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`