prepare_taxa_charts.py: A Python program to automate generation of publication ready taxonomic pie chart images from QIIME
QIIME (Quantitative Insights Into Microbial Ecology) is one of the most popular open-source bioinformatics suite for performing metagenome, 16S rRNA amplicon and Internal Transcribed Spacer (ITS) data analysis. Although, it is very comprehensive and powerful tool, it lacks a method to provide public...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2017-06-01
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| Series: | Genomics Data |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2213596016302070 |
| _version_ | 1818684442604994560 |
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| author | Vijay Lakhujani Chandan Badapanda |
| author_facet | Vijay Lakhujani Chandan Badapanda |
| author_sort | Vijay Lakhujani |
| collection | DOAJ |
| description | QIIME (Quantitative Insights Into Microbial Ecology) is one of the most popular open-source bioinformatics suite for performing metagenome, 16S rRNA amplicon and Internal Transcribed Spacer (ITS) data analysis. Although, it is very comprehensive and powerful tool, it lacks a method to provide publication ready taxonomic pie charts. The script plot_taxa_summary.py bundled with QIIME generate a html file and a folder containing taxonomic pie chart and legend as separate images. The images have randomly generated alphanumeric names. Therefore, it is difficult to associate the pie chart with the legend and the corresponding sample identifier. Even if the option to have the legend within the html file is selected while executing plot_taxa_summary.py, it is very tedious to crop a complete image (having both the pie chart and the legend) due to unequal image sizes. It requires a lot of time to manually prepare the pie charts for multiple samples for publication purpose. Moreover, there are chances of error while identifying the pie chart and legend pair due to random alphanumeric names of the images. To bypass all these bottlenecks and make this process efficient, we have developed a python based program, prepare_taxa_charts.py, to automate the renaming, cropping and merging of taxonomic pie chart and corresponding legend image into a single, good quality publication ready image. This program not only augments the functionality of plot_taxa_summary.py but is also very fast in terms of CPU time and user friendly. |
| first_indexed | 2024-12-17T10:50:42Z |
| format | Article |
| id | doaj.art-d6fce360b712429885186b8e699073fb |
| institution | Directory Open Access Journal |
| issn | 2213-5960 |
| language | English |
| last_indexed | 2024-12-17T10:50:42Z |
| publishDate | 2017-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Genomics Data |
| spelling | doaj.art-d6fce360b712429885186b8e699073fb2022-12-21T21:51:59ZengElsevierGenomics Data2213-59602017-06-0112C9710110.1016/j.gdata.2017.03.009prepare_taxa_charts.py: A Python program to automate generation of publication ready taxonomic pie chart images from QIIMEVijay LakhujaniChandan BadapandaQIIME (Quantitative Insights Into Microbial Ecology) is one of the most popular open-source bioinformatics suite for performing metagenome, 16S rRNA amplicon and Internal Transcribed Spacer (ITS) data analysis. Although, it is very comprehensive and powerful tool, it lacks a method to provide publication ready taxonomic pie charts. The script plot_taxa_summary.py bundled with QIIME generate a html file and a folder containing taxonomic pie chart and legend as separate images. The images have randomly generated alphanumeric names. Therefore, it is difficult to associate the pie chart with the legend and the corresponding sample identifier. Even if the option to have the legend within the html file is selected while executing plot_taxa_summary.py, it is very tedious to crop a complete image (having both the pie chart and the legend) due to unequal image sizes. It requires a lot of time to manually prepare the pie charts for multiple samples for publication purpose. Moreover, there are chances of error while identifying the pie chart and legend pair due to random alphanumeric names of the images. To bypass all these bottlenecks and make this process efficient, we have developed a python based program, prepare_taxa_charts.py, to automate the renaming, cropping and merging of taxonomic pie chart and corresponding legend image into a single, good quality publication ready image. This program not only augments the functionality of plot_taxa_summary.py but is also very fast in terms of CPU time and user friendly.http://www.sciencedirect.com/science/article/pii/S221359601630207016S rRNA amplicon/ITS analysisMetagenomeQIIMEPythonTaxonomyPie chart |
| spellingShingle | Vijay Lakhujani Chandan Badapanda prepare_taxa_charts.py: A Python program to automate generation of publication ready taxonomic pie chart images from QIIME Genomics Data 16S rRNA amplicon/ITS analysis Metagenome QIIME Python Taxonomy Pie chart |
| title | prepare_taxa_charts.py: A Python program to automate generation of publication ready taxonomic pie chart images from QIIME |
| title_full | prepare_taxa_charts.py: A Python program to automate generation of publication ready taxonomic pie chart images from QIIME |
| title_fullStr | prepare_taxa_charts.py: A Python program to automate generation of publication ready taxonomic pie chart images from QIIME |
| title_full_unstemmed | prepare_taxa_charts.py: A Python program to automate generation of publication ready taxonomic pie chart images from QIIME |
| title_short | prepare_taxa_charts.py: A Python program to automate generation of publication ready taxonomic pie chart images from QIIME |
| title_sort | prepare taxa charts py a python program to automate generation of publication ready taxonomic pie chart images from qiime |
| topic | 16S rRNA amplicon/ITS analysis Metagenome QIIME Python Taxonomy Pie chart |
| url | http://www.sciencedirect.com/science/article/pii/S2213596016302070 |
| work_keys_str_mv | AT vijaylakhujani preparetaxachartspyapythonprogramtoautomategenerationofpublicationreadytaxonomicpiechartimagesfromqiime AT chandanbadapanda preparetaxachartspyapythonprogramtoautomategenerationofpublicationreadytaxonomicpiechartimagesfromqiime |