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

add_exclusivityAdd exclusivity of phylogroups
add_gcdAdd gene content distance
add_genome_metadataAdd genome metadata to tidygenomes object
add_orthogroup_measuresAdd various orthogroup measures to the orthogroup table
add_patternsAdd presence/absence patterns to a tidygenomes object
add_phylogroup_colorAdd color variable for phylogroups
add_phylogroup_measuresAdd various phylogroup measures to the phylogroup table
add_phylogroupsAdd phylogroups to a tidygenomes object
add_rootbranchAdd a branch to the root of the tree
add_tidygenomesAdd a tidygenomes object to a tidygenomes object
as_tidygenomesCreate a new tidygenomes object
collapse_speciesCollapse species pangenomes
complete_pairsComplement the pairs of a pair table
filter_genomesFilter the genomes of a tidygenomes object
filter_orthogroupsFilter the orthogroups of a tidygenomes object
genomesReturn a genome table
ggtree_augmentedCall 'ggtree()' and add metadata
heatmapConstruct an heatmap to explore a pair variable
inflate_pangenomeInflate one of the pangenomes of a metapangenome
map_patternsMap presence/absence patterns to the tree
pairsReturn a pair table
pangenome_matrixReturn a pangenome matrix
prepare_tidygenomesPrepare tidygenomes object
read_pangenomeRead pangenome from a file or folder
read_phylip_distmatRead a phylip formatted distance matrix
remove_phylogroupsRemove phylogroups from a tidygenomes object
root_treeRoot tree given three genomes
root_tree.phyloRoot tree given three tips
tidygenomestidygenomes: A Grammar of Genome Data Manipulation
update_genomesUpdate the names of the genomes
upset_plotConstruct an "upset plot" to explore gene presence/absence
SWittouck/tidyorthogroups documentation built on Feb. 21, 2020, 11:16 p.m.