summarize_taxa_through_plots.py
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