scientific-writer 2.1.1__py3-none-any.whl → 2.2.2__py3-none-any.whl

scientific_writer/.claude/skills/scientific-schematics/references/diagram_types.md

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+# Scientific Diagram Types: Catalog and Examples
+
+## Overview
+
+This guide catalogs common scientific diagram types used in research publications, with guidance on when to use each type, design considerations, and example implementations.
+
+## 1. Methodology Flowcharts
+
+### Purpose
+Visualize study design, participant flow, data processing pipelines, and experimental workflows.
+
+### When to Use
+- Clinical trial participant flow (CONSORT diagrams)
+- Systematic review selection process (PRISMA flowcharts)
+- Data processing and analysis pipelines
+- Experimental procedure workflows
+- Algorithm or computational workflows
+
+### Key Elements
+- **Start/End nodes**: Rounded rectangles (terminals)
+- **Process boxes**: Rectangles for actions/steps
+- **Decision diamonds**: For conditional branches
+- **Data boxes**: Parallelograms for data inputs/outputs
+- **Arrows**: Show sequence and flow direction
+- **Annotations**: Numbers (n=X) for participant counts, exclusion criteria
+
+### Design Guidelines
+- Flow top-to-bottom or left-to-right consistently
+- Align nodes for professional appearance
+- Include sample sizes at each step
+- Use color sparingly (colorblind-safe palette)
+- Keep text concise within nodes
+- Add legends for symbols if needed
+
+### Example Use Cases
+
+**CONSORT Participant Flow**
+```
+Assessed for eligibility (n=500)
+    ↓
+Excluded (n=150)
+- Age < 18: n=80
+- Declined: n=50
+- Other: n=20
+    ↓
+Randomized (n=350)
+    ↓
+  /   \
+Treatment  Control
+(n=175)   (n=175)
+```
+
+**Data Processing Pipeline**
+```
+Raw Data → Quality Control → Normalization → 
+Statistical Analysis → Visualization → Report
+```
+
+**Systematic Review Selection**
+```
+Records identified → Duplicates removed → 
+Title/Abstract screening → Full-text review → 
+Studies included in meta-analysis
+```
+
+## 2. Circuit Diagrams
+
+### Purpose
+Illustrate electrical circuits, signal processing systems, and electronic schematics.
+
+### When to Use
+- Electronics and electrical engineering papers
+- Sensor system designs
+- Signal processing workflows
+- Measurement apparatus descriptions
+- Control system diagrams
+- Communication protocol implementations
+
+### Key Elements
+- **Voltage/current sources**: Standard symbols
+- **Resistors, capacitors, inductors**: Standard component symbols
+- **Integrated circuits**: Rectangular blocks with pins
+- **Connections**: Solid lines (wires), dots at junctions
+- **Ground symbols**: Standard ground notation
+- **Labels**: Component values, node voltages
+
+### Design Guidelines
+- Follow IEEE/IEC standard symbols
+- Wire connections: dots at junctions, no dots for crossovers
+- Label all components with values and units
+- Use consistent wire thickness
+- Indicate signal direction with arrows when helpful
+- Group functional blocks with dashed boxes
+
+### Example Use Cases
+
+**Simple RC Circuit**
+```
+Voltage Source --- Resistor (R1) --- Capacitor (C1) --- Ground
+                                  |
+                              Output node
+```
+
+**Amplifier Circuit**
+```
+Input → Coupling Capacitor → Transistor → Load Resistor → Output
+                              ↑
+                          Bias Network
+```
+
+**Signal Processing Block Diagram**
+```
+Sensor → Amplifier → Filter → ADC → Microcontroller → DAC → Actuator
+```
+
+## 3. Biological Diagrams
+
+### Purpose
+Visualize cellular processes, molecular interactions, signaling pathways, and biological systems.
+
+### When to Use
+- Signaling cascade illustrations
+- Metabolic pathways
+- Gene regulatory networks
+- Protein-protein interactions
+- Cellular processes and organelle functions
+- Experimental procedures (cloning, assays)
+
+### Key Elements
+- **Proteins/genes**: Rounded rectangles or ovals
+- **Small molecules**: Circles or hexagons
+- **Activation arrows**: Standard arrows (→)
+- **Inhibition**: Blunt-ended lines (⊣)
+- **Transcription**: Bent arrows
+- **Translocation**: Dashed arrows across membranes
+- **Complex formation**: Connecting lines
+
+### Design Guidelines
+- Use standard Systems Biology Graphical Notation (SBGN) when possible
+- Italicize gene names, regular font for proteins
+- Show subcellular location (cytoplasm, nucleus, membrane)
+- Use color to distinguish entity types (proteins, metabolites, genes)
+- Include legends for arrow types
+- Indicate time progression if relevant
+
+### Example Use Cases
+
+**MAPK Signaling Pathway**
+```
+Growth Factor → Receptor → RAS → RAF → MEK → ERK → 
+Transcription Factor → Gene Expression
+```
+
+**Metabolic Pathway**
+```
+Glucose → Glucose-6-P → Fructose-6-P → Fructose-1,6-BP →
+(enzymes labeled at each arrow)
+```
+
+**Gene Regulation Network**
+```
+         ┌─────────┐
+         │ Gene A  │
+         └────┬────┘
+              ↓ activates
+         ┌─────────┐
+         │ Gene B  │ ⊣ inhibits
+         └────┬────┘     ↓
+              ↓      ┌─────────┐
+         ┌─────────┐│ Gene C  │
+         │ Protein │└─────────┘
+         └─────────┘
+```
+
+**Cell Signaling with Compartments**
+```
+Membrane: [Receptor] → [G-protein]
+              ↓
+Cytoplasm: [2nd Messenger] → [Kinase Cascade]
+              ↓
+Nucleus:   [Transcription Factor] → [Gene]
+```
+
+## 4. Block Diagrams / System Architecture
+
+### Purpose
+Show system components and their relationships, data flow, or hierarchical organization.
+
+### When to Use
+- Software architecture
+- Hardware system design
+- Data flow diagrams
+- Control systems
+- Network architecture
+- Experimental apparatus setup
+- Conceptual frameworks
+
+### Key Elements
+- **Components**: Rectangles with labels
+- **Subsystems**: Grouped components in larger boxes
+- **Connections**: Arrows showing data/signal/control flow
+- **Interfaces**: Labeled connection points
+- **External entities**: Distinct styling for external components
+- **Annotations**: Data types, protocols, frequencies
+
+### Design Guidelines
+- Organize hierarchically (high-level to low-level)
+- Align blocks in rows or columns
+- Use consistent block sizes for similar components
+- Label all connections with data types or protocols
+- Use colors to distinguish component types
+- Include legends for line types (data, control, power)
+
+### Example Use Cases
+
+**Data Acquisition System**
+```
+┌────────┐    ┌─────┐    ┌──────────────┐    ┌──────────┐
+│ Sensor │ → │ ADC │ → │ Microcontrol.│ → │ Database │
+└────────┘    └─────┘    └──────────────┘    └──────────┘
+                              ↓
+                         ┌─────────┐
+                         │ Display │
+                         └─────────┘
+```
+
+**Software Architecture (Three-Tier)**
+```
+Presentation Layer: [Web UI] [Mobile App]
+        ↓
+Business Logic Layer: [API Server] [Auth Service]
+        ↓
+Data Layer: [Database] [Cache] [File Storage]
+```
+
+**Experimental Setup**
+```
+[Light Source] → [Sample Chamber] → [Detector] → [Amplifier] → 
+[Data Acquisition] → [Computer]
+      ↑                                              ↓
+[Temperature Controller] ←───────────────── [Control Software]
+```
+
+## 5. Process Flow Diagrams
+
+### Purpose
+Illustrate sequential processes, decision logic, and workflows.
+
+### When to Use
+- Manufacturing processes
+- Quality control procedures
+- Algorithm logic flow
+- Decision trees
+- Standard operating procedures (SOPs)
+- Troubleshooting guides
+
+### Key Elements
+- **Start/End**: Ovals or rounded rectangles
+- **Process**: Rectangles
+- **Decision**: Diamonds with yes/no branches
+- **Input/Output**: Parallelograms
+- **Subprocess**: Rectangle with double borders
+- **Arrows**: Show flow direction
+- **Connectors**: Circles for off-page or looping connections
+
+### Design Guidelines
+- Single entry and exit points
+- Clear decision branch labels (Yes/No, True/False)
+- Avoid crossing lines when possible
+- Use connectors for complex flows
+- Number steps if sequence is critical
+- Keep decision questions simple and binary
+
+### Example Use Cases
+
+**Quality Control Decision Tree**
+```
+Start → Measure Parameter → [Within Spec?] 
+                              Yes ↓    No ↓
+                           Accept   Adjust Settings → Retest
+                              ↓         ↓
+                             End ← [Pass?] → Reject
+```
+
+**Algorithm Flowchart**
+```
+Initialize Variables → Read Input → [Data Valid?]
+                                      No ↓      Yes ↓
+                                Error Message  Process Data
+                                      ↓             ↓
+                                   End ←──── Output Results
+```
+
+## 6. Network Diagrams
+
+### Purpose
+Visualize relationships, connections, and network topology.
+
+### When to Use
+- Computer networks
+- Social networks
+- Protein interaction networks
+- Collaboration networks
+- Communication pathways
+- Graph-based data structures
+
+### Key Elements
+- **Nodes**: Circles, rectangles, or custom shapes
+- **Edges**: Lines connecting nodes
+- **Directed edges**: Arrows showing direction
+- **Weighted edges**: Line thickness or labels showing weights
+- **Node attributes**: Color, size, or labels
+- **Clusters**: Grouped nodes with boundaries
+
+### Design Guidelines
+- Use layout algorithms for complex networks (force-directed, hierarchical)
+- Size nodes by importance/degree if relevant
+- Color-code node types or communities
+- Show edge weights if important
+- Minimize edge crossings
+- Include network statistics if relevant (N nodes, M edges)
+
+### Example Use Cases
+
+**Communication Network**
+```
+    [Server]
+    /  |  \
+  /    |    \
+[PC1] [PC2] [PC3]
+  \    |    /
+   \   |   /
+    [Router] ← [Internet]
+```
+
+**Protein Interaction Network**
+```
+Nodes = proteins (colored by function)
+Edges = experimentally verified interactions
+Node size = expression level
+```
+
+**Collaboration Network**
+```
+Nodes = researchers
+Edges = co-authorship
+Node color = institution
+Edge thickness = number of collaborations
+```
+
+## 7. Timeline Diagrams
+
+### Purpose
+Show events, phases, or changes over time.
+
+### When to Use
+- Study design timelines
+- Treatment schedules
+- Historical progressions
+- Project milestones
+- Developmental stages
+- Longitudinal study visits
+
+### Key Elements
+- **Time axis**: Horizontal or vertical line
+- **Events**: Markers, dots, or boxes at time points
+- **Durations**: Bars or shaded regions
+- **Labels**: Time points and event descriptions
+- **Phases**: Color-coded segments
+- **Annotations**: Additional information for events
+
+### Design Guidelines
+- Use consistent time scale
+- Clearly label all time points
+- Use color to distinguish phases or types
+- Include scale bar or time units
+- Align events vertically for clarity
+- Show overlapping events with vertical offset
+
+### Example Use Cases
+
+**Clinical Trial Timeline**
+```
+Week:     0    4    8   12   16   20   24
+          |----|----|----|----|----|----|
+Events:   ●    ●    ●    ●    ●         ●
+       Baseline Randomize   Follow-ups  End
+          |=========|=========|
+        Screening Treatment  Follow-up
+```
+
+**Experimental Protocol**
+```
+Day 0: Baseline measurements
+  ↓
+Days 1-7: Treatment A
+  ↓
+Day 8: Washout period
+  ↓
+Days 9-15: Treatment B
+  ↓
+Day 16: Final measurements
+```
+
+**Project Gantt Chart Style**
+```
+Task 1  |████████|
+Task 2     |██████████|
+Task 3           |████████|
+        0  2  4  6  8  10 (months)
+```
+
+## 8. Hierarchical / Tree Diagrams
+
+### Purpose
+Show hierarchical relationships, classifications, or organizational structure.
+
+### When to Use
+- Organizational charts
+- Taxonomic classifications
+- Decision trees
+- File system structures
+- Phylogenetic trees
+- Category hierarchies
+
+### Key Elements
+- **Root node**: Top-level element
+- **Parent nodes**: Intermediate levels
+- **Child nodes**: Terminal elements
+- **Branches**: Connections showing relationships
+- **Levels**: Horizontal tiers of hierarchy
+- **Labels**: Node names and attributes
+
+### Design Guidelines
+- Organize top-to-bottom or left-to-right
+- Align nodes at same hierarchical level
+- Use consistent spacing between levels
+- Size nodes by importance if relevant
+- Keep branch angles consistent
+- Label branch points if needed (e.g., evolutionary distances)
+
+### Example Use Cases
+
+**Organizational Structure**
+```
+         [Director]
+            /  \
+           /    \
+    [Manager A] [Manager B]
+      /    \       /    \
+   [Staff] [Staff] [Staff] [Staff]
+```
+
+**Taxonomic Classification**
+```
+Kingdom
+  ↓
+Phylum → [Multiple branches]
+  ↓
+Class
+  ↓
+Order
+  ↓
+Family → [Species groups]
+```
+
+**Decision Tree (Classification)**
+```
+[Feature 1 > threshold?]
+  Yes /        \ No
+[Class A]   [Feature 2 > threshold?]
+            Yes /          \ No
+         [Class B]      [Class C]
+```
+
+## 9. Venn Diagrams / Set Relationships
+
+### Purpose
+Show overlaps, intersections, and relationships between sets.
+
+### When to Use
+- Shared features or categories
+- Overlap analysis (gene lists, patient cohorts)
+- Logical relationships
+- Comparison of groups
+- Inclusion/exclusion criteria
+
+### Key Elements
+- **Circles/ovals**: Representing sets
+- **Overlaps**: Intersecting regions
+- **Labels**: Set names and sizes
+- **Numbers**: Element counts in each region
+- **Color**: Distinguish sets (use transparency for overlaps)
+
+### Design Guidelines
+- Use 2-3 circles maximum for clarity
+- Label all regions with counts
+- Use colorblind-safe palette with transparency
+- Ensure circles overlap proportionally if area matters
+- Include total counts for each set
+- Consider alternatives for >3 sets (UpSet plots)
+
+### Example Use Cases
+
+**Gene Expression Overlap**
+```
+    [Treatment A]  [Treatment B]
+         200          150
+           \    80   /
+            \───────/
+         Differentially expressed genes
+```
+
+**Patient Eligibility**
+```
+[Age 18-65]  ∩  [No contraindications]  ∩  [Willing to participate]
+     = Eligible participants
+```
+
+## 10. Heatmaps / Matrix Diagrams
+
+### Purpose
+Visualize matrix data, correlations, or relationships between two categorical variables.
+
+### When to Use
+- Correlation matrices
+- Gene expression across samples
+- Confusion matrices (classification)
+- Pairwise comparisons
+- Presence/absence data
+- Intensity measurements across conditions
+
+### Key Elements
+- **Grid cells**: Representing matrix values
+- **Color scale**: Mapping values to colors
+- **Row/column labels**: Categories or variables
+- **Color bar**: Legend for color scale
+- **Annotations**: Values within cells if readable
+
+### Design Guidelines
+- Use perceptually uniform colormap (viridis, plasma)
+- Include color bar with scale
+- Order rows/columns meaningfully (hierarchical clustering)
+- Annotate cells if space permits
+- Use diverging colormap for centered data (correlations)
+- Keep cell aspect ratio square
+
+### Example Use Cases
+
+**Correlation Matrix**
+```
+       Var1  Var2  Var3
+Var1 [ 1.0   0.7   0.3 ]
+Var2 [ 0.7   1.0   0.5 ]
+Var3 [ 0.3   0.5   1.0 ]
+
+Color scale: -1 (blue) to +1 (red)
+```
+
+**Gene Expression Heatmap**
+```
+Rows = genes
+Columns = samples/conditions
+Color = expression level (low to high)
+Hierarchical clustering on both axes
+```
+
+## Diagram Selection Guide
+
+| **Goal** | **Diagram Type** | **Best For** |
+|----------|-----------------|--------------|
+| Show sequence | Flowchart, Timeline | Processes, events over time |
+| Show components | Block diagram | System architecture |
+| Show relationships | Network, Tree | Connections, hierarchies |
+| Show overlap | Venn diagram | Set intersections |
+| Show pathway | Biological diagram | Signaling, metabolism |
+| Show circuit | Circuit diagram | Electronics, signals |
+| Show data matrix | Heatmap | Correlations, patterns |
+| Show decisions | Decision tree, Flowchart | Logic, classification |
+| Show organization | Tree, Org chart | Hierarchies, structure |
+
+## Combining Diagram Types
+
+Often, complex figures combine multiple diagram types:
+
+**Example: Experimental Design + Timeline**
+```
+[Flowchart showing participant groups]
+    +
+[Timeline showing intervention schedule]
+    +
+[Measurement points indicated]
+```
+
+**Example: System Architecture + Data Flow**
+```
+[Block diagram of components]
+    +
+[Arrows showing data flow with annotations]
+    +
+[Network diagram of connections]
+```
+
+## Common Mistakes to Avoid
+
+1. **Too much information**: Simplify, create multiple figures if needed
+2. **Inconsistent styling**: Use templates and style files
+3. **Poor alignment**: Use grids and alignment tools
+4. **Unclear flow**: Ensure arrows and sequence are obvious
+5. **Missing labels**: Label all components, axes, and connections
+6. **Color overuse**: Stick to colorblind-safe palette, use sparingly
+7. **Tiny text**: Ensure readability at final print size
+8. **Crossing lines**: Minimize or use bridges/gaps to indicate
+9. **No legend**: Include legends for symbols, colors, line types
+10. **Inconsistent scale**: Maintain proportions and spacing
+
+## Accessibility Checklist
+
+- [ ] Colorblind-safe palette (Okabe-Ito)
+- [ ] Works in grayscale
+- [ ] Text minimum 7-8 pt at final size
+- [ ] High contrast between elements
+- [ ] Redundant encoding (not just color)
+- [ ] Clear, descriptive labels
+- [ ] Comprehensive figure caption
+- [ ] Logical reading order
+
+## Further Reading
+
+- **CONSORT Flow Diagram**: http://www.consort-statement.org/consort-statement/flow-diagram
+- **PRISMA Flow Diagram**: http://prisma-statement.org/
+- **Systems Biology Graphical Notation (SBGN)**: https://sbgn.github.io/
+- **IEEE Standard Graphic Symbols for Electrical and Electronics Diagrams**: IEEE Std 315
+- **Graph Visualization**: Graphviz documentation
+
+Use this catalog to select the appropriate diagram type for your scientific communication needs, then refer to the TikZ guide and templates for implementation.
+