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Plot the summary output from Kraken.

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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:

>>> 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()])

Simple Tree Example

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