Spatial Random Effects Clustering of Single Cell Data

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Documentation for package ‘spruce’ version 0.99.1

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build_knn_graph Make KNN network
coords_df_sim stx Mouse brain coordinates
fit_msn Multivariate skew-normal mixture model clustering
fit_msn_PG_smooth Multivariate skew normal mixture model clustering - PG multinom regression Spatial smoothing
fit_msn_smooth Spatial multivariate skew normal mixture model clustering
fit_mvn Multivariate normal mixture model clustering
fit_mvn_MCAR Multivariate normal spatial mixture model clustering
fit_mvn_PG Multivariate normal mixture model clustering - PG multinom regression
fit_mvn_PG_CAR Multivariate normal mixture model clustering - PG multinom regression w/ CAR random effect
fit_mvn_PG_CAR_MCAR Multivariate normal spatial mixture model clustering w/ PG multinomial regression on membership probabilities
fit_mvn_PG_CAR_MCAR_smooth Multivariate normal spatial mixture model clustering w/ PG multinomial regression on membership probabilities with spatial smoothing
fit_mvn_PG_CAR_smooth Multivariate normal mixture model clustering - PG multinom regression w/ CAR random effect and spatial smoothing
fit_mvn_PG_MCAR Multivariate normal spatial mixture model clustering w/ PG multinomial regression on membership probabilities
fit_mvn_PG_MCAR_smooth Multivariate normal spatial mixture model clustering w/ PG multinomial regression on membership probabilities and spatial smoothing
fit_mvn_PG_smooth Multivariate normal mixture model clustering - PG multinom regression Spatial smoothing
fit_mvn_smooth Spatial multivariate normal mixture model clustering
fit_spruce Fit spruce Bayesian spatial mixture model
get_map Get MAP estimate of cluster indicators
get_psi_sums Sum all neighboring psis
get_scores Calculate cluster uncertainty
plot_deltas Plot delta parameters from multinomial regression model
psi_sums Sum neighboring psis in spot i
remap_canonical2 Canonical re-mapping of mixture component labels
spruce SPRUCE