getClusterSimilarity: getClusterSimilarity

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

getClusterSimilarity

Description

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

Usage

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

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.

Value

data.table

Examples

data("mini_giotto_single_cell")

cluster_similarities = getClusterSimilarity(mini_giotto_single_cell,
                                            cluster_column = 'leiden_clus')

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.