Plot and Figure Generating Tools for Researchers and Scientists
A practical guide to the tools researchers use for workflow diagrams, statistical plots, vector illustrations, and paper figures.
Plots, process flows, vector curves, and diagrams for academic research.
Plots and figures are an integral part of research and analytics. A single figure can describe more than 2-3 pages of essays. However, researchers around the world use different tools for different purposes.
Here is a breakdown of the most useful tools for methodology flowcharts, statistical plots, vector illustrations, and study designs.
1. Overview Table
Quick comparison of tools, primary strengths, learning curves, and export formats.
| Category | Tool | Best For | Learning Curve | Export Formats |
|---|---|---|---|---|
| Visual Editors | draw.io | Flowcharts, system architecture, workflows, study designs | Low | SVG, PDF, PNG, XML |
| Excalidraw | Hand-drawn sketches, brainstorming, whiteboard figures | Very Low | SVG, PNG, JSON | |
| Inkscape | Custom vector illustrations, multi-panel figure assembly | Medium | SVG, EPS, PDF | |
| Diagrams as Code | Mermaid | Flowcharts, sequence diagrams, Gantt charts | Low | SVG, PNG |
| Graphviz | Networks, DAGs, hierarchical layouts | Medium | SVG, PDF, PostScript | |
| PlantUML | UML, component, and sequence diagrams | Medium | SVG, PNG, LaTeX | |
| TikZ / PGFPlots | Mathematical diagrams matching paper typography | High | Native PDF vector | |
| Statistical Plotting | Matplotlib + Seaborn | Publication plots, training curves, statistical graphics | Medium | PDF, SVG, EPS, PNG |
| ggplot2 (R) | Grammar-of-graphics statistical visualizations | Medium | PDF, SVG, EPS, TIFF | |
| gnuplot | Scriptable, command-line scientific plotting | Medium | PostScript, PDF, SVG | |
| Plotly | Interactive exploratory plots and static exports | Low–Medium | HTML, SVG, PDF, PNG | |
| Icons & AI Tools | Open Icon Libraries | Reusable scientific vectors (bio, organisms, medical) | None | SVG, PNG |
| Automated / AI Tools | PRISMA flowcharts, paper schematics, knowledge graphs | Low | SVG, Code |
2. Diagram & Flowchart Tools (GUI / Visual Editors)
These tools give you an interactive canvas to draw, arrange, and export figures without writing code.
draw.io (diagrams.net)
Author's PickBest For: Flowcharts, architecture diagrams, workflows, study designs.
Notes: Completely free, open-source, and works both in the browser and as an offline desktop app. It has rich shape libraries, supports transparent background rendering, and exports SVG, PNG, and PDF. You can also re-edit exported SVGs because the diagram data is stored inside the file.
Excalidraw
Hand-Drawn StyleBest For: Hand-drawn sketches, quick brainstorming, collaborative diagrams.
Notes: Open-source, browser-based, and end-to-end encrypted. It supports Mermaid syntax import and is great for informal, whiteboard-style figures.
Inkscape
Vector IllustrationBest For: Complex custom illustrations, multi-panel figures, vector polishing.
Notes: Full-featured free alternative to Illustrator (SVG-native). Ideal for assembling multi-panel publication figures (Panel A, B, C) with exact column widths and 300+ DPI.
3. Diagrams as Code (Text → Diagram)
Write markup or code to define nodes and connections. Diagrams are generated automatically, making them easy to version control in Git and modify quickly.
Mermaid
Best For: Flowcharts, sequence diagrams, Gantt charts, class/state diagrams, mind maps.
Notes: Uses Markdown-like syntax. Renders directly in GitHub, GitLab, Notion, Obsidian, and docs. Fast for reproducible diagrams.
graph TD
A[Data Ingestion] --> B{Validation}
B -- Pass --> C[Feature Extraction]
B -- Fail --> D[Log Error]
C --> E[Model Training]
Graphviz
Best For: Graphs, networks, hierarchical layouts, complex node-edge diagrams.
Notes: Automatic layout engine. Excellent for large or structured graphs without manual positioning.
digraph G {
rankdir=LR;
"Input" -> "Filter" -> "Classifier" -> "Output";
}
PlantUML
Best For: UML, sequence, activity, and component diagrams.
Notes: Text-based and highly flexible. Integrates with IDEs and exports SVG, PNG, or LaTeX.
plantuml.com →TikZ / PGFPlots (LaTeX)
LaTeX NativeBest For: High-precision methodology diagrams, flowcharts, plots that match paper fonts.
Notes: Steeper learning curve, but unmatched quality and reproducibility in LaTeX papers. Fonts and math symbols match your paper body text exactly. Part of any modern LaTeX distribution.
\begin{tikzpicture}
\node [draw] (a) {Raw Data};
\node [draw, right of=a, node distance=2.5cm] (b) {$\int f(x)dx$};
\draw [->] (a) -- (b);
\end{tikzpicture}
4. Data Plots & Statistical Figures
For empirical data, benchmark comparisons, and statistical distributions, scripted plotting libraries give you full reproducibility.
Matplotlib + Seaborn
Best For: Publication plots, training curves, statistical graphics.
Notes: Python standard. Full control over every axis, spine, and label, highly customizable.
pip install matplotlib seaborn
ggplot2 (R)
Best For: Grammar-of-graphics statistical visualizations.
Notes: Reproducible, elegant plots. Pairs well with cowplot, ggpubr, and patchwork for multi-panel publication figures.
install.packages("ggplot2")
gnuplot
Best For: Command-line scientific plotting.
Notes: Lightweight, scriptable, high-quality vector output (PostScript, PDF, SVG). Great for fast terminal workflows.
Plotly (Open-Source Core)
Best For: Interactive + static scientific plots.
Notes: Good for exploratory analysis and web dashboards, with static publication exports via Kaleido.
5. Scientific Icon & Illustration Libraries (Free / Open)
These provide reusable vector icons and drawings you can drop directly into Inkscape, draw.io, or other tools:
Bioicons
Open SourceOpen-source scientific icons (especially life sciences, molecular biology, and biochemistry).
PhyloPic
Free SilhouetteSilhouette vector icons of organisms across the tree of life.
SciDraw
Community DrawingsCommunity-contributed scientific drawings for research rigs, apparatuses, and setups.
NIH BioArt
BiomedicalFree biomedical illustrations provided by the National Institute of Allergy and Infectious Diseases (NIAID / NIH).
Servier Medical Art (SMART)
CC BY 4.0High-quality medical illustrations (free for academic and educational use).
Health Icons
Public DomainOpen health-related icons for clinical, healthcare, and public health projects.
6. Emerging Open-Source AI / Automated Tools
Automated tools for generating diagrams, knowledge graphs, and standardized flows from text:
SciSketch (Yale NLP)
Framework for generating schematic diagrams from scientific papers (open-source).
GitHub: yale-nlp/SciSketch →OpenDiagram
AI diagram generator (Excalidraw-based, self-hostable) for architecture, sequence, and ER diagrams.
GitHub: Itz-Agasta/OpenDiagram →Napkin AI
Excellent knowledge graph generator (free version available, with paid options).
napkin.ai →SchemaTex
Text DSL → industry-standard diagrams (including PRISMA flow diagrams) as pure SVG.
GitHub: SchemaTex/SchemaTex →About the Author
Md. Muqtadir Fuad is an Industrial & Production Engineering researcher and software engineer at BUET specializing in applied machine learning, computer-aided engineering design (CAD/FEA), and full-stack computational tools.