output.md

Output

The output of the simulations are saved in the directory given by the user. If the directory path given by the user is /path/to/save/, then the output of the simulations will look like this:

/path/to/save/
test/
├── 10cells
│   ├── burden # single cell mutational burden mapping
│   │   ├── 0dot0years
│   │   │   ├── 0.json  # run 0
│   │   │   ├── 1.json  # run 1
│   │   │   └── ...
│   │   ├── 1dot0years
│   │   │   ├── 0.json
│   │   │   ├── 1.json
│   │   │   └── ...
│   │   └── ...
│   ├── sfs # site frequency spectrum vector
│   │   ├── 0dot0years
│   │   │   ├── 0.json
│   │   │   ├── 1.json
│   │   │   └── ...
│   │   ├── 1dot0years
│   │   │   ├── 0.json
│   │   │   ├── 1.json
│   │   │   └── ...
│   │   └── ...
│   └── variant_fraction # the subclones' abbundance
│       ├── 0dot0years
│       │   ├── 0.csv
│       │   ├── 1.csv
│       │   └── ...
│       ├── 1dot0years
│       │   ├── 0.csv
│       │   ├── 1.csv
│       │   └── ...
│       └── ...
└── rates
    ├── 0.csv
    ├── 1.csv
    └── ...

that is those measurements are saved at the end of the simulations, for each timepoint, for each run.

The file name of the runs (here 0.csv and 1.csv or 0.json and 1.json) have changed such that they incorportate the parameters that have been used to generate them, starting from version v1.1.0.

Measurements

• burden: a json file with keys being the number of mutations (single-cell mutational burden x-axis) and values being the cells with those mutations (single-cell mutational burden y-axis)
• sfs: a json file with keys being the jcells (x-axis) and values being the number of variants with jcells (y-axis).
• variant_fraction: the abbundance of all subclones
• rates: the birth-rates of the subclones, where the first entry represents the birth-rate of the wild-type b0