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Improve cdf supplement figure - #116

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zacharopoulou wants to merge 45 commits into
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improve-cdf-supplement-figure
Open

Improve cdf supplement figure#116
zacharopoulou wants to merge 45 commits into
mainfrom
improve-cdf-supplement-figure

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@zacharopoulou

@zacharopoulou zacharopoulou commented Jul 23, 2026

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Summary

This PR improves the per-dataset top 100 perturbation-aware effect CDF plots generated during evaluation and adds a
manuscript supplementary figure assembler.

Changes include:

  • Restyled top_100_effect_cdfs plots for clearer manuscript use:
    • tighter x-axis range
    • black dashed all-gene reference curve
    • compact in-panel median summary
    • smaller internal legend
  • Added scripts/supplement_top_effect_cdfs.py to combine per-dataset CDF plots into supplementary figure parts.
  • Generated two supplementary figure parts with 3 plots per row:
    • manuscript_assets/supplement/supplement_top_100_effect_cdfs_part1.png/svg
    • manuscript_assets/supplement/supplement_top_100_effect_cdfs_part2.png/svg

zacharopoulou and others added 30 commits July 23, 2026 12:51
@zacharopoulou
Add script for manuscript Figure 2 coverage panels
6fb5b92
@zacharopoulou
Fix perturbation aliases and separate Figure 2 outputs
4a02355
@zacharopoulou
Use evaluation colors in Figure 2 panels
368bc9b
@zacharopoulou
Align Figure 2 coverage script with benchmark outputs
5a0c312
@zacharopoulou
Clarify Figure 2 coverage panels
b660964
@zacharopoulou
Move Figure 2 counts to supplementary table
25e46c4
@zacharopoulou
Set benchmark FDR threshold
c7b9df0
@zacharopoulou
Use counts for Figure 2A labels
fad0f0c
@zacharopoulou
Clean Figure 2 supplementary table
2a3aacf
@zacharopoulou
Add Figure 2 pairwise gene overlap table
bed4346
@zacharopoulou
Add Figure 2 multiway gene overlap table
470023c
@zacharopoulou
Combine Figure 2 gene overlap tables
ef3a59d
@zacharopoulou
Annotate Figure 2 pair denominators
9944096
@zacharopoulou
Add Figure 2 UTR length and conservation panels
3af8b0c
@zacharopoulou
Read Figure 2 thresholds from run config
478403e
@zacharopoulou
Handle phastCons download resume fallback
7c583d0
@zacharopoulou
modify benchmark.yaml for the final run
3a58e08
@zacharopoulou
Clarify Figure 2 ground-truth filter log
be5b7b1
@zacharopoulou
Organize Figure 2 manuscript tables
6b2dff4
@zacharopoulou
Use logger in Figure 2 scripts
4afc2cd
@zacharopoulou
Add Figure 2 conservation table generation
4ccbd34
@zacharopoulou
Refresh final Figure 2 outputs
bdc2f35
@zacharopoulou
Keep Figure 2 outputs in manuscript assets
e65e855
@zacharopoulou
Generalize Figure 2 README run path
e62050a
@zacharopoulou
Generate vector combined Figure 2 SVG
b5a74a1
@zacharopoulou
Rename effect threshold plumbing
a3f7192
@zacharopoulou
Use benchmark defaults for Figure 2 thresholds
624a4ee
@zacharopoulou
Align Figure 2 panel labels
eb079f4
@zacharopoulou
Update metadata info
8b09aaf
@zacharopoulou
Add Figure 2 overlap supplement table
c3f042d
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@zacharopoulou