plotnineSeqSuite: a Python package for visualizing sequence data using ggplot2 style.

Journal: BMC genomics
PMID: 37789265

Abstract

BACKGROUND: The visual sequence logo has been a hot area in the development of bioinformatics tools. ggseqlogo written in R language has been the most popular API since it was published. With the popularity of artificial intelligence and deep learning, Python is currently the most popular programming language. The programming language used by bioinformaticians began to shift to Python. Providing APIs in Python that are similar to those in R can reduce the learning cost of relearning a programming language. And compared to ggplot2 in R, drawing framework is not as easy to use in Python. The appearance of plotnine (ggplot2 in Python version) makes it possible to unify the programming methods of bioinformatics visualization tools between R and Python.

Authors

  • Tianze Cao
    School of Mathematics, Hangzhou Normal University, Hangzhou, Zhejiang Province, China.
  • Qian Li
    Emergency and Critical Care Center, Department of Emergency Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China.
  • Yuexia Huang
    School of Mathematics, Hangzhou Normal University, Hangzhou, Zhejiang Province, China. yxhuang@hznu.edu.cn.
  • Anshui Li
    Department of Statistics, Shaoxing University, Shaoxing, Zhejiang Province, China. anshuili@usx.edu.cn.

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