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 tumorevoUsage
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 ifmode> 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 --removeThis 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.
