Coming from R

Coming from R#

Every public biotapy function names its R equivalent in its docstring. This table is generated from those lines each time the docs are built, plus a short list of phyloseq accessors that are plain AnnData/TreeData code (docs/_data/r_idioms.toml). Rows marked “not in 0.2” have no biotapy equivalent yet.

biotapy keeps samples as rows, so tdata.X is phyloseq’s otu_table with taxa_are_rows = FALSE. Functions return new objects instead of changing yours; tl functions store their result in the object only with inplace=True.

R	biotapy
`ALDEx2::aldex`	`bt.da.aldex2`
`ANCOMBC::ancombc2`	`bt.da.ancombc2`
`ape::pcoa`	`bt.tl.pcoa`
`base::load`	`bt.io.read_phyloseq`
`base::readRDS`	`bt.io.read_phyloseq`
`biomformat::write_biom`	`bt.io.write_biom`
`maaslin3::maaslin3`	`bt.da.maaslin3`
`mia::agglomerateByRank`	`bt.pp.tax_glom`
`mia::importHUMAnN`	`bt.io.read_humann`
`mia::importMetaPhlAn`	`bt.io.read_metaphlan`
`mia::transformAssay`	`bt.pp.clr`, `bt.pp.philr`, `bt.pp.relative`
`MicrobiomeStat::linda`	`bt.da.linda`
`philr::philr`	`bt.pp.philr`
`phyloseq::distance`	`bt.tl.beta`
`phyloseq::estimate_richness`	`bt.tl.alpha`
`phyloseq::filter_taxa`	`bt.pp.filter_features`
`phyloseq::get_taxa_unique`	`tdata.var[rank].unique()`
`phyloseq::get_variable`	`tdata.obs[column]`
`phyloseq::import_biom`	`bt.io.read_biom`
`phyloseq::merge_samples`	not in 0.2
`phyloseq::nsamples`	`tdata.n_obs`
`phyloseq::ntaxa`	`tdata.n_vars`
`phyloseq::ordinate`	`bt.tl.nmds`, `bt.tl.pcoa`
`phyloseq::otu_table`	`tdata.X` (samples x features)
`phyloseq::phy_tree`	`tdata.vart["phylo"]`
`phyloseq::phyloseq`	`bt.io.read_dada2`
`phyloseq::plot_bar`	`bt.pl.bar`
`phyloseq::plot_heatmap`	`bt.pl.heatmap`
`phyloseq::plot_net`	not in 0.2
`phyloseq::plot_ordination`	`bt.pl.ordination`
`phyloseq::plot_richness`	`bt.pl.richness`
`phyloseq::plot_scree`	`bt.pl.scree`
`phyloseq::plot_tree`	not in 0.2
`phyloseq::prune_samples`	`tdata[keep].copy()`
`phyloseq::prune_taxa`	`tdata[:, keep].copy()`
`phyloseq::psmelt`	not in 0.2
`phyloseq::rank_names`	`tdata.var.columns`
`phyloseq::rarefy_even_depth`	`bt.pp.rarefy`
`phyloseq::refseq`	`tdata.var["sequence"]`, which only `bt.io.read_dada2` fills
`phyloseq::sample_data`	`tdata.obs`
`phyloseq::sample_names`	`tdata.obs_names`
`phyloseq::sample_sums`	`tdata.X.sum(axis=1)`
`phyloseq::sample_variables`	`tdata.obs.columns`
`phyloseq::subset_samples`	`tdata[tdata.obs["SampleType"] == "Feces"].copy()`
`phyloseq::subset_taxa`	`tdata[:, tdata.var["phylum"] == "Chlamydiae"].copy()`
`phyloseq::tax_glom`	`bt.pp.tax_glom`
`phyloseq::tax_table`	`tdata.var`, one column per rank
`phyloseq::taxa_names`	`tdata.var_names`
`phyloseq::taxa_sums`	`tdata.X.sum(axis=0)`
`phyloseq::tip_glom`	not in 0.2
`phyloseq::transform_sample_counts`	`bt.pp.relative`
`phyloseq::UniFrac`	`bt.tl.unifrac`
`picante::pd`	`bt.tl.alpha`
`qiime2R::qza_to_phyloseq`	`bt.io.read_qiime2`
`utils::data`	`bt.datasets.enterotype`, `bt.datasets.esophagus`, `bt.datasets.global_patterns`
`vegan::adonis2`	`bt.tl.permanova`
`vegan::decostand`	`bt.pp.clr`
`vegan::metaMDS`	`bt.tl.nmds`