Package index • SpNeigh

All functions

addBoundary(): Add boundary outlines to a spatial ggplot
addBoundaryPoly(): Add boundary polygons or linestrings to a spatial plot
boundaryPolyToPoints(): Convert boundary polygons to boundary point coordinates
buildBoundaryPoly(): Convert boundary points into valid polygon geometries
computeBoundaryWeights(): Compute spatial weights based on distance to nearest boundary
computeCentroidWeights(): Compute spatial weights based on distance to the centroid
computeSEI(): Compute Spatial Enrichment Index (SEI)
computeSpatialEnrichmentIndex(): Compute Spatial Enrichment Index (SEI) for Each Gene
computeSpatialInteractionMatrix(): Compute a spatial neighborhood interaction matrix using K-nearest neighbors (KNN)
extractCoords(): Extract spatial coordinates and cluster information
factorNaturalOrder(): Create a factor with natural (human-friendly) ordering
getBoundary(): Extract spatial boundary points for a cluster or cell population
getCellsInside(): Identify cells located within spatial boundaries or ring regions
getInnerBoundary(): Generate an inner boundary polygon by shrinking an existing boundary inward
getOuterBoundary(): Generate an outer or inner boundary polygon by buffering an existing boundary
getRingRegion(): Generate ring regions between a boundary and its outer buffer
plotBoundary(): Plot spatial cell coordinates with cluster boundaries
plotCellsInside(): Plot cells located within spatial boundaries or ring regions
plotEdge(): Plot boundary edges or segmented boundary lines
plotExpression(): Plot gene expression across spatial coordinates
plotInteractionMatrix(): Plot a heatmap of a row-scaled spatial interaction matrix
plotRegion(): Plot filled spatial regions inside boundaries or rings
plotSpatialExpression(): Plot average gene expression along spatial distance
plotStatsBar(): Bar plot of cluster statistics for cells inside boundaries or ring regions
plotStatsPie(): Pie chart or donut chart of cluster proportions inside spatial regions
plotWeights(): Plot spatial weights for cells on a spatial plot
removeOutliers(): Removes spatial outlier cells based on local k-nearest neighbor distances
runLimmaDE(): Differential expression analysis between two groups of cells using limma
runSpatialDE(): Differential expression along spatial distance gradients using splines
safeColorPalette(): Generate a safe color palette for discrete clusters
splineDesign(): Generate an orthonormal spline-based design matrix
splitBoundaryPolyByAnchor(): Split a polygon boundary into two parts using anchor points
statsCellsInside(): Summarize cell counts and proportions inside spatial regions
colors15_cheng: Custom Color Palette
theme_spneigh(): Custom ggplot2 theme