Spatial cell-type inter-correlation by density in R

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Documentation for package ‘scider’ version 1.7.2

• 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
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.
plotDensCor	Plot density correlation between two cell types
plotDensity	Plot grid-based density.
plotDR	Plot reduced dimensions.
plotGrid	Plot grid from metadata.
plotImage	Plot background image of spe
plotLISA	Plotting LISA (e.g. moran)
plotPCA	Plot reduced dimensions.
plotROI	Plot ROIs on spatial.
plotSpatial	Plot cells based on spatial coordinates.
plotUMAP	Plot reduced dimensions.
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
[-method	Subset for grid level analysis