Skip to content

I-diagram matrix: connected hollow/filled dots and Jurgens atom labels #16

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
Autoplectic merged 2 commits into from
Oct 6, 2026
Merged

I-diagram matrix: connected hollow/filled dots and Jurgens atom labels #16

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
bf75f88
I-diagram matrix: connect all dots, fill included variables and hollo…
Oct 6, 2026
49bbbf9
I-diagram matrix: label each atom with its Jurgens & Crutchfield taxo…
Oct 6, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
21 changes: 9 additions & 12 deletions sofic/viz/idiagram.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -241,7 +241,7 @@ def plot_information_diagram(
)

if figsize is None:
figsize = (max(9.0, 0.55 * n + 1.2), 5.6)
figsize = (max(9.0, 0.55 * n + 1.2), 6.4)
n_legend = len(handles_by_group)
ncol = _legend_ncols(figsize[0], n_legend)
empty_patch = mpatches.Patch(facecolor="none", edgecolor="none", label=" ")
Expand Down Expand Up @@ -300,16 +300,11 @@ def plot_information_diagram(
for x, atom in zip(xs, plotted, strict=True):
inside = set(atom.indices)
color = colors[atom.role]
ys_inside = []
ax_mat.plot([x, x], [0, n_vars - 1], color=color, lw=2.0, zorder=2)
for var_index in range(n_vars):
y = n_vars - 1 - var_index
if var_index in inside:
ax_mat.plot(x, y, "o", color=color, ms=8, zorder=3)
ys_inside.append(y)
else:
ax_mat.plot(x, y, "o", color="0.86", ms=8, zorder=2)
if len(ys_inside) > 1:
ax_mat.plot([x, x], [min(ys_inside), max(ys_inside)], color=color, lw=2.0, zorder=2)
face = color if var_index in inside else "white"
ax_mat.plot(x, y, "o", mfc=face, mec=color, mew=1.5, ms=8, zorder=3)

ax_mat.set_xlim(-1.4, n - 0.5)
# First gray strip is the top row at y = n_vars - 1, spanning
Expand All @@ -319,8 +314,9 @@ def plot_information_diagram(
ax_mat.set_ylim(-0.5, top)
ax_mat.axhline(top, color="0.15", lw=1.0, solid_capstyle="butt", zorder=10)
ax_mat.set_yticks([])
ax_mat.set_xticks([])
ax_mat.tick_params(axis="x", bottom=False, labelbottom=False)
ax_mat.set_xticks(xs)
ax_mat.set_xticklabels([atom.jurgens_label or atom.label for atom in plotted], rotation=90, fontsize=8)
ax_mat.tick_params(axis="x", length=0, pad=4)
for spine in ax_mat.spines.values():
spine.set_visible(False)

Expand All @@ -339,7 +335,8 @@ def plot_information_diagram(
title_fontsize=8,
)

fig.subplots_adjust(left=0.075, right=0.98, top=0.93, bottom=0.05)
# Reserve a fixed ~0.85 in strip at the bottom for the rotated atom labels.
fig.subplots_adjust(left=0.075, right=0.98, top=0.93, bottom=0.85 / figsize[1])
# After layout, seat the matrix flush under the bar so the bar x-axis
# (bottom spine) borders the top of the first gray strip.
bar_pos = ax_bar.get_position()
Expand Down
Loading