# Spatial cellular neighbourhood scanning in R

## Documentation for package ‘hoodscanR’ version 1.4.0

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

## Help Pages

calcMetrics | Calculate metrics for probability matrix
clustByHood | Cluster the probability matrix with K-means
clustByHood-method | Cluster the probability matrix with K-means
findNearCells | Find the k-th nearest cells for each cell
mergeByGroup | Merge probability matrix based on annotations
mergeHoodSpe | Merge probability matrix into SpatialExperiment object.
perplexityPermute | Compute p-value for perplexity via permutation
plotColocal | Plot heatmap for neighbourhood analysis
plotColocal-method | Plot heatmap for neighbourhood analysis
plotHoodMat | Plot probability matrix as a heatmap
plotHoodMat-method | Plot probability matrix as a heatmap
plotProbDist | Plot probability distribution
plotProbDist-method | Plot probability distribution
plotTissue | Plot cells based on cell position on tissue.
readHoodData | Read cellular position and annotation data into a list object.
scanHoods | Scan cellular neighbourhoods.