The R script DownsampledReads.R aims at performing 4-way figures and linear regressions based on estimations of depth and breadth coverages from downsampled paired-end reads described in the "Listeria-cgMLST-Additional-file-1.tsv" of the article entitled "In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes".
The R script DownsampledReads.R was prepared and tested with R version 3.6.3 and RStudio 1.3.1093.
- library(ggplot2)
- library(plyr)
- library(reshape2)
- library(ggpubr)
- library(ggpmisc)
sudo apt update
sudo apt install r-base
R --version
sudo apt install gdebi-core
sudo gdebi /home/Downloads/rstudio-1.3.1093-amd64.deb
rstudio --version
R --version
sudo apt-get update
sudo apt-get upgrade
sudo apt-cache showpkg r-base
sudo apt-get install r-base
R --version
rstudio DownsampledReads.R
Palma F., Mangone I., Janowicz A., Moura A., Chiaverini A., Torresi M., Garofolo G., Criscuolo A., Brisse S., Di Pasquale A., Cammà C. and Radomski N. In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes. 2022, BMC Genomics, 23(235): 1-24, https://doi.org/10.1186/s12864-022-08437-4
My former colleague Laurent Guillier with whom I learned a lot about R
Nicolas Radomski