add_exclusivity | Add exclusivity of phylogroups |
add_gcd | Add gene content distance |
add_genome_metadata | Add genome metadata to tidygenomes object |
add_orthogroup_measures | Add various orthogroup measures to the orthogroup table |
add_patterns | Add presence/absence patterns to a tidygenomes object |
add_phylogroup_color | Add color variable for phylogroups |
add_phylogroup_measures | Add various phylogroup measures to the phylogroup table |
add_phylogroups | Add phylogroups to a tidygenomes object |
add_rootbranch | Add a branch to the root of the tree |
add_tidygenomes | Add a tidygenomes object to a tidygenomes object |
as_tidygenomes | Create a new tidygenomes object |
collapse_species | Collapse species pangenomes |
complete_pairs | Complement the pairs of a pair table |
dist2pairs | Convert dist object to pair table |
filter_genomes | Filter the genomes of a tidygenomes object |
filter_orthogroups | Filter the orthogroups of a tidygenomes object |
fix_pair_order | Fix the pair order of a genome pair table |
genomes | Return a genome table |
get_tree | Return the tree of a tidygenomes object |
ggtree_augmented | Call 'ggtree()' and add metadata |
heatmap | Construct an heatmap to explore a pair variable |
inflate_pangenome | Inflate one of the pangenomes of a metapangenome |
map_patterns | Map presence/absence patterns to the tree |
nodes_postorder | Perform postorder tree traversal |
nodes_preorder | Perform preorder tree traversal |
pairs | Return a pair table |
pairs2matrix | Convert pair table to matrix |
pangenome_matrix | Return a pangenome matrix |
prepare_tidygenomes | Prepare tidygenomes object |
read_pangenome | Read pangenome from a file or folder |
read_phylip_distmat | Read a phylip formatted distance matrix |
remove_phylogroups | Remove phylogroups from a tidygenomes object |
root_tree | Root tree given three genomes |
root_tree.phylo | Root tree given three tips |
tidygenomes | tidygenomes: A Grammar of Genome Data Manipulation |
update_genomes | Update the names of the genomes |
upset_plot | Construct an "upset plot" to explore gene presence/absence |
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