High resolution plottiong tool for micro detection of the molecular structure of the organelle genomes
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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.
The .R files above contain the main functions.
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.
You can install Chloroplot from this GitHub repository:
install.packages("devtools")
library(devtools)
- To install Chloroplot from GitHub, you'd type:
devtools::install_github("shuyuzheng/Chloroplot")
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
[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.
Distributed under the Mozilla Public License 2.0
ali.amiryousefi@helsinki.fi - Ali Amiryousefi
Project Link: https://github.com/amiryousefilab/Chloroplot