I’m using Rstudio rmd to generate the figures and have them organized with an outline where u can click to whichever figure to see how it is generated. The file is script_result_vis.rmd
It's fine to use R Studio instead of Jupyter to make your figures, but I'd still recommend making this clearer from a reproducible research standpoint. I'd suggest:
Make a new top-level directory called figures/ in the repo
Split out your current 3800 line (!) file script_result_vis.rmd into five files titled figure_1.Rmd, figure_2.Rmd, etc... that each produce just one figure.
The PNG output from each of these files should be exactly what gets versioned in manuscript/figures/.
Add a README.md under top-level figures/ directory that describes how to install necessary R packages (maybe with something like install.packages(c("dplyr", "ggplot2", "tidyverse")), but I don't know R very well at all) and how to load and run a file in R Studio.
It's fine to use R Studio instead of Jupyter to make your figures, but I'd still recommend making this clearer from a reproducible research standpoint. I'd suggest:
figures/in the reposcript_result_vis.rmdinto five files titledfigure_1.Rmd,figure_2.Rmd, etc... that each produce just one figure.manuscript/figures/.README.mdunder top-levelfigures/directory that describes how to install necessary R packages (maybe with something likeinstall.packages(c("dplyr", "ggplot2", "tidyverse")), but I don't know R very well at all) and how to load and run a file in R Studio.