srishtidoi / extinction-therapy Goto Github PK

Code for the preprint Preventing evolutionary rescue in cancer, Srishti Patil, Armaan Ahmed, Yannick Viossat, Robert John Noble; bioRxiv 2023.11.22.568336; doi: https://doi.org/10.1101/2023.11.22.568336

Simulation data is generated using a Gillepsie implementation to generate extinction probability plots and heatmaps. Find further description in the subfolders.

The folder plotting contains scripts to calculate extinction probabilities using the analytical model and plot them along with simulation data:

1. EP_parameter_space.R and high_prob_regions.R for plots shown in Fig3A, Fig4B and FigA.4.
2. extinction_probability.R, plotting_Nq.R and plotting_extinction_probability.R for plots shown in Fig2, Fig3B,C, Fig4A, FigA.2, FigA.5 and FigA.6.
3. heatmaps_analytical.R and plotting_heatmaps.R generate the data and plots shown in FigA.7.