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Example Gallery

The gallery recreates reference-style oncoplot figures from deterministic local inputs. Active goal plots are limited to figures that can be rendered directly through the public oncoplot() API with renderer: oncoplot.

Runtime choices live in python_refactor_goal_sources/config.yaml under the gallery_params block. recreate_gallery.py loads that YAML and renders clean runs by passing params.oncoplot to public oncoplot(), including table sources, gene choices, sample or mutation filters, metadata tracks, legends, and layout options.

Render The Clean Gallery

python3 python_refactor_goal_sources/recreate_gallery.py

Outputs are written to:

python_refactor_goal_sources/generated_plots/clean/

Regenerate Gallery Inputs

python3 python_refactor_goal_sources/generate_synthetic_inputs.py

This regenerates the deterministic non-fuc fixtures. The Python/fuc AML fixtures are derived from upstream sbslee/fuc-data files with:

python3 python_refactor_goal_sources/fuc_sources/rebuild_fuc_fixtures.py --source-dir /path/to/fuc-data

Gallery inputs are checked in under:

python_refactor_goal_sources/syntheitic_goal_data/

BRCA Comparison Sheets

python3 python_refactor_goal_sources/recreate_gallery.py --style comparison --preset brca_large
python3 python_refactor_goal_sources/recreate_gallery.py --style comparison --preset brca_compact_complex

Comparison sheets contain two panels: the original source image and the clean generated image.

Outputs are written to:

python_refactor_goal_sources/generated_plots/comparison/

Accepted Clean Baselines

The generated AML metadata plots are treated as approved clean baselines:

python_refactor_goal_sources/generated_plots/clean/gen.goal_plot_11.png
python_refactor_goal_sources/generated_plots/clean/gen.goal_plot_12.png
python_refactor_goal_sources/generated_plots/clean/gen.goal_plot_13.png

Do not tune these toward the originals if it makes the generated versions worse.

Presets

Goal plots are compactly numbered by source family: ggoncoplot/R oncoplot examples first, other R-based oncoplot-style examples next, and Python/fuc AML examples last.

Preset Output Size Notes
brca_large gen.goal_plot_01.png 3600 x 1800 ggoncoplot/R large BRCA oncoplot
ggoncoplot_readme_small gen.goal_plot_02.png 672 x 480 ggoncoplot/R small README oncoplot
ggoncoplot_readme_basic gen.goal_plot_03.png 7200 x 3000 ggoncoplot/R README basic oncoplot
ggoncoplot_readme_marginal gen.goal_plot_04.png 7200 x 3600 ggoncoplot/R oncoplot with marginal bars
ggoncoplot_readme_metadata gen.goal_plot_05.png 7200 x 3600 ggoncoplot/R oncoplot with clinical metadata
paper_gbm_oncoplot gen.goal_plot_06.png 864 x 432 ggoncoplot/R compact paper-style GBM oncoplot
brca_compact_complex gen.goal_plot_07.png 850 x 683 other R-based paper compact BRCA oncoplot
cssc_compact gen.goal_plot_08.png 1400 x 700 other R-based paper alteration matrix
gbm_clinical_molecular gen.goal_plot_09.png 1080 x 436 other R-based paper GBM clinical/molecular heatmap
aml_basic gen.goal_plot_10.png 1080 x 720 Python/fuc basic AML oncoplot
aml_metadata_unsorted gen.goal_plot_11.png 1080 x 720 Python/fuc accepted clean baseline
aml_metadata_sorted gen.goal_plot_12.png 1080 x 720 Python/fuc accepted clean baseline
aml_metadata_survival gen.goal_plot_13.png 1080 x 720 Python/fuc survival-filtered AML baseline

Config-Driven Runs

Each plot_runs entry declares its renderer, output file, source goal plot, expected size, run toggle, and renderer params:

gallery_params:
  plot_runs:
    brca_large:
      run: true
      renderer: oncoplot
      style: clean
      output_name: gen.goal_plot_01.png
      goal_plot: goal_plot_01.png
      expected_size: [3600, 1800]
      params:
        oncoplot:
          data: {path: syntheitic_goal_data/brca_mutations.tsv, sep: "\t"}
          gene_col: gene
          sample_col: sample
          mutation_type_col: mutation_type
          include_genes: [PIK3CA, TP53, CDH1]
          options:
            width: 3600
            height: 1800

Generated outputs keep the zero-padded numbered naming convention: gen.goal_plot_NN.png for generated plots and compare.goal_plot_NN.png for comparison sheets.

Input Families

Family Files
AML/fuc aml_mutations.tsv, aml_metadata.tsv, aml_tmb.tsv, aml_palette.json, aml_gallery_params.json
BRCA brca_mutations.tsv, brca_metadata.tsv, brca_tmb.tsv, brca_palette.json
CSSC cssc_mutations.tsv, cssc_tmb.tsv, cssc_palette.json
GBM gbm_clinical_tracks.tsv, gbm_events.tsv, gbm_palette.json
ggoncoplot README ggoncoplot_readme_mutations.tsv, ggoncoplot_readme_metadata.tsv, ggoncoplot_readme_tmb.tsv, ggoncoplot_readme_palette.json

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