beta_diversity.py – Calculate beta diversity (pairwise sample dissimilarity) on one or many otu tables

Description:

The input for this script is the OTU table containing the number of sequences observed in each OTU (rows) for each sample (columns). For more information pertaining to the OTU table refer to the documentation for make_otu_table. If the user would like phylogenetic beta diversity metrics using UniFrac, a phylogenetic tree must also be passed as input (see make_phylogeny.py). The output of this script is a distance matrix containing a dissimilarity value for each pairwise comparison.

A number of metrics are currently supported, including unweighted and weighted UniFrac (pass the -s option to see available metrics). In general, because unifrac uses phylogenetic information, one of the unifrac metrics is recommended, as results can be vastly more useful (Hamady & Knight, 2009). Quantitative measures (e.g. weighted unifrac) are ideally suited to revealing community differences that are due to changes in relative taxon abundance (e.g., when a particular set of taxa flourish because a limiting nutrient source becomes abundant). Qualitative measures (e.g. unweighted unifrac) are most informative when communities differ primarily by what can live in them (e.g., at high temperatures), in part because abundance information can obscure significant patterns of variation in which taxa are present (Lozupone et al., 2007). Most qualitative measures are referred to here e.g. “binary_jaccard”. Typically both weighted and unweighted unifrac are used.

Usage: beta_diversity.py [options]

Input Arguments:

Note

[OPTIONAL]

-i, --input_path

Input path: otu table, or dir of otu tables for batch mode

-r, --rows

Compute only these rows of the distance matrix. pass a list of sample names, e.g. “s1,s3” [by default, + the full n x n matrix is generated]

-o, --output_dir

Output directory, will be created if doesn’t exist

-m, --metrics

Metrics to use, comma delimited if >1 metric, no spaces

-s, --show_metrics

Show available beta diversity metrics and quit. “binary_...” specifies that a metric is qualitative, and considers only the presence or absence of each taxon

-t, --tree_path

Path to newick tree file, required for phylogenetic metrics [default: None]

-f, --full_tree

By default, we first compute the intersection of the tree with the otus present in the otu table. pass -f if you already have a minimal tree, and this script will run faster

Output:

Each file in the input directory should be an otu table, and the output of beta_diversity.py is a folder containing text files, each a distance matrix between samples corresponding to an input otu table.

Single File Beta Diversity:

To perform beta diversity (using e.g. euclidean distance) on a single OTU table, where the results are output to beta_div.txt, use the following command:

beta_diversity.py -i otu_table.txt -m euclidean -o beta_div/

Note: Since this is a non-phylogenetic metric, the tree does not need to be supplied.

In the case that you would like to perform beta diversity using a phylogenetic metric (e.g. weighted_unifrac), you can use the following command:

beta_diversity.py -i otu_table.txt -m weighted_unifrac -o beta_div/ -t repr_set.tre

Multiple File (batch) Beta Diversity:

To perform beta diversity on multiple OTU tables (resulting files from multiple_rarefactions.py), specify an input directory (e.g. rarefaction_tables/) as shown by the following command:

beta_diversity.py -i rarefaction_tables/ -m weighted_unifrac -o beta_div/ -t repr_set.tre