Data types

qdiv uses five primary data types:

• tab: A table with counts or relative abundances. Features (e.g. species, OTUs, ASVs, MAGs, or bins) are row indices and samples are column headings.

• tax: A table with taxonomic information for the features. Column headings are typically Domain, Phylum, Class, Order, Family, Genus, and Species, although other taxonomic levels are also supported.

• seq: A table containing the sequence of each feature. This is typically used for amplicon sequencing data and is loaded from a FASTA file.

• meta: A table containing metadata about the samples. Sample names are row indices and the columns contain sample attributes such as treatment, location, time point, or environmental measurements.

• tree: A phylogenetic tree loaded from a Newick-formatted file.

  The tree representation consists of two components:

  • tree: A pandas DataFrame containing all nodes, branches, and branch lengths.

  • leaf_order: A list containing the names of all leaf nodes ordered internally by qdiv.

All data are stored as pandas DataFrames (and, for phylogenetic trees, a DataFrame together with a corresponding leaf_order list) within a qdiv.MicrobiomeData object.

The underlying data can be accessed and exported directly. For example, to save the abundance table:

obj.tab.to_csv("your_chosen_file_name.csv")

To save all data present in a MicrobiomeData object to the appropriate file formats:

obj.save(savename = "My_data")