extract_hrchy_seurat: Extract hierarchy from Seurat object (Data-driven approach)

In byzhang23/TreeCorTreat: Tree-based correlation screen for phenotype-associated transcriptomic features and cell types

Extract hierarchy from Seurat object (Data-driven approach)

Description

This function takes in either Seurat object or phylogenetic tree and generates hierarchy information.

Usage

extract_hrchy_seurat(input, type = "phylo_tree")

Arguments

input	An input data
type	Input data type, must be one of 'phylo_tree' (default) or 'seurat_object'.

Value

A list of hierarchy information:

• edges: a data frame that documents that parent-children relationship.

• layout: a data frame that contains id, xy coordiates, label and a leaf indicator for each node.

• immediate_children: a data frame that captures immediate children for each node.

• leaves_info: a data frame that summarizes leaf children for each node.

Author(s)

Boyang Zhang <[e-mail]>, Hongkai Ji

Examples

# Assume seurat_object is obtained after running treecor_harmony()
extract_hrchy_seurat(seurat_object, type = 'seurat_object')

byzhang23/TreeCorTreat documentation built on May 7, 2024, 8:37 a.m.