Add scatterplots to C pages

config.yaml

@@ -1 +1 @@
-config/config.fafb.yaml
+config/config.cns.yaml

config/config.cns.yaml

@@ -22,6 +22,10 @@ discovery:
   # Randomize selection (true) or use alphabetical order (false)
   randomize: true
 
+# Scatter plot settings. It was 9
+scatter:
+  min_col_count_threshold: null
+
 html:
   title_prefix: "Male CNS"
   github_repo: "https://github.com/reiserlab/celltype-explorer-drosophila-male-cns"
@@ -48,6 +52,25 @@ subsets:
     - "'AOTU103m'"
     - '"KCa''b''-ap1"'
     - "'Acc. ti flexor MN'"
+  subset-medium-optic:
+    - "Cm5"
+    - "Dm8a"
+    - "Li30"
+    - "C2"
+    - "MeLo14"
+    - "TmY5a"
+    - "Y3"
+    - "dCal1"
+    - "LC17"
+    - "LoVP3"
+    - "MeVP62"
+    - "LT79"
+    - "vCal3"
+    - "LoVC23"
+    - "aMe30"
+    - "OLVC7"
+    - "AN27X013"
+    - "DNp30"
   subset-small:
     - "SAD103"
     - "Tm3"

config/config.example.yaml

@@ -10,5 +10,8 @@ output:
 neuroglancer:
   base_url: "https://clio-ng.janelia.org/"
 
+scatter:
+  min_col_count_threshold: null
+
 html:
   title_prefix: "Neuron Type Report"

config/config.fafb.yaml

@@ -22,6 +22,9 @@ discovery:
   # Randomize selection (true) or use alphabetical order (false)
   randomize: true
 
+scatter:
+  min_col_count_threshold: null
+
 html:
   title_prefix: "Female Adult Fly Brain"
   fathom_id: "GDMDXQVG"

config/config.optic-lobe.yaml

@@ -23,6 +23,9 @@ discovery:
   # Randomize selection (true) or use alphabetical order (false)
   randomize: true
 
+scatter:
+  min_col_count_threshold: null
+
 html:
   title_prefix: "Neuron Type Report"
 

docs/user-guide.md

@@ -104,8 +104,35 @@ html:
 performance:
   max_workers: 4
   cache_enabled: true
+
+scatter:
+  # Minimum column count threshold for data quality filtering
+  # Data points with cols_innervated <= this value will be excluded from scatter plots
+  # Set to null to disable this filter
+  min_col_count_threshold: null
+```
+
+### Scatter Plot Configuration
+
+Configure scatter plot generation for optic lobe datasets:
+
+```yaml
+scatter:
+  min_col_count_threshold: 9.0  # Default threshold
 ```
 
+**Configuration Options:**
+- `min_col_count_threshold`: Minimum number of columns a neuron type must innervate to be included in scatter plots
+  - Default: `9.0` (excludes types with ≤ 9 columns)
+  - Set to `null` to disable filtering and include all data points
+  - This filter helps exclude low-quality or sparse data from visualizations
+  - Can be overridden per-command using `--min-col-count` CLI option
+
+**Use Cases:**
+- **Strict quality control** (default 9.0): Only well-sampled types with sufficient column coverage
+- **Relaxed filtering** (e.g., 5.0): Include more types with moderate column coverage
+- **No filtering** (null): Include all types regardless of column count
+
 ### Dataset-Specific Configurations
 
 Different datasets may require specific settings:
@@ -166,6 +193,15 @@ pixi run neuview build --types "Tm3,Mi1,T4"
 # Use a subset from config
 pixi run neuview build --subset small-test
 
+# Generate scatter plots (for optic lobe datasets)
+pixi run neuview create-scatter
+
+# Generate scatter plots with custom quality threshold
+pixi run neuview create-scatter --min-col-count 5
+
+# Generate scatter plots without quality filtering
+pixi run neuview create-scatter --min-col-count -1
+
 # Verbose output for debugging
 pixi run neuview build --verbose
 ```
@@ -184,6 +220,16 @@ pixi run neuview build --verbose
 - `neuview inspect <type>` - Show detailed information about a neuron type
 - Displays: neuron count, soma distribution, connectivity stats
 
+**`create-scatter` command:**
+- `neuview create-scatter` - Generate SVG scatter plots of spatial metrics for optic lobe types
+- `--min-col-count <value>` - Set minimum column count threshold for data quality filtering
+  - Default: 9.0 (excludes points with cols_innervated ≤ 9)
+  - Set to -1 to disable filtering
+  - Can also be configured in `config.yaml` under `scatter.min_col_count_threshold`
+- Generates plots for ME, LO, and LOP regions
+- Creates both combined (both hemispheres) and hemisphere-specific (L/R) plots
+- Output: `output/scatter/*.svg` files
+
 ## Generated Website Features
 
 ### Interactive Index Page
@@ -712,4 +758,4 @@ A: Yes! The `data/neurons.json` file is a standard JSON API endpoint.
 A: Same data, different formats. JSON for web servers/APIs, JS for local file access.
 
 **Q: Why do some neurons have L/R pages and others don't?**
-A: Automatically determined by soma distribution. Bilateral neurons get separate pages.
+A: Automatically determined by soma distribution. Bilateral neurons get separate pages.