make_rarefaction_plots.py – Generate Rarefaction Plots

Description:

Once the batch alpha diversity files have been collated, you may want to compare the diversity using plots. Using the results from collate_alpha.py, you can plot the samples and or by category in the mapping file using this script.

This script creates an html file of rarefaction plots based on the supplied collated alpha-diversity files in a folder or a comma-separated list of files, by passing the “-i” option. Be aware that this script produces many images for the interactive html pages, so you may choose to not create these pages. The user may also supply optional arguments like an image type (-g), and a resolution (-d).

Usage: make_rarefaction_plots.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_dir

Name of folder containing rarefaction files, takes output from collate_alpha.py. The user can also supply a list of files, which are comma-separated. [REQUIRED]

-m, --map_fname

Name of mapping file [REQUIRED]

[OPTIONAL]

-b, --colorby

Name of columns to make rarefaction graphs of, comma delimited no spaces.

-p, --prefs_path

Preferences file for coloring of columns.

-k, --background_color

Background color for graphs.

-g, --imagetype

Extension for image type choose from (png, svg, pdf). WARNING: Some formats may not properly open in your browser! [default: png]

-d, --resolution

Output image resolution, [default: 75]

-y, --ymax

This is the ymax value to be used for the plots, so you can compare rarefaction plots between two different analyses [default: None]

-w, --webpage

This is allows to user to not create the webpage, which may be slow with large datasets [default: True]

-o, --output_dir

Path to the output directory

Output:

The result of this script produces a folder and within that folder there is a sub-folder containing image files. Within the main folder, there is an html file.

Default Example:

For generated rarefaction plots using the default parameters, including the mapping file and one rarefaction file, you can use the following command:

make_rarefaction_plots.py -i collated_alpha/ -m mapping_file.txt

Specify Image Type and Resolution:

Optionally, you can change the resolution (“-d”) and the type of image created (“-i”), by using the following command:

make_rarefaction_plots.py -i collated_alpha/ -m mapping_file.txt -d 180 -g pdf

Use Prefs File:

You can also supply a preferences file “-p”, as follows

make_rarefaction_plots.py -i collated_alpha/ -m mapping_file.txt -d 180 -p prefs.txt

Set Background Color:

Alternatively, you can set the plot background “-k”, as follows: a preferences file “-p”, as follows

make_rarefaction_plots.py -i collated_alpha/ -m mapping_file.txt -k black

Generate raw data without interactive webpages:

The user can choose to not create an interactive webpage (“-w” option). This is for the case, where the user just wants the average plots and the raw average data.

make_rarefaction_plots.py -i collated_alpha/ -m mapping_file.txt -w