mergeClusters#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/clustering.R#L2218

Description#

Merge selected clusters based on pairwise correlation scores and size of cluster.

Usage#

mergeClusters(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  cluster_column,
  cor = c("pearson", "spearman"),
  new_cluster_name = "merged_cluster",
  min_cor_score = 0.8,
  max_group_size = 20,
  force_min_group_size = 10,
  max_sim_clusters = 10,
  return_gobject = TRUE,
  verbose = TRUE
)

Arguments#

Argument

Description

gobject

giotto object

spat_unit

spatial unit

feat_type

feature type

expression_values

expression values to use

cluster_column

name of column to use for clusters

cor

correlation score to calculate distance

new_cluster_name

new name for merged clusters

min_cor_score

min correlation score to merge pairwise clusters

max_group_size

max cluster size that can be merged

force_min_group_size

size of clusters that will be merged with their most similar neighbor(s)

max_sim_clusters

maximum number of clusters to potentially merge to reach force_min_group_size

return_gobject

return giotto object

verbose

be verbose

Details#

Merge selected clusters based on pairwise correlation scores and size of cluster. To avoid large clusters to merge the max_group_size can be lowered. Small clusters can be forcibly merged with their most similar pairwise cluster by adjusting the force_min_group_size parameter. Clusters smaller than this value will be merged independent on the provided min_cor_score value. The force_min_group_size might not always be reached if clusters have already been merged before list() A giotto object is returned by default, if FALSE then the merging vector will be returned.

Value#

Giotto object