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 ...
Prepackage for APEC-2021 analyses
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)
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())