diversity.py

Calculate the alpha diversity of a set of samples using one or more metrics and output a kernal density estimator-smoothed histogram of the results.

usage: diversity.py [-h] [-d DIVERSITY [DIVERSITY ...]] [--plot_title PLOT_TITLE] [--image_type IMAGE_TYPE] [--save_calculations SAVE_CALCULATIONS] [--show_significance] [--show_available_metrics] -m MAP_FILE -i BIOM_FP -c CATEGORY --color_by COLOR_BY -o OUT_DIR

Required arguments

-m MAP_FILE, --map_file MAP_FILE

QIIME mapping file.

-i BIOM_FP, --biom_fp BIOM_FP

BIOM table file name

-c CATEGORY, --category CATEGORY

Specific category from the mapping file.

--color_by COLOR_BY

A column name in the mapping file containing hexadecimal (#FF0000) color values that will be used to color the groups. Each sample ID must have a color entry.

-o OUT_DIR, --out_dir OUT_DIR

The directory all plots will be saved to.

Optional arguments

-h, --help

show this help message and exit

-d DIVERSITY [DIVERSITY ...], --diversity DIVERSITY [DIVERSITY ...]

The alpha diversity metric. Default value is ‘shannon’, which will calculate the Shannon entropy. Multiple metrics can be specified (space separated). The full list of metrics is available at: http://scikit-bio.org/docs/latest/generated/skbio.diversity.alpha.html.

--plot_title PLOT_TITLE

The name of a PDF file the pathway map will be written to.

-p IMAGE_TYPE, --image_type IMAGE_TYPE

The type of image to save: PNG, SVG, etc.

--save_calculations SAVE_CALCULATIONS

Path and name of text file to store the calculated diversity metrics.

--show_significance

Display significance testing results. The results will be shown by default.

--show_available_metrics

Supply this parameter to see which alpha diversity metrics are available for usage. No calculations will be performed if this parameter is provided.