Man pages for SWittouck/tidyorthogroups
A Grammar of Genome Data Manipulation
| 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 |
