/Chloroplot

A R tool to parse and visualize chloroplast genomes

Primary LanguageR

Contributors MPL2.0 License


Chloroplot

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Table of Contents

About the Package

The R package Chloroplot wrapped the functions for visualizing the organelle genomes. We also provide a web application at https://irscope.shinyapps.io/chloroplot/ for users who prefere interactive GUI.

Built with

Getting Start

Prerequistes

Chloroplot is a package written with R programming language. Please make sure that you have installed R project ( >= V3.6) on your local machine. You can download and install R from CRAN.

Installation

You can install Chloroplot from this GitHub repository:

  1. Install and load the devtools package. You can do this from CRAN. Invoke R and then type
install.packages("devtools")
library(devtools)
  1. To install Chloroplot from GitHub, you'd type:
devtools::install_github("shuyuzheng/Chloroplot")

Usage

There are 3 main functions in Chloroplot for visualizing the organelle genomes: "PlotTab", " PlotMitGenome"and "PlotPlastidGenome". Following are two examples for utality:

library(chloroplot)
# Plot Ppchloroplast genome.

# 1. Parsing the GenBank file.
#"EU549769" is the GenBank accession for Guizotia abyssinica chloroplast 
t <- PlotTab(gbfile = "EU549769")
# 2. Generate plot
PlotPlastidGenome(t) # The plot will be saved in a pdf file under your work directory.
PlotPlastidGenome(t, save = FALSE) # The plot will be shown in the "plot" panel if you are using Rstudio.

# Plot mitochondrion genome.

# 1. Parsing the GenBank file
# "NC_012920.1" is the GenBank accession for Homo sapiens mitochondrion
t <- PlotTab(gbfile = "NC_012920.1")
# 2. Generate plot
PlotMitGenome(t) # The plot will be saved in a pdf file under your work directory.
PlotMitGenome(t, save = FALSE) # The plot will be shown in the "plot" panel if you are using Rstudio.

For further details about manipulating the visualizations. Please check the documentations for the functions, by typing following commands in the R console.

help(PlotMitGenome) # or ?PlotMitGenome
help(PlotPlastidGenome) # or ?PlotPlastidGenome

Reference

[1]: Zheng, S.; Poczai, P.; Hyvönen, J.; Tang, J.; Amiryousefi, A. Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes. Front. Genet. 2020, 11. https://doi.org/10.3389/fgene.2020.576124.

License

Distributed under the Mozilla Public License 2.0

Contact

Shuyu Zheng - shuyu.zheng@helsinki.fi ali.amiryousefi@helsinki.fi - Ali Amiryousefi

Project Link: https://github.com/shuyuzheng/Chloroplot

Acknowledgements