silhouetteRank | R Documentation |
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
)
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 |
data.table with spatial scores
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.