https://github.com/pedrofale/tumorevo
Simulate tumor evolution and generate bulk and single-cell data from it.
https://github.com/pedrofale/tumorevo
cancer simulation single-cell spatial-transcriptomics tumor-evolution
Last synced: 21 days ago
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Simulate tumor evolution and generate bulk and single-cell data from it.
- Host: GitHub
- URL: https://github.com/pedrofale/tumorevo
- Owner: pedrofale
- License: mit
- Created: 2021-11-21T00:24:51.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2025-01-21T19:33:59.000Z (4 months ago)
- Last Synced: 2025-04-10T03:18:41.864Z (about 1 month ago)
- Topics: cancer, simulation, single-cell, spatial-transcriptomics, tumor-evolution
- Language: Jupyter Notebook
- Homepage:
- Size: 805 KB
- Stars: 6
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# tumorevo
[](https://pypi.python.org/pypi/tumorevo)
[](https://github.com/pedrofale/tumorevo/actions/workflows/main.yaml)
Simulate tumor evolution under different spatial constraints. This package aims to be as awesome as [demon](https://github.com/robjohnnoble/demon_model).
`tumorevo` simulates tumor growth and and produces a Muller plot, a 2D slice of the tumor, and a clone tree.
## Installation
```bash
$ pip install tumorevo
```
## Usage
`tumorevo` contains two command line utilities: `tumorsim` and `tumorfig`.
### Simulating tumor evolution
`tumorsim` can be used to simulate the evolution of a tumor according to a specified spatial structure.
```bash
$ tumorsim --mode 1 --steps 2000 --genes 20 --carrying-capacity 5 --grid-size 20 --division-rate 0.2 --dispersal-rate 0.1
100%|████████████████████| 1999/1999 [00:07<00:00, 251.69it/s]
```
This will create a folder containing:
* `parents.csv`: file indicating each clones's parent;
* `trace_counts.csv`: file indicating the number of cells of each clone at each time step;
* `genotypes.csv`: file containing the genotypes of each clone;
* `grid.csv`: file containing the regular grid of genotypes if `mode` > 0.
Full overview:
```
$ tumorsim --help
Usage: tumorsim [OPTIONS]
Simulate tumor evolution under different spatial constraints.
Options:
-m, --mode INTEGER Spatial structure.
-k, --carrying-capacity INTEGER
Deme carrying capacity.
-g, --genes INTEGER Number of genes.
-s, --steps INTEGER Number of steps in simulation.
--grid-size INTEGER Grid size.
--division-rate FLOAT Divison rate.
--mutation-rate FLOAT Mutation rate.
--dispersal-rate FLOAT Dispersal rate.
-r, --random_seed INTEGER Random seed for the pseudo random number
generator.
--log INTEGER Logging level. 0 for no logging, 1 for info,
2 for debug.
-o, --output-path TEXT Output directory
--help Show this message and exit.
```
### Plotting tumor evolution
`tumorfig` can be used to create a Muller plot of the tumor's evolution, the 2D spatial organization of the tumor cells, and a clone tree.
```bash
$ tumorfig out/trace_counts.csv out/parents.csv --plot --grid-file out/grid.csv --normalize --remove
```
This will open a figure like this:
Full overview:
```
$ tumorfig --help
Usage: tumorfig [OPTIONS] GENOTYPE_COUNTS GENOTYPE_PARENTS
Plot the evolution of a tumor.
Options:
-c, --cells INTEGER Number of cells in slice plot.
-r, --average-radius INTEGER Average radius of circles in slice plot.
--grid-file TEXT Path to grid file.
--colormap TEXT Colormap for genotypes.
--dpi INTEGER DPI for figures.
--plot Plot all the figures.
--do-muller Make a Muller plot.
--do-slice Make a slice plot.
--do-tree Make a clone tree plot.
--normalize Normalize the abundances in the Muller plot.
--labels Annotate the clone tree plot.
--remove Remove empty clones in the clone tree plot.
-o, --output-path TEXT Directory to write figures into.
--help Show this message and exit.
```