demesdraw 0.4.1

drawing tools for Demes demographic models

DemesDraw

demesdraw is a Python package that contains drawing functions for Demes demographic models, using matplotlib to create the figures. DemesDraw offers both a command line interface, and a Python API. Feedback is very welcome.

Installation

Install with pip:

$ python3 -m pip install demesdraw

Or with conda:

$ conda install -c conda-forge demesdraw

Example usage

Command line interface (CLI)

The CLI can be used to quickly plot a Demes YAML file. Any image format supported by matplotlib can be specified as the output, but a vector format such as svg or pdf is recommended.

demesdraw tubes --log-time \
	examples/stdpopsim/HomSap__AmericanAdmixture_4B11.yaml \
	AmericanAdmixture_4B11_tubes.svg

Interactive plots

If an output file is not specified, then an interactive plotting window will be shown. Hovering the mouse over parts of the plot will show an annotation. The example below combines this with demes CLI support for ms commands, to visualise a command from the ms manual.

# Figure 2 from the ms manual (pp. 17 & 18 of msdoc.pdf):
# Calculate N0, the scaling parameter to convert coalescent units into
# generation times and population sizes.
N0=`python -c 'theta=11.2; mu=1e-8; length=7000; print(theta/(4*mu*length))'`
demes ms \
    -N0 $N0 \
    -I 2 3 12 \
    -g 1 44.36 \
    -n 2 0.125 \
    -eg 0.03125 1 0.0 \
    -en 0.0625 2 0.05 \
    -ej 0.09375 2 1 \
| demesdraw tubes --scale-bar -

Python API

Compared with the CLI, the Python API provides additional control. In the following example, the horizontal positions of the demes are chosen manually and the names of extinct demes are moved to a legend.

import demes
import demesdraw

graph = demes.load("examples/stdpopsim/HomSap__AmericanAdmixture_4B11.yaml")
w = demesdraw.utils.separation_heuristic(graph)
positions = dict(ancestral=0, AMH=0, AFR=0, OOA=1.5 * w, EAS=1 * w, EUR=2 * w, ADMIX=-w)
ax = demesdraw.tubes(graph, log_time=True, positions=positions, labels="xticks-legend")
ax.figure.savefig("AmericanAdmixture_4B11_tubes_custom.svg")

Documentation

Complete API and CLI details are available in the DemesDraw documentation.