Pyggseqlogo

October 21, 2023 ยท View on GitHub

Python version of ggseqlogo. Based on plotnine (Python version of ggplot2). A derivative of plotnineSeqSuite.

Cite this work

Cao, T., Li, Q., Huang, Y. et al. plotnineSeqSuite: a Python package for visualizing sequence data using ggplot2 style. BMC Genomics 24, 585 (2023). https://doi.org/10.1186/s12864-023-09677-8

Installation

pip install pyggseqlogo

Getting Started

from plotnine import ggplot
from plotnineseqsuite import geom_logo
from plotnineseqsuite.data import seqs_dna
from pyggseqlogo import ggseqlogo, theme_logo

The code is based on plotnineSeqSuite.

ggplot() + geom_logo(data=seqs_dna['MA0001.1']) + theme_logo()

https://caotianze.github.io/pyggseqlogo/started_1.png
Pyggseqlogo provides a wrapper function for the above code.

ggseqlogo(seqs_dna['MA0001.1'])

https://caotianze.github.io/pyggseqlogo/started_2.png
facet_wrap

ggseqlogo(seqs_dna, ncol=4)

https://caotianze.github.io/pyggseqlogo/started_3.png

Where to go next

If you want to draw more complex sequence logos or other sequence-related diagrams, we recommend visiting the plotnineSeqSuite homepage for details.