Plot the summary output from Kraken.
Project description
krakenplot
Analysis and plotting library for base substitution spectra and signatures.
❯ 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
>>> 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);'
>>> 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()])
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