# Spatial cell-type inter-correlation by density in R

## Documentation for package ‘scider’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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