Probabilistic RNA Folding Visualization Tool

Donut Diagram

File: donut.py
Author: Vincent Beaulieu
Date: 14 September 2022

Suggestion from Dr. Nawwaf Kharma - Concordia University

Info:

Display in a circular diagram the folding probabilities of an RNA sequence using a coolwarm colormap. The generated output can then be used to detect genotypic patterns from a population displaying similar phenotypes by overlaying their diagrams.

Requirements:

• The probability matrix ".prob" generated by VARNA RNA.
• The whole rna sequence used for the folding (eg.: a fasta/txt/csv/etc. file containing the sequence).
• The networkx library available at https://networkx.org.
• The csv, matplotlib, and numpy libraries.

Comments:

This code is mostly generalized and may require minimal modification to adapt it to your particular file input.
These modifications are:

• The filepath.
• The line number at which the whole RNA sequence is situated in the input file.
• The styles parameters:
  • Relative edge thickness enabled/disabled (parameter: edge_thickness_control)
  • Edge thickness multiplier (parameter: weight)
  • Plot style white/grey/black

Output Example:

Black/White/Grey background with Relative Edges Thickness

Grey background with Constant Edges Thickness

This software is licensed under the MIT license. See the "LICENSE" file for more details.