This repo provides code and files to reproduce analyses for my paper on the evolution of hypermutated tumors. This readme will explain the file structure, documentation and reproducibility instructions.
Environment: All jupyter notebooks and python scripts within this repository are run in python 2.7. All R scripts are run using R version 3.5. Scripts not contained in this notebook and used to generate files are referred to in generate_all_files_and_plots.ipynb and are hosted on the juno computational cluster
Files This repository contains all ipython, R and python scripts used to generate project plots except where otherwise specified in generate_all_files_and_plots.ipynb. All files in the /files directory are hosted on google drive at link_. Download the directory at this link and drag it to the files directory
Directory Map
evolution_of_hypermutation
│ README.md
│ fileDirectory.txt (identifiers and paths to all project files)
│ generate_all_files_and_plots.ipynb (ipython cells/written documentation of where files came from/how to create them)
│
└───scripts
│ └───figure1
| | | make_figure_1.ipynb (all code to make figure 1 dataframes)
| | | make_figure1_supplementary_figures.ipynb (all code to make figure S1 dataframes)
| | | plotFigure1.R (plots all figure1 panels)
| | | plotSupplementaryFiguresFig1.R (plots all Supplemental Figure 1 panels)
| | |
| | └───FIGURE1_PLOTTING_FILES (figure plots and dataframes used to generate them)
| | |
| | | └───figurePdfs (PDFs of figures)
| | | | | figure1.pdf (combined pdf with all figure 1 plots)
| | | | | figureS1.pdf (combined pdf with all figure 1 supplemental plots)
| | | | | figure1a.pdf (indidual panel figures)
| | | | | figureS1a.pdf (individual supplemental figures)
| | | | | ...
| | | |
| | | └───plotDataFiles (tsvs used to generate pdf plots--note not all figures have individual tsvs)
| | | | | figure_1b.tsv
| | | | | figure_S1a.tsv
| | | | | ...
| | | | |
│ └───figure2 (same structure figure 1)
| |
│ └───figure3 (same structure figure 1)
| |
│ └───utilityScripts (various python scripts imported throughout project or used for standalone file generation)
│
└───files
| |
| └───infoFiles (files with general reference data: i.e cancer type, gene expression, msi scores)
| |
| └───expectedMutationInfo (files specific to analysis modules related to estimating expected mutation burdens)
| |
| └───mafs (all maf files--annotated, unannotated, cohort specific, pan cohort)