getClusterSimilarity

Creates data.table with pairwise correlation scores between each cluster.

getClusterSimilarity(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  cluster_column,
  cor = c("pearson", "spearman")
)

Arguments

gobject

giotto object

expression_values

expression values to use

cluster_column

name of column to use for clusters

cor

correlation score to calculate distance

Value

data.table

Details

Creates data.table with pairwise correlation scores between each cluster and the group size (# of cells) for each cluster. This information can be used together with mergeClusters to combine very similar or small clusters into bigger clusters.

Examples

data("mini_giotto_single_cell")
#> Warning: data set ‘mini_giotto_single_cell’ not found

cluster_similarities = getClusterSimilarity(mini_giotto_single_cell,
                                            cluster_column = 'leiden_clus')
#> Warning: restarting interrupted promise evaluation
#> Warning: restarting interrupted promise evaluation
#> Error: object 'mini_giotto_single_cell' not found