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.