lineage_tree: Lineage Figures - Lineage Tree

In KathrynCampbell/MADDOG: Lineage Designation and Assignment

Lineage Figures - Lineage Tree

Description

This group of Lineage Figure functions produce figures to assist in interpretation of lineage data.

Usage

lineage_tree(lineage_info, node_data, tree, metadata, sequence_data)

Arguments

lineage_info	The output of the lineage_info function
node_data	The output of the node_info function
tree	A phylogenetic tree
metadata	The metadata corresponding to the sequences in the tree, including "ID" "assignment" "country" and "year"
sequence_data	The output of the seq_designation function

Details

This function produces a lineage tree with a lineage bar to visualise the phylogenetic positions of the lineages. The outputs of the seq_designation, node_info and lineage_info functions are required, along with the phylogenetic tree and corresponding metadata file used as input for the sequence data, node info and lineage information.

Value

A lineage tree with a lineage bar to visualise the phylogenetic positions of the lineages

KathrynCampbell/MADDOG documentation built on April 14, 2025, 10:40 a.m.