Open source diagram tools for research, compared on licence, offline use, self-hosting, vector export, and keeping diagrams reproducible in version control.
SciFig Team
SciFig editorial team
Open source diagram tools solve two research problems: cost and reproducibility.
Cost is the obvious one: open source diagram software is free to use, which matters especially for students and for labs outside well-funded institutions. Reproducibility is the more interesting one. A diagram defined as text, under version control, regenerated by a script, is a research artifact in the same sense your analysis code is — and it does not stop working when a licence lapses.
A repository tree showing diagram source files stored alongside analysis code, with the rendered figure output beside it (Figure generated with SciFig)
Three Families
Open source diagram tools split into three groups that suit different jobs.
Family
Tools
You get
You give up
Text-to-diagram
Graphviz, Mermaid, PlantUML, D2
Version control, regeneration, automation
Fine visual control
Direct manipulation
Inkscape, draw.io, Excalidraw, Krita
Precise composition
Reproducibility, diffability
Plot libraries
matplotlib, ggplot2
Data-bound figures, full automation
Suitability for conceptual diagrams
Most research groups end up using one from each family of open source diagramming tools, and the common mistake is trying to force one tool across all three jobs.
Pick by Output
With any software for diagrams, the family matters less than what you need to hand over at the end:
LaTeX source. Write the figure in TikZ / PGF inside your LaTeX document. Graphviz, Mermaid, PlantUML and D2 also stay as text, but they output SVG or PDF rather than LaTeX code.
An editable project. Keep the native file, such as a .drawio file from draw.io. It stores shapes, connectors and pages as diagram data that draw.io reopens for editing; a plain SVG export is a drawing, and draw.io can only reopen it as a diagram if you embed the diagram data at export.
Just an image file. Export SVG (or PDF) from any tool on this page. SVG stays sharp at any size and opens in Inkscape for a final pass.
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Graphviz is the veteran. You describe nodes and edges in DOT and it computes the layout. For anything graph-shaped — pathways, dependency structures, phylogenies, state machines — it produces a defensible layout without manual fiddling, and exports SVG and PDF.
Mermaid trades some layout power for readability and renders natively in many Markdown environments, which makes it convenient for documentation and lab notebooks.
PlantUML targets software diagrams — sequence, class, component — and is the right choice if you are documenting a computational pipeline.
D2 is the newest and has the strongest layout engine of the four, with a syntax designed to stay readable as diagrams grow.
Direct Manipulation
Inkscape is the reference open source vector editor. Full SVG control, exports PDF and EPS at journal requirements, handles CMYK conversion. It is where figures should finish when appearance matters. The interface takes real time to learn.
draw.io is faster for structured diagrams and requires almost no learning. Open XML format, runs offline, and a common open source Lucidchart alternative.
Excalidraw is for thinking rather than finishing, with a deliberately provisional hand-drawn look. In a draw.io vs Excalidraw choice, pick draw.io for finished structured diagrams with connectors and shape libraries, and Excalidraw as a lighter alternative to draw.io for whiteboard sketches.
Krita is a raster painting application, relevant when a figure needs illustration rather than diagramming — anatomical drawings, textured biological structures.
A comparison of the same pathway rendered by Graphviz automatic layout and by hand in Inkscape, showing the trade-off between speed and control (Figure generated with SciFig)
Three example diagrams representing the text-to-diagram, direct manipulation, and plot library families (Figure generated with SciFig)
Free to start, not open source: SciFig
SciFig (scifig.ai) is not open source and runs in the browser, so it is not one of the tools compared here. It is worth knowing when the constraint is time rather than licence. SciFig FlowChart (flowcharts and diagrams) turns a plain-language description into a native SVG diagram with every box, label and connector editable — try the text to diagram generator. SciFig DataChart (data-driven charts) plots charts precisely from your CSV or Excel data and lets you download the Python code, and SciFig AI Illustration (AI scientific illustration) creates concept figures you can convert to editable SVG. Exports carry no watermark, and a free publication license PDF covers publication and commercial use.
Free to start · 3 figures on day one · up to ~44 in your first month, no card required. SVG exports open in Inkscape for a final pass, just like the output of any open source tool on this page.
Reproducibility in Practice
The concrete benefit of text-defined open source diagrams is that they participate in your existing workflow:
Diffs are meaningful. A pull request shows that one edge was added, not that a binary file changed.
Regeneration is automatic. If the diagram is generated from a data file, updating the data updates the figure.
Provenance is preserved. The commit history records who changed what and why.
The limit is aesthetic. Automatic layout produces defensible diagrams, not beautiful ones. A pragmatic pattern is to generate structure automatically, export SVG, and do a final pass in Inkscape — accepting that the last step breaks regeneration, and doing it only once the science is settled.
Tip
Check licences before publishing, not after. Most of these tools are GPL, MPL, or Apache licensed and place no restriction on the figures you create, but a few icon and font libraries bundled with them carry separate terms. The tool's licence and the asset's licence are different things.
Create Scientific Figures Now
Describe your scientific figure in natural language — get publication-ready illustrations in minutes.
When you want structure without writing DOT syntax, SciFig FlowChart turns plain language into a native editable SVG diagram, and SciFig AI Illustration (text to figure) handles publication figures you can convert to editable SVG. Our BioRender alternatives comparison covers the figure-library category alongside these.
A diagram distinguishing the software licence from the bundled asset licence for open source diagram tools (Figure generated with SciFig)
There is no single best open source diagram software for every job. Graphviz and D2 lead for generated structural diagrams, Inkscape for final publication artwork, and draw.io for quick structured diagrams. Most research groups use one from each category.
Yes. Inkscape exports SVG, PDF and EPS, and draw.io exports SVG and PDF, at journal specifications, and Graphviz and D2 export vector formats directly. No major publisher restricts which software produced a figure.
Diagrams stored as text diff meaningfully in version control, regenerate automatically when underlying data changes, and carry commit history as provenance. The trade-off is reduced control over fine visual composition.
For scientific figures, yes. It provides full vector editing, journal-grade export formats, and CMYK conversion. Its interface is less polished, which mainly costs learning time rather than capability.
The tools generally do not. However, icon sets, fonts, and template assets bundled with a tool may carry their own licences, so check the asset terms separately from the software terms before publishing.
Graphviz or D2, because both compute layouts automatically. Manual placement stops being practical beyond roughly thirty nodes, and automatic layout also produces a more defensible arrangement.
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