createSpatialEnrich#

Last Updated: May 20, 2025

Description#

Function to calculate gene signature enrichment scores per spatial position using an enrichment test.

createSpatialEnrich(...)

...

Arguments passed on to runSpatialEnrich

gobject: Giotto object
spat_unit: spatial unit
feat_type: feature type
enrich_method: method for gene signature enrichment calculation
sign_matrix: Matrix of signature genes for each cell type / process
expression_values: expression values to use
reverse_log_scale: reverse expression values from log scale
min_overlap_genes: minimum number of overlapping genes in sign_matrix required to calculate enrichment (PAGE)
logbase: log base to use if reverse_log_scale = TRUE
p_value: calculate p-value (default = FALSE)
n_times: (page/rank) number of permutation iterations to calculate p-value
rbp_p: (rank) fractional binarization threshold (default = 0.99)
num_agg: (rank) number of top genes to aggregate (default = 100)
max_block: number of lines to process together (default = 20e6)
top_percentage: (hyper) percentage of cells that will be considered to have gene expression with matrix binarization
output_enrichment: how to return enrichment output
name: to give to spatial enrichment results, default = PAGE
verbose: be verbose
return_gobject: return giotto object