Expression Report

Expression Report Skill

Generate reproducible .qmd scripts for single-cell gene expression reports. The skill discusses setup with the user, then writes a complete Python/scanpy/matplotlib .qmd template encoding all decisions as configuration variables.

Reference implementations:

• Python: exploration/scripts/scmicrobiome/spongilla/02_nonmetazoan_expression.qmd
• R: TiHKAL/scripts/signaling_pathway_reports/generate_pathway_reports.qmd

Bundled resources:

• templates/report_template.py — script body chunks (config, normalization, gene matching, expression computation, combined heatmap, report loop, cross-analysis, archive)
• templates/helpers.py — reusable plotting functions (two-panel heatmap, barplot Style A)
• references/species_notes.md — species-specific cell type configurations and quirks

Overview: Two-Phase Workflow

1. Discuss — Resolve all setup decisions with the user (inputs, cell types, gene labels, barplot style, cross-analysis)
2. Generate — Write a complete .qmd script following quarto-docs and script-organization conventions
3. Render — User renders with quarto render, producing all outputs in outs/<subdirectory>/XX_script_name/

Phase 1: Discussion

Resolve these questions before generating the script. Present recommendations where possible; don't just list options.

1. Inputs

Validation steps:

• Load the h5ad, report n_obs x n_vars, check if counts are raw (max > 20) or log-normalized (max < 20)
• Load the gene list TSV, show columns and first few rows
• Test gene ID matching: how many gene list IDs match h5ad var_names? Report match rate. If < 80%, investigate ID format mismatch (underscores vs dashes, prefix differences)

2. Gene labeling

Default: use the full gene name from the single-cell object's var_names. Do not parse or abbreviate — show what's in the object. This ensures labels match the authoritative gene naming in the dataset.

• The gene list's h5ad_name column (populated during gene ID matching) contains the full var_name from the object. Use this directly as the plot label.
• Do NOT parse gene symbols out of var_names. The full annotation is the label.
• Deduplication: append #2, #3 for duplicate display names if needed.

3. Cell type setup

Check references/species_notes.md for known species-specific quirks before proposing defaults. If the species has an entry, pre-populate family assignments, ordering, and colors from it.

Default: named cell types only. Numbered/transitional clusters are excluded unless the user specifically requests them.

Read cell type info directly from the h5ad .obs:

1. Detect columns — scan .obs for likely cell type columns (look for "cell_type", "cluster", "annotation", "celltype" in column names). Show the user what you find.
2. Detect family column — look for a family/group column. If found, propose family-based ordering and coloring.
3. Ask which clusters are transitional — not all transitional clusters are just numbers. Some datasets have named transitional types. Ask the user to mark exclusions.
4. Named vs all — Recommend named cell types only. Offer "all clusters" and "both (two versions of every plot)" as alternatives.
5. Propose ordering — present cell types grouped by family, ask user to confirm or reorder.
6. Assign colors — auto-assign from Nature palette by family. User can override.

4. Cell type ordering

Ordering is family-grouped, user-confirmed. The skill proposes an order, the user adjusts if needed. The final order must be explicitly confirmed by the user. Store it as a list in the configuration chunk so it can be edited later.

5. Barplot style

All barplots use linear scale (mean CPT). Present the two styles:

Style A: Cell type family coloring (recommended for exploratory / large gene sets)

• Bars colored by cell type family (Nature palette)
• 2 columns x 6 rows grid, portrait orientation
• Gene ordering by hierarchical clustering of expression profiles
• Dashed family separators + family legend on page 1
• X-axis labels on every subplot

Style B: Gene category coloring (recommended for curated functional categories)

• Bars colored by gene's functional category
• facet_wrap style with 4 columns
• Gene ordering by category, then alphabetical

Recommendation logic: If the gene list has a functional category column with <=8 categories, recommend Style B. Otherwise recommend Style A.

6. Sub-grouping

• Ask if there's a secondary column for splitting within primary groups
• Sub-group threshold: minimum 5 genes for own plots; smaller groups lumped into "Other"

7. Cross-analysis

• Expression summary — bar chart: genes per group, fraction expressed (always include)
• Cell type enrichment — fraction of top-expressed genes per cell type vs genome-wide base rate. Only meaningful when the gene set is a defined fraction of the genome.
• Group x cell type heatmap — mean expression per group, two panels: linear + z-score. Useful when there are >=4 groups.

8. Integration markers (optional)

Ask if other datasets should be intersected with the gene list to add markers (e.g., * for phosphoproteomics hits). This is optional and project-specific.

Phase 2: Template Generation

Once all decisions are resolved, generate a .qmd script.

Naming and placement

Follow the script-organization skill:

• Script: scripts/<subdirectory>/XX_name.qmd (next available number — always ls first)
• Outputs: outs/<subdirectory>/XX_name/
• Register in project CLAUDE.md script table

.qmd structure

Generate a Python .qmd with these sections in order. Read templates/report_template.py and templates/helpers.py for the code patterns to insert into each chunk:

1. YAML frontmatter (standard quarto-docs Python template)
2. Setup chunk (PROJECT_ROOT, out_dir, git_hash, imports, archive logic)
3. Configuration chunk — all user decisions as named variables
4. Inputs chunk (load h5ad + gene list, validate)
5. Gene ID mapping chunk (match gene list IDs to h5ad var_names)
6. Cell type setup chunk (ordering, families, colors, boundaries)
7. Expression computation chunk (normalize, compute mean per cell type)
8. Helper functions chunk (heatmap + barplot functions from templates/helpers.py)
9. Combined all-genes heatmap (if <=100 genes — with category color sidebar)
10. Report generation loop (per-group, per-sub-group)
11. Cross-analysis chunk (summary, enrichment, group x cell type heatmap)
12. Build info chunk (standard BUILD_INFO.txt)

Color Palettes

Nature palette (cell type families and categories)

NATURE_PALETTE = [
    "#BC3C29",  # Brick red
    "#0072B5",  # Steel blue
    "#20854E",  # Forest green
    "#E18727",  # Amber
    "#7876B1",  # Muted purple
    "#6F99AD",  # Slate blue
    "#EE4C97",  # Rose
    "#868686",  # Gray
]

Expression heatmap colormap

White -> steel blue -> navy (#FFFFFF -> #3182BD -> #08306B)

Z-score heatmap

Diverging RdBu_r with TwoSlopeNorm centered at 0.

Anti-Patterns (MUST AVOID)

These were learned through iterative development. Do not repeat them.

Data handling

• NEVER apply expm1() without checking — if X.max() > 20, it's raw counts
• NEVER parse or abbreviate gene names — use the full var_name from the h5ad object
• NEVER trust a single best hit — require hits from >=3 species for kingdom signals

Visualization

• NEVER omit x-axis labels on barplots — every subplot must show rotated cell type names
• NEVER use garish primary colors — use Nature-style muted palette
• NEVER use 3x4 landscape barplots — portrait 2x6 is more readable
• NEVER save individual page PDFs — combine into single multi-page PDF
• NEVER sort barplots by max expression — hierarchical clustering is more informative
• NEVER show only top-N genes — show all expressed genes (up to max_pages)
• NEVER show all clusters by default — recommend named cell types only

Analytical

• NEVER assume DE testing filters pre-selected gene sets — it's overpowered (~75-85% pass)
• NEVER show only z-scored heatmaps — show linear + z-score side by side
• NEVER show only family-level averages — cell-type-level is the primary view
• NEVER leave stale outputs — archive must capture files AND subdirectories

Output Structure

outs/<subdirectory>/XX_name/
  all_genes_heatmap.pdf/.png      # Combined heatmap if <=100 genes
  expression_summary.pdf/.png     # Genes per group, fraction expressed
  group_celltype_heatmap.pdf/.png # Group x cell type (linear + z-score)
  gene_summary.tsv                # All genes with expression info
  BUILD_INFO.txt                  # Provenance
  _archive/                       # Previous runs
  group_slug_1/                   # Per-group subdirectory
    gene_list.tsv
    heatmap.pdf/.png
    barplots.pdf/.png
  group_slug_2/
    ...

Combined all-genes heatmap layout

When <=100 expressed genes, the combined heatmap uses:

• Category color sidebar on the RIGHT side (not left) to avoid overlapping gene labels
• Two heatmap panels: linear (mean CPT) + z-score
• Category legend at bottom

Future: R/Seurat Template

Not yet implemented. When added, the R template will use:

• Seurat DotPlot for dotplots
• pheatmap with category row annotations for heatmaps
• ggplot2 + facet_wrap for Style B barplots
• Same configuration-at-top pattern, adapted to R syntax