This repository contains code and data required to reproduce the results in ().

More detailed instructions are given in the markdown files in the code/ subdirectory.

figure_1.Rmd Contains code to reproduce figure 1. Provides instructions on how to reproduce the Ilastik image analysis. Saves output of image analysis for use in downstream parameter estimation.

figure_2.Rmd Contains code to reproduce figures 2 & S1. Saves output of tumour volume analysis for use in downstream parameter estimation.

figure_3.Rmd Contains code to reproduce figure 3. Saves output of gene expression analysis for use in downstream parameter estimation.

figure_4.Rmd Contains code to reproduce figures 4 & S2.

figure_5.Rmd Contains code to reproduce figures 5 &S2-9.