Automatically Infer Lineage Tree (hclust) from scRNA-seq Counts & Cell Types

Builds a hierarchical clustering lineage tree between cell-type centroids from scRNA-seq expression data.

Usage

infer_scrna_lineage_tree(data, cell_types, method = "ward.D2")

Arguments

data

Expression or count matrix (genes x cells).

cell_types

Factor or vector of cell-type annotations for each cell.

method

Linkage method for hierarchical clustering (default "ward.D2").

Value

An hclust tree object representing the cell-type lineage tree.

Examples

data(example_scrna, package = "scSimEval")
infer_scrna_lineage_tree(example_scrna$ref, example_scrna$cell_types)
#> 
#> Call:
#> stats::hclust(d = dist_mat, method = method)
#> 
#> Cluster method   : ward.D2 
#> Distance         : euclidean 
#> Number of objects: 2 
#>