GPGraph

Genotype-phenotype maps in NetworkX

Port a GenotypePhenotypeMap to a NetworkX Digraph.

Basic Example

GPGraph follows NetworkX syntax. Initialize a graph, add the genotype-phenotype map object, and draw the graph. This library even comes with a draw method, draw_gpgraph, suited for genotype-phenotype graphs.

from gpmap.simulate import MountFujiSimulation
from gpgraph import GenotypePhenotypeGraph
from gpgraph.pyplot import draw_gpgraph, draw_edges

# Simulate a genotype-phenotype map
sim = MountFujiSimulation.from_length(4, roughness_width=1)

# Turn the genotype-phenotype map into a networkx object
G = GenotypePhenotypeGraph(sim)

# Draw the graph
figure = draw_gpgraph(G,
                      edge_colors = 'gray', 
                      node_size=400)

Install

Clone this repo and install with pip:

pip install -e .

To develop

Clone this repo and run setup.py as follows

python setup.py develop --user

This way, if only python scripts are being changed nothing has to be reinstalled.