Metadata-Version: 2.1
Name: krakenplot
Version: 0.1.0
Summary: Plot the summary output from Kraken.
Home-page: https://github.com/clintval/krakenplot
Author: clintval
Author-email: valentine.clint@gmail.com
License: MIT
Download-URL: https://github.com/clintval/krakenplot/archive/v0.1.0.tar.gz
Project-URL: Documentation, https://krakenplot.readthedocs.io
Project-URL: Issue-Tracker, https://github.com/clintval/krakenplot/issues
Description: # krakenplot
        
        [![Testing Status](https://travis-ci.org/clintval/krakenplot.svg?branch=master)](https://travis-ci.org/clintval/krakenplot)
        [![codecov](https://codecov.io/gh/clintval/krakenplot/branch/master/graph/badge.svg)](https://codecov.io/gh/clintval/krakenplot)
        [![Documentation Build Status](https://readthedocs.org/projects/krakenplot/badge/?version=latest)](https://krakenplot.readthedocs.io/en/latest/?badge=latest)
        [![PyPi Release](https://badge.fury.io/py/krakenplot.svg)](https://badge.fury.io/py/krakenplot)
        [![Python Versions](https://img.shields.io/pypi/pyversions/krakenplot.svg)](https://pypi.python.org/pypi/krakenplot/)
        [![MyPy Checked](http://www.mypy-lang.org/static/mypy_badge.svg)](http://mypy-lang.org/)
        [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
        
        Analysis and plotting library for base substitution spectra and signatures.
        
        ```bash
        ❯ pip install krakenplot
        ```
        
        Features that may be implemented include:
        
        - Bar plot or scatter plot integration showing the magnitude of sequences assigned to each node in the phylogenetic tree.
        - Method for _forcing_ all counts either up or down a linear branch to simplify sequence classification.
        - Clade collapsing based on taxonomic assignment and phylogenetic order.
        
        Read the documentation at: [krakenplot.readthedocs.io](http://krakenplot.readthedocs.io/)
        
        ```python
        >>> from krakenplot import KrakenSummary
        >>> summary = KrakenSummary('sample-report.txt')
        >>> summary.newick
        '(((Mus musculus musculus:1):1,(Rattus norvegicus albus:1):1,Homo sapiens:1),unclassified:1);'
        ```
        
        ```python
        >>> canvas, coords = summary.toytree.draw(
        >>>     width=500,
        >>>     height=175,
        >>>     tip_labels_color=['red', 'black', 'black', 'black'],
        >>>     # Make Carl Linnaeus proud and italicize those species names!
        >>>     tip_labels=[f'<i>{l}</i>' for l in summary.toytree.get_tip_labels()])
        ```
        
        ![Simple Tree Example](docs/img/simple-tree.png "Simple Tree Example")
Keywords: kraken tree phylogeny taxonomy classification
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Description-Content-Type: text/markdown
