# Spatial Neighborhood Modeling and Differential Expression Analysis for Transcriptomics

## Documentation for package ‘SpNeigh’ version 1.1.0

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

## Help Pages

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
colors15_cheng | Custom Color Palette
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
theme_spneigh | Custom ggplot2 theme