This code is for my AM 881 (Introduction to Mathematical Oncology) final project. The code replicates and analyzes the PKPD model presented in Kirouac et al., Nature Biotechnology, 2023.
- mod_eqns model equations
- driver_allpatients.m Run simulations for all the VPs presented in Kirouac et al., 2023. Model results are saved to directory "sims_patients"
- plot_allpatients.m Plot the results from driver_allpatients.m. This is used to make Fig. B.1, B.2, and B.3
- parameter_PCA.m conduct PCA and plot results for the 36 VPs from Kirouac et al., 2023. This is used to make Fig. B.4 and B.5
- param_hists.m Loads and creates histograms of the parameters for the 36 VPs from Kirouac et al., 2023. This is used to make Fig. B.6, B.7, B.8
- generateVPparams.m Generates parameter set for VPs. Results are saved to directory "VP"
- simulateVP.m Simulate CART therapy for each VP in the VP set generated from generateVPparams
- sortVP.m Creates labels for each of the VP based on the simulation results. NOTE: This requires the directory VPsims (see below) or will need to conduct simulations using simulateVP.m first.
- VP_paramPCA.m Conduct PCA on the VP population results. Makes Fig. C.1.
- VPparams_hist.m Conducts ANOVA test for each parameter and plots a histogram of the values for diverges, responders, and non-responders. Makes Fig. C.2 and C.3 - C.8
The VP simulation data directory VPsims has been uploaded to https://figshare.com/articles/dataset/VP_simulations_for_CART_project/25612824. This is required to run "sortVP.m".