semvec/pypi-packages huggingface dataset:
krakenplot 0.1.0
Plot the summary output from Kraken.
License: MIT
Keywords: kraken tree phylogeny taxonomy classification

# krakenplot

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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")