The ImageAnalysis folder contains code and data related to image analysis of tumour histology slides.
Within ModelOutput, each folder contains the input and output files from an instance of the demon model, which can be analysed using functions in the demonanalysis R package. For example, the following R code will draw a Muller plot, tumour clone grid, and clonal origin times plot:
install.packages("devtools")
library(devtools)
install_github("robjohnnoble/demonanalysis")
library(demonanalysis)
plot_figure2("ModelOutput/FissionModelK2046")ModesFigures.R contains code for plotting other figures from the paper.
RealTumourTreesData contains data for constructing the evolutionary trees of real tumours, sourced from published studies.