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Use log rank for p-adic fold chart and surface top tags #69

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Use log rank for p-adic fold chart and surface top tags #69

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32 changes: 25 additions & 7 deletions padjective/build_site.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1755,7 +1755,7 @@ def _generate_log_nonzero_proportion_chart(
tag_data.sort(key=lambda x: x[0])

# Calculate cumulative proportion of non-zero coefficients
x_positions = []
log_rank_positions = []
log_proportions = []

for i in range(len(tag_data)):
Expand All @@ -1770,20 +1770,25 @@ def _generate_log_nonzero_proportion_chart(

# Skip positions where proportion is 0 (can't take log)
if proportion > 0:
x_positions.append(i)
current_rank = tag_data[i][0]
# Rank must be positive to take a logarithm. If ranks are 0 or negative,
# fall back to the 1-based index position to maintain monotonic growth.
if current_rank <= 0:
current_rank = i + 1
log_rank_positions.append(math.log(current_rank))
log_proportions.append(math.log(proportion))

if len(x_positions) < 2:
if len(log_rank_positions) < 2:
return None

# Create line chart
fig, ax = plt.subplots(figsize=(12, 6))

ax.plot(x_positions, log_proportions, color='#0b6ce3', linewidth=2, alpha=0.8)
ax.plot(log_rank_positions, log_proportions, color='#0b6ce3', linewidth=2, alpha=0.8)

ax.set_xlabel('Tag Position (ordered by battle rank)', fontsize=12, fontweight='bold')
ax.set_xlabel('log(Tag Rank)', fontsize=12, fontweight='bold')
ax.set_ylabel('log(Proportion of Non-Zero Coefficients)', fontsize=12, fontweight='bold')
ax.set_title(f'Log Proportion of Non-Zero Coefficients by Tag Rank', fontsize=14, fontweight='bold', pad=15)
ax.set_title('Log-Log Proportion of Non-Zero Coefficients by Tag Rank', fontsize=14, fontweight='bold', pad=15)
ax.grid(True, alpha=0.3, linestyle='--')

# Add horizontal reference line at y=0 (proportion=1, or 100%)
Expand Down Expand Up @@ -2002,7 +2007,7 @@ def _write_umllr_pages(output_dir: Path, summary: Dict[str, Any], conn=None, sch
<h2>Log Proportion of Non-Zero Coefficients</h2>
<figure class="chart">
<img src="fold_{fold}_log_nonzero_proportion.png" alt="Log proportion of non-zero coefficients" />
<figcaption>Logarithm of the cumulative proportion of tags with non-zero coefficients (excludes infinite p-adic valuation). Shows how the proportion of informative tags changes as more tags are included by battle ranking.</figcaption>
<figcaption>Logarithms of the cumulative proportion of tags with non-zero coefficients (excludes infinite p-adic valuation) plotted against the logarithm of their battle ranking. Shows how the proportion of informative tags changes as more tags are included by battle ranking.</figcaption>
</figure>
"""

Expand Down Expand Up @@ -2243,6 +2248,14 @@ def _build_index_html(
if not class_rows:
class_rows = '<tr><td colspan="5">No taxonomy class data available</td></tr>'

top_tags = taxonomy_summary.get("top_tags", [])[:10]
top_tag_rows = "\n".join(
f"<tr><td>{html.escape(row.get('tag') or '')}</td><td>{html.escape(row.get('top_taxonomy_path') or 'Unknown')}</td><td>{row.get('top_weight', 0.0):.4f}</td><td>{row.get('max_abs_weight', 0.0):.4f}</td></tr>"
for row in top_tags
)
if not top_tag_rows:
top_tag_rows = '<tr><td colspan="4">No tag signal data available</td></tr>'

chart_html = ""
if taxonomy_dist_chart_path:
chart_rel_path = taxonomy_dist_chart_path.relative_to(output_dir).as_posix()
Expand All @@ -2261,6 +2274,11 @@ def _build_index_html(
<thead><tr><th>Taxonomy ID</th><th>Name</th><th>Path</th><th>Samples</th><th>Share</th></tr></thead>
<tbody>{class_rows}</tbody>
</table>
<h3>Tags with strongest signal</h3>
<table class="tag-taxonomy-table">
<thead><tr><th>Tag</th><th>Top taxonomy</th><th>Weight</th><th>Max |weight|</th></tr></thead>
<tbody>{top_tag_rows}</tbody>
</table>
</section>"""

html_document = f"""<!DOCTYPE html>
Expand Down
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