Spatial Neighborhood Modeling and Differential Expression Analysis for Transcriptomics

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Documentation for package ‘SpNeigh’ version 0.99.43

• 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