Triangle Plot for Ribosome Profiling Data#

Overview#

This script is an additional tool for ORFribo located in the Extra_Scripts directory on Github. It generates a triangle plot that helps analyze in-frame and out-of-frame ribosome occupancy across coding sequences (CDS).

Installation & Dependencies#

The script automatically checks for and installs missing dependencies. If you want to ensure all required packages are installed manually, run:

install.packages(c("ggplot2", "ggbeeswarm", "ggpubr", "plotrix", "RColorBrewer", "ineq", 
                    "ggExtra", "ggridges", "proxy", "dplyr", "seqinr", "stringr"), 
                 repos = "http://cran.rstudio.com/")

Usage#

1. Running the Script#

To execute the script from the command line:

Rscript triangle_plot.R input_data.csv output_plot.pdf feature_column blue grey red

Parameters:

input_data.csv: Path to the input CSV file.

output_plot.pdf: Path to the output PDF file.

blue grey red : (Optional) Colors for low, mid, and high intensity.

2. Example :#

Rscript triangle_plot.R data.csv output.pdf HCA "darkblue" "lightgrey" "darkred"

My Image