the selectRegion function to SpatialExperiment. |
| 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 |