https://github.com/grahamgower/demesdraw
Drawing functions for Demes demographic models
https://github.com/grahamgower/demesdraw
demes drawing figures python
Last synced: about 1 year ago
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Drawing functions for Demes demographic models
- Host: GitHub
- URL: https://github.com/grahamgower/demesdraw
- Owner: grahamgower
- License: isc
- Created: 2021-03-05T18:23:44.000Z (over 5 years ago)
- Default Branch: main
- Last Pushed: 2024-04-08T08:36:25.000Z (about 2 years ago)
- Last Synced: 2024-04-08T10:00:32.576Z (about 2 years ago)
- Topics: demes, drawing, figures, python
- Language: Python
- Homepage: https://grahamgower.github.io/demesdraw/
- Size: 188 MB
- Stars: 18
- Watchers: 2
- Forks: 4
- Open Issues: 11
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
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README
# DemesDraw
`demesdraw` is a Python package that contains drawing functions for
[Demes](https://popsim-consortium.github.io/demes-spec-docs/main/)
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 file format supported by matplotlib can be specified,
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
```
## 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.
```python
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](https://grahamgower.github.io/demesdraw).