summarize_taxa_through_plots.py – A workflow script for performing taxonomy summaries and plots

Description:

The steps performed by this script are: Summarize OTU by Category (optional, pass -c); Summarize Taxonomy; and Plot Taxonomy Summary

Usage: summarize_taxa_through_plots.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --otu_table_fp

The input otu table [REQUIRED]

-o, --output_dir

The output directory [REQUIRED]

[OPTIONAL]

-p, --parameter_fp

Path to the parameter file, which specifies changes to the default behavior. See http://www.qiime.org/documentation/file_formats.html#qiime-parameters. [if omitted, default values will be used]

-m, --mapping_fp

Path to the mapping file [REQUIRED if passing -c]

-f, --force

Force overwrite of existing output directory (note: existing files in output_dir will not be removed) [default: None]

-w, --print_only

Print the commands but don’t call them – useful for debugging [default: False]

-c, --mapping_category

Summarize OTU table using this category. [default: None]

-s, --sort

Sort the OTU Table [default: False]

Output:

The results of this script is a folder (specified by -o) containing taxonomy summary files (at different levels) and a folder containing taxonomy summary plots. Additionally, if a mapping_catgory is supplied there will be a summarized OTU table. The primary interface for this output are the OUTPUT_DIR/taxa_summary_plots/*html files which are interactive plots that can be opened in a web browser (see the mouse-overs for interactivity).

Plot taxa summaries for all samples:

summarize_taxa_through_plots.py -o taxa_summary -i otu_table.biom -m Fasting_Map.txt

Plot taxa summaries on a categorical basis:

Alternatively, the user can supply a mapping_category, where the OTU is summarized based on a sample metadata category:

summarize_taxa_through_plots.py -o taxa_summary_by_treatment -i otu_table.biom -m Fasting_Map.txt -c Treatment