This repository contains the figures generated for the manuscript publication of RADSuite.

Large data files

To clone this repository to your device, you'll need access to Github's Large File Storage. If you don't already have this downloaded, first download it at https://git-lfs.com/

Next, run this command in a terminal such as git bash:

# shell
git lfs install

You should now be ready to clone the repository.

Set working directory

After all dependencies have been installed, set the working directory to the figures directory:

    # R
    setwd("your/path/to/figures")

Dependencies

Figure 2 has three package dependencies: Biostrings, tidyverse, and here. If any of these dependencies are not installed, run the corresponding line in the R command line to install them:

Biostrings

    # R
    install.packages("BiocManager")
    BiocManager::install("Biostrings")

tidyverse

    # R
    install.packages("tidyverse")

here

    # R
    install.packages("here")

data.table

    # R
    install.packages("data.table")

ggtext

    # R
    install.packages("ggtext")

Instructions on generating figure 1

Because figure 1 contains no numerical data, it was created manually using the draw.io free software. A copy of the figure has been included here for completeness.

Instructions on generating figure 2

Figure 2 can be generated by first running the rscript "access_data.r" and then "create_figure_2.r". Both of the files needed for creating figure 2 can be found in the figure-2 directory.

To run a file in RStudio, open the file by going to File -> Open File and selecting the correct file, then use the "Source" button in the top right corner of the file window in RStudio.

Instructions on generating figure 3

First, clone this repository to your device.

After all dependencies have been installed, figure 3 can be generated by running these rscripts in this order: "load_data.r", "figure_3_presentable.R".

FAQ

I'm encountering an error that says that a data file for the figures doesn't exist.

Things to try:

Check your working directory is the figures/ directory you cloned from Github.

# R
getwd()

If it's not the figures/ directory, use the setwd() function to change your working directory to be figures/.

Restart RStudio: Sometimes, installing the dependencies requires a restart to allow the here package to correctly locate the files.