tumorevo 0.0.1

Simulate and illustrate tumor evolution under different spatial constraints.

tumorevo

Simulate tumor evolution under different spatial constraints. This package aims to be as awesome as demon. tumorevo simulates tumor growth and and produces a Muller plot, a cartoon of the 2D spatial organization of the tumor cells, and a clone tree.

Installation

$ 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.

$ 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.

$ 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.