createSpatialEnrich

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

createSpatialEnrich(...)

Arguments

...

...	Arguments passed on to `runSpatialEnrich` `gobject` Giotto object `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

Arguments passed on to runSpatialEnrich

gobject: Giotto object
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