compare_alpha_diversity.py – This script compares alpha diversities based on a two sample t-test

Description:

This script compares the alpha diversity of entries in a rarefaction file after they have been grouped based on some category found in the mapping file based on a two sample t-test. The output file contains the (Category: (Subcategories): t, prob). By default the two sample t-test will be nonparametric (i.e. using Monte Carlo permutations to calculate the p-value), though the user has the option to make the test a parametric t-test.

Usage: compare_alpha_diversity.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --alpha_diversity_filepath

Path to collated alpha diversity file (as generated by collate_alpha.py) [REQUIRED]

-m, --mapping_filepath

Path to the mapping file [REQUIRED]

-c, --category

Category for comparison [REQUIRED]

-d, --depth

Depth of rarefaction file to use [REQUIRED]

-o, --output_filepath

Output file path [REQUIRED]

[OPTIONAL]

-t, --test_type

The type of test to perform when calculating the p-values. Valid choices: parametric, nonparametric. If test_type is nonparametric, Monte Carlo permutations will be used to determine the p-value. If test_type is parametric, the num_permutations option will be ignored and the t-distribution will be used instead [default: nonparametric]

-n, --num_permutations

The number of permutations to perform when calculating the p-value. Must be greater than zero. Only applies if test_type is nonparametric [default: 999]

Output:

Script generates an output nested dictionary which has as a first key:value pair the category passed, and a dictionary which gives the t_two_sample score for every possible combination of the values under that category in the mapping file, saved as a text file into the directory specified by the output path.

Comparing alpha diversities:

The following command takes the following input: a mapping file (which associaties each sample with a number of characteristics), alpha diversity metric (the results of collate_alpha for an alpha diverity metric, like PD_whole_tree), depth (the rarefaction depth to use for comparison), category (the category in the mapping file to determine which samples to compare to each other), and output file path (a path to the output file). A nonparametric two sample t-test is run to compare the alpha diversities using the default number of Monte Carlo permutations (999).

compare_alpha_diversity.py -i PD_whole_tree.txt -m mapping.txt -c Treatment -d 100 -o PD_d100.txt

Parametric t-test:

The following command runs a parametric two sample t-test using the t-distribution instead of Monte Carlo permutations.

compare_alpha_diversity.py -i PD_whole_tree.txt -m mapping.txt -c Treatment -d 100 -o PD_d100_parametric.txt -t parametric