diversity.py

Calculate and plot for two sample categories: Shannon diversity, Chao1 diversity, and a Jaccard similiarity distance matrix heatmap.

usage: usage: diversity.py [-h][-c {shannon,chao1,jaccard} [{shannon,chao1,jaccard} ...]] [-p IMAGE_TYPE] map_file biom_file category plot_title out_dir

Required arguments

map_file

QIIME mapping file.

biom_file

BIOM table file name

category

Specific category from the mapping file.

plot_title

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

out_dir

The directory all plots will be saved to.

Optional arguments

-h, --help

show this help message and exit

-c {shannon,chao1,jaccard} [{shannon,chao1,jaccard} ...]

Choose the type of calculation needed. Default value is “None”, which will output all 3 types of calculations.

-p IMAGE_TYPE, --image_type IMAGE_TYPE

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