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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]
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.
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 alpha_div_collated/ -m Fasting_Map.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 alpha_div_collated/ -m Fasting_Map.txt -d 180 -g pdf
Use Prefs File:
You can also supply a preferences file ‘-p’, as follows
make_rarefaction_plots.py -i alpha_div_collated/ -m Fasting_Map.txt -d 180 -p prefs.txt
Set Background Color:
Alternatively, you can set the plot background ‘-k’
make_rarefaction_plots.py -i alpha_div_collated/ -m Fasting_Map.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 alpha_div_collated/ -m Fasting_Map.txt -w
Generate average tables and per-sample plots:
Pass –generate_average_tables and –generate_per_sample_plots to generate average tables of results as tab-separated text and per-sample plots for each of the metadata categories
make_rarefaction_plots.py -i alpha_div_collated/ -m Fasting_Map.txt --generate_average_tables --generate_per_sample_plots