spatial_patterns {spatialDE} | R Documentation |
Group spatially variable genes into spatial patterns using automatic expression histology (AEH)
spatial_patterns( x, coordinates, de_results, qval_thresh = 0.05, n_patterns, length, verbose = FALSE )
x |
|
coordinates |
|
de_results |
|
qval_thresh |
|
n_patterns |
|
length |
|
verbose |
|
list
of two dataframe (pattern_results, patterns):
pattern_results
dataframe with pattern membership information for each
gene.
patterns
the posterior mean underlying expression fro genes in given
spatial patterns.
Svensson, V., Teichmann, S. & Stegle, O. SpatialDE: identification of spatially variable genes. Nat Methods 15, 343–346 (2018). https://doi.org/10.1038/nmeth.4636
set.seed(42) mock <- mockSVG(size = 10, tot_genes = 500, de_genes = 10) stabilized <- stabilize(mock$counts) sample_info <- mock$coordinates sample_info$total_counts <- colSums(mock$counts) regressed <- regress_out(counts = stabilized, sample_info = sample_info) ## Run SpatialDE de_results <- run(x = regressed, coordinates = mock$coordinates) ## Run Spatial_patterns sp <- spatial_patterns( x = regressed, coordinates = mock$coordinates, de_results = de_results, qval_thresh = NULL, n_patterns = 5, length = 1.5 ) sp$pattern_results sp$patterns