getClusterTree: getClusterTree This function takes a CATALYST sce with...

In adam2o1o/treekoR: Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations

getClusterTree This function takes a CATALYST sce with clusters and creates a hierarchical tree

Description

getClusterTree This function takes a CATALYST sce with clusters and creates a hierarchical tree

Usage

getClusterTree(
  exprs,
  clusters,
  hierarchy_method = "hopach",
  hopach_kmax = 5,
  hopach_K = 10,
  scale_exprs = TRUE
)

Arguments

exprs	a dataframe containing single cell expression data
clusters	a vector representing the cell type or cluster of each cell (can be character or numeric). If numeric, cluster names need to be consecutive starting from 1.
hierarchy_method	a string indicating the hierarchical tree construction method to be used
hopach_kmax	integer between 1 and 9 specifying the maximum number of children at each node in the tree
hopach_K	positive integer specifying the maximum number of levels in the tree. Must be 15 or less, due to computational limitations (overflow)
scale_exprs	boolean indicating whether to scale median cluster expression data before constructing hierarchical tree

Value

a list containing the cluster median frequencies and a phylogram of the hierarchical tree

Examples

library(SingleCellExperiment)
data(COVIDSampleData)

sce <- DeBiasi_COVID_CD8_samp
exprs <- t(assay(sce, "exprs"))
clusters <- colData(sce)$cluster_id
classes <- colData(sce)$condition
samples <- colData(sce)$sample_id

clust_tree <- getClusterTree(exprs,
                             clusters,
                             hierarchy_method="hopach")

adam2o1o/treekoR documentation built on June 2, 2023, 11:42 p.m.