202409245 Archiving this project Functions for APEC-2021 - could have been a package but is currently not worked on anymore (no time) - but may might be recyclabe Some nice functions for distances and phylogeny heatmap though ...

APEC-2021-Rprepackage

Prepackage for APEC-2021 analyses

Documentation

Tree visualization

packages ggtree

function: prepare_metadata function: join_metadata_assembly_names

function import: treeio::read.iqtree read.iqtree

function prepare_visualisation_tree function standard_treeplot_eve1 function save_eve function import: ggtree::get_taxa_name function root_tree_data function import is.rooted - treio or ape function import ggplot2::xlim function subset_tree ... start here function import ape::getMRCA function import ape::root

Note that rooting the tree (either midpoint or rooting according to an outgroup has to be done before linking the tree and metadata)

Distances and statistics

function import distance function distance_density_plots (make also the stats, correcting for duplicates) function distance_tree_heatmap gradient 3 colors (ok if not too many data) function distance_tree_heatmap2 (binned version < value > value and gradient in middle ) reorder_distance_matrix.R to be able to follow ordering from the plot (.packages())