coloc module

Focused on differential co-localization

OvsE_coloc_test	Observed vs Expected log2 ratios filtered by p-value obtained from comparing them against a background distribution
OvsE_coloc_test_adjPval	Observed vs Expected log2 ratios filtered by adjusted p-value from a per-pair background distribution.
cellCatContained	Check if a cell group (niche/type/category) is contained in a cell type pair
colocNW	(Differential) co-localization network
compute_sc_spatial_knn_coloc_matrix	Compute a kNN-based co-localization probability matrix between cell type pairs.
compute_sc_spatial_radius_coloc_matrix	Compute a radius-based co-localization probability matrix between cell type pairs.
diffColoc_test	Differential co-localization test with table of scores and p-values as output
getColocProbs	Vectorized calculation of cell type pair co-localization probabilities per sample (sum across spots of probabilities of each cell type pair being in the same spot)
reshapeColoc	Transforms matrix obtained with getColocProbs into a matrix of CT pairs x samples CTcoloc=previously obtained colocalisation matrix from getColocprobs complete=list with repeated values (ct1_x_ct2 and ct2_x_ct1)
spatialCTPlot	Plot cell types in spatial data (MERFISH / visium slices)
spatialNichePlot	Plot niches in spatial data (MERFISH / visium slices)
spatialSingleCTPlot	Plot a single cell type proportions in spatial data (MERFISH / visium slices)