Chloroplot
Tidy drug combination high-throughput screening data for DrugComb portal
Web Application
Report Bug
·
Request Feature
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:
install.packages("devtools")
library(devtools)
- 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