Ultra fast program to generate publication ready taxonomic pie charts from QIIME.
This script parses the pie_chart.html
file coming from plot_taxa_summary.py
script from QIIME (for details, visit http://qiime.org/scripts/plot_taxa_summary.html.) and do the following:
1.Maps the pie chart and legend image names to corresponding samples.
2.Copies the files to user defined directory
3.Rename the files according to sample ids
4.Merges the pie charts and legends
S. No. | Module |
---|---|
1. | fnmatch |
2. | os |
3. | getopt |
4. | PIL |
5. | re |
6. | shutil |
7. | sys |
8. | timeit |
prepare_taxa_charts.py -p path_to_pie_charts.html -c path_to_charts_folder -o output_path_to_final_images
Prerequisites for prepare_taxa_charts.py
-
Python version 2.7
-
The legend files should be generated in png format (default is pdf). This could be achieved by running the script
plot_taxa_summary.py
with the option-t/--type_of_file as png
. Given below is an example:
plot_taxa_summary.py -i phylum.txt -l phylum -c pie -o phylum_charts/ -t png
** Note: High resolution images can be generated using the -d, --dpi option for the script plot_taxa_summary.py. See below example (setting the dpi to 100 produce good quality images):
plot_taxa_summary.py -i phylum.txt -l phylum -c pie -o phylum_charts/ -t png -d 100
This script is released under GNU GENERAL PUBLIC LICENSE, v3, 29 June 2007
Developed by - Vijay Lakhujani:
Project Scientist, Bioinformatics
NGS division, Xcelris Labs Ltd
vijay.lakhujani@xcelrislabs.com
Let's connect!
Click here