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

## Documentation for package ‘scider’ version 1.10.0

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

## 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
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
getHVG | Get top highly variable genes.
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.
plotDensCor | Plot density correlation between two cell types
plotDensity | Plot grid-based density.
plotDots | Dot plot of gene expression by groups
plotDR | Plot reduced dimensions.
plotGrid | Plot grid from metadata.
plotImage | Plot background image of spe
plotLISA | Plotting LISA (e.g. moran)
plotLISAscatter | Scatterplot for local moran's I
plotPCA | Plot reduced dimensions.
plotROI | Plot ROIs on spatial.
plotSpatial | Plot cells based on spatial coordinates.
plotUMAP | Plot reduced dimensions.
plotViolin | Violin plot using genes or cell data
postSelRegion | Merge sel_region from the selectRegion function to SpatialExperiment.
readProseg | Read Proseg V2 output into spe
readVisium | Read Visium output into spe
readVisiumHD | Read VisiumHD output into spe
readXenium | Read Xenium output into spe
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
[-method | Subset for grid level analysis