--- name: scientific-illustration-guide description: "Create graphical abstracts, schematic diagrams, and scientific illustrations" metadata: openclaw: emoji: "🖍️" category: "tools" subcategory: "diagram" keywords: ["scientific illustration", "graphical abstract", "schematic diagram", "architecture diagram", "vector graphics"] source: "wentor" --- # Scientific Illustration Guide A skill for creating clear, professional scientific illustrations including graphical abstracts, schematic diagrams, workflow visualizations, and architecture diagrams. Covers both programmatic and design tool approaches. ## Graphical Abstract Design ### Composition Principles ``` Layout Guidelines for Graphical Abstracts: - Dimensions: typically 500x300px to 1200x800px (check journal spec) - Flow direction: left-to-right or top-to-bottom - Maximum 5-7 visual elements - Use arrows to show process flow - Include 1-2 key data points or results - Minimal text (30-50 words maximum) - Consistent color scheme (3-4 colors) Structure: [Input/Problem] --> [Method/Process] --> [Output/Finding] ``` ### Programmatic Diagrams with Python ```python import matplotlib.pyplot as plt import matplotlib.patches as patches from matplotlib.patches import FancyBboxPatch, FancyArrowPatch def create_workflow_diagram(steps: list[dict], output: str = 'workflow.pdf'): """ Create a horizontal workflow diagram. Args: steps: List of dicts with 'label', 'color', and optional 'sublabel' output: Output file path """ fig, ax = plt.subplots(figsize=(12, 3)) n = len(steps) box_width = 0.12 gap = (1 - n * box_width) / (n + 1) for i, step in enumerate(steps): x = gap + i * (box_width + gap) y = 0.3 # Draw box box = FancyBboxPatch( (x, y), box_width, 0.4, boxstyle="round,pad=0.01", facecolor=step.get('color', '#3B82F6'), edgecolor='#1E293B', linewidth=1.5, alpha=0.9 ) ax.add_patch(box) # Add label ax.text(x + box_width/2, y + 0.2, step['label'], ha='center', va='center', fontsize=9, fontweight='bold', color='white') if 'sublabel' in step: ax.text(x + box_width/2, y - 0.08, step['sublabel'], ha='center', va='center', fontsize=7, color='#475569') # Draw arrow to next step if i < n - 1: ax.annotate('', xy=(x + box_width + gap*0.2, 0.5), xytext=(x + box_width + gap*0.8, 0.5), arrowprops=dict(arrowstyle='->', color='#64748B', lw=1.5)) ax.set_xlim(0, 1) ax.set_ylim(0, 1) ax.axis('off') fig.savefig(output, dpi=300, bbox_inches='tight', facecolor='white', edgecolor='none') plt.close() return output # Example: research pipeline steps = [ {'label': 'Data\nCollection', 'color': '#3B82F6', 'sublabel': 'N=1,200'}, {'label': 'Preprocessing', 'color': '#6366F1', 'sublabel': 'QC + Filtering'}, {'label': 'Analysis', 'color': '#8B5CF6', 'sublabel': 'ML Pipeline'}, {'label': 'Validation', 'color': '#A855F7', 'sublabel': 'Cross-validation'}, {'label': 'Results', 'color': '#EC4899', 'sublabel': 'AUC = 0.92'} ] create_workflow_diagram(steps, 'research_pipeline.pdf') ``` ## Schematic Diagrams ### System Architecture Diagrams ```python import matplotlib.pyplot as plt from matplotlib.patches import FancyBboxPatch, FancyArrowPatch def create_architecture_diagram(components: list[dict], connections: list[tuple], output: str = 'architecture.pdf'): """ Create a system architecture diagram. Args: components: List of {'name', 'x', 'y', 'width', 'height', 'color', 'type'} connections: List of (source_name, target_name, label) tuples """ fig, ax = plt.subplots(figsize=(10, 7)) # Draw components comp_positions = {} for comp in components: x, y = comp['x'], comp['y'] w, h = comp.get('width', 1.5), comp.get('height', 0.8) color = comp.get('color', '#3B82F6') if comp.get('type') == 'database': # Cylinder shape for databases ellipse_h = 0.15 ax.add_patch(patches.Rectangle((x, y), w, h-ellipse_h, facecolor=color, edgecolor='#1E293B', linewidth=1.2)) ax.add_patch(patches.Ellipse((x+w/2, y+h-ellipse_h), w, ellipse_h*2, facecolor=color, edgecolor='#1E293B', linewidth=1.2)) ax.add_patch(patches.Ellipse((x+w/2, y), w, ellipse_h*2, facecolor=color, edgecolor='#1E293B', linewidth=1.2)) else: box = FancyBboxPatch((x, y), w, h, boxstyle="round,pad=0.05", facecolor=color, edgecolor='#1E293B', linewidth=1.2, alpha=0.9) ax.add_patch(box) ax.text(x + w/2, y + h/2, comp['name'], ha='center', va='center', fontsize=10, fontweight='bold', color='white') comp_positions[comp['name']] = (x + w/2, y + h/2, w, h) # Draw connections for src, tgt, label in connections: sx, sy, sw, sh = comp_positions[src] tx, ty, tw, th = comp_positions[tgt] ax.annotate('', xy=(tx, ty + th/2 if sy > ty else ty - th/2), xytext=(sx, sy - sh/2 if sy > ty else sy + sh/2), arrowprops=dict(arrowstyle='->', color='#64748B', lw=1.5, connectionstyle='arc3,rad=0.1')) mid_x = (sx + tx) / 2 mid_y = (sy + ty) / 2 if label: ax.text(mid_x + 0.1, mid_y, label, fontsize=7, color='#475569') ax.set_xlim(-0.5, 10) ax.set_ylim(-0.5, 8) ax.set_aspect('equal') ax.axis('off') fig.savefig(output, dpi=300, bbox_inches='tight', facecolor='white') plt.close() ``` ## Vector Graphics with Drawio For complex diagrams, use draw.io (diagrams.net) which exports to SVG, PDF, and PNG: ```xml ``` ### Recommended Tools by Diagram Type | Diagram Type | Best Tool | Output Format | Learning Curve | |-------------|-----------|---------------|----------------| | Flowcharts | draw.io / Mermaid | SVG, PDF | Low | | Molecular structures | ChemDraw / RDKit | SVG, PNG | Medium | | Biological pathways | BioRender / KEGG | PNG, SVG | Low | | Network graphs | Cytoscape / NetworkX | SVG, PDF | Medium | | 3D protein structures | PyMOL / ChimeraX | PNG, TIFF | High | | Circuit diagrams | KiCad / CircuiTikZ | PDF, SVG | Medium | | Math diagrams | TikZ/PGF | PDF | High | | UML diagrams | PlantUML / Mermaid | SVG, PNG | Low | ## Color and Accessibility Use colorblind-safe palettes consistently. The key rules: 1. Never use red and green together to encode different categories 2. Use both color and shape/pattern to distinguish elements 3. Ensure sufficient contrast (WCAG AA: 4.5:1 ratio for text) 4. Test your diagram in grayscale to verify it remains interpretable 5. Label elements directly rather than relying solely on a color legend ## Export and Journal Compliance - Export vector formats (SVG, PDF, EPS) for line art and diagrams - Minimum 300 DPI for raster elements within diagrams - Embed fonts or convert text to paths in final SVG/PDF - Check journal-specific requirements for graphical abstract dimensions and file size - Name files following journal convention (e.g., "Figure_1.pdf", "graphical_abstract.tiff") --- Source attribution: wentorai Original project: https://github.com/wentorai/research-plugins/blob/bf44b3cd617fa94c8a1b254c5d1987142ca3d631/skills/tools/diagram/scientific-illustration-guide/SKILL.md License: MIT License information: https://opensource.org/license/mit Original upstream instructions; downloaded from Mega AI Hub. ## Upstream license notice MIT License Copyright (c) 2026 Wentor AI Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. # Mega AI Hub resource metadata Creator / publisher: wentorai Original project: https://github.com/wentorai/research-plugins/blob/bf44b3cd617fa94c8a1b254c5d1987142ca3d631/skills/tools/diagram/scientific-illustration-guide/SKILL.md Attribution basis: Source repository record Fields of work: Design, Education & Research Roles: Graphic Designer, Researcher, UX Designer Specialties: API, Design Tools: Matplotlib Country applicability: Country not specified Classification basis: Source catalog labels Instruction SHA-256: fb54e1e1a963d4e5ef4f086f76d753d5bf1b36986e78aef8fd6e2eff2f163ac4