def model_image(self, species, model):
import demesdraw
import matplotlib.pyplot as plt
mid = self.get_demographic_model_id(species, model)
_, ax = plt.subplots(1, 1, figsize=(4, 4), tight_layout=True)
# Conversion into demes object for easier plotting
graph = model.model.to_demes()
demesdraw.tubes(graph, ax=ax, log_time=True)
ax.set_title(f"{model.id}", fontsize=10)
ax.set_xticklabels(
[p.name for p in model.populations],
rotation=45,
ha="right",
rotation_mode="anchor",
fontsize=10,
)
ax.set_ylabel("Time (generations)", fontsize=10)
os.makedirs(f"parameter_images/{species.id}/", exist_ok=True)
img_name = f"parameter_images/{species.id}/{mid}.png"
plt.savefig(img_name, dpi=150)
section = nodes.image(uri=img_name)
return section
#!/usr/bin/env python3
import demes
import demesdraw
def size_max(graph):
return max(
max(epoch.start_size, epoch.end_size) for deme in graph.demes
for epoch in deme.epochs)
graph = demes.load("models/IM.yaml")
w = 0.8 * size_max(graph)
positions = dict(A=0, X=-w, Y=w)
fig, ax = demesdraw.utils.get_fig_axes(aspect=1)
ax = demesdraw.tubes(graph, ax=ax, positions=positions, seed=1, inf_ratio=0.4)
ax.figure.savefig(
"fig/IM.pdf",
# Save with a transparent background.
transparent=True,
)
def draw_model(args):
dg = demes.load(args.yaml)
outfile = os.path.basename(args.yaml).replace(".yml", "_draw.png")
_ = demesdraw.tubes(dg)
plt.savefig(outfile)
return outfile