Skip to main content

Plot the summary output from Kraken.

Project description

krakenplot

Testing Status codecov Documentation Build Status PyPi Release Python Versions MyPy Checked Code style: black

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()])

Simple Tree Example

Project details


Release history Release notifications

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for krakenplot, version 0.1.0
Filename, size File type Python version Upload date Hashes
Filename, size krakenplot-0.1.0.tar.gz (4.7 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page