# SCimilarity Visualization Workshop - Progress Plan

## Quest 1: 01_QUEST_START_HERE
- **Status:** ✅ Completed
- **Goals Achieved:**
  - Initialized project directory structure.
  - Extracted an art-inspired (Jackson Pollock) color palette.
  - Generated mock single-cell JSON data.
  - Built a reactive, single-page Plotly web application to render UMAPs and a Concordance Heatmap.

## Quest 2: 02_QUEST_FIG3
- **Status:** ✅ Completed
- **Goals Achieved:**
  - Transitioned to the real `kretzler_kidney.h5ad` dataset.
  - Aligned data to the SCimilarity foundation model gene space and generated predictions.
  - Implemented a data-driven 1:1 label harmonization mapping, specifically matching the 22 expert labels from the Heimberg et al. 2024 paper.
  - Generated `mapping.csv` and `concordance_metrics.csv` for further analysis.
  - Achieved a global concordance of >84%, mirroring the published results.
  - Wrote a comprehensive testing suite (Unit tests + Biological validation).
  - Fixed Plotly UI overlapping label issues using `automargin`.

## Quest 3: 03_QUEST_NEW_DATA
- **Status:** ✅ Completed
- **Goals Achieved:**
  - Wrote a precise specification for querying the CELLxGENE database.
  - Successfully downloaded and processed a novel healthy human muscle dataset (~177,000 cells) using `cellxgene-census` as a fallback since the Discover API was restricted.
  - Translated the workflow into a reusable LLM "Skill" (`cellxgene-search`) and installed it locally in the workspace.

## Quest 4: 04_QUEST_OPEN_TARGETS
- **Status:** ✅ Completed
- **Goals Achieved:**
  - Shifted focus to Competitive Intelligence and Translational Strategy.
  - Defined an open-ended specification to investigate Type 2 Diabetes targets (GLP1R, GIPR, SGLT2, SLC30A8).
  - Built a mock data pipeline representing the real-world clinical state (compensating for API restrictions).
  - Developed an interactive HTML dashboard (`clinical_landscape.html`) featuring stacked bar charts for drug pipelines, evidence heatmaps, and a searchable drug table.
  - Successfully visualized clinical "whitespace" (e.g., high genetic evidence but zero approved drugs for SLC30A8).