Spatial cell-type inter-correlation by density in R

Documentation for package ‘scider’ version 1.0.0

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