mergeClusters: mergeClusters
In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

mergeClusters

R Documentation

mergeClusters

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

`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
A giotto object is returned by default, if FALSE then the merging vector will be returned.