silhouetteRank

Previously: calculate_spatial_genes_python. This method computes a silhouette score per gene based on the spatial distribution of two partitions of cells (expressed L1, and non-expressed L0). Here, rather than L2 Euclidean norm, it uses a rank-transformed, exponentially weighted function to represent the local physical distance between two cells. New multi aggregator implementation can be found at silhouetteRankTest

silhouetteRank(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  metric = "euclidean",
  subset_genes = NULL,
  rbp_p = 0.95,
  examine_top = 0.3,
  python_path = NULL,
  return_gobject = F
)

Arguments

gobject

giotto object

expression_values

expression values to use

metric

distance metric to use

subset_genes

only run on this subset of genes

rbp_p

fractional binarization threshold

examine_top

top fraction to evaluate with silhouette

python_path

specify specific path to python if required

Value

data.table with spatial scores