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.. _summarize_taxa_through_plots:
.. index:: summarize_taxa_through_plots.py
*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:** :file:`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
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