Practical diagram guide
Plan a scientific graphical abstract from your mechanism notes
A useful graphical abstract explains one result or proposed mechanism at a glance. Plan the scientific story first, then choose an editable diagram or an AI illustration according to what you need to change later.
By PathwayFig · Reviewed
Decide what the figure must communicate
Before drawing, finish this sentence: “In this model, this intervention is associated with this outcome, and this is the mechanism we can support.” If your work only proposes a mechanism, say so in the title or caption. Avoid turning a pathway overview into a claim that every interaction was demonstrated in your experiment.
| Research task | What to show | What to prepare first |
|---|---|---|
| Explain a perturbation in a lab meeting | The intervention, affected branch, and measured readout | Which links are established versus hypothesized in your model |
| Compare control and treatment | Two panels with the same orientation and consistent labels | Your observed differences; never ask the model to invent effect sizes |
| Summarize a proposed mechanism for a manuscript | A compact chain connecting the experimental question to the proposed outcome | References, limitations, and the target journal’s artwork and AI rules |
Choose an editable diagram or an image draft
Choose the editable-diagram workflow when collaborators will change molecule names, adjust an inhibition relationship, or rearrange branches. PathwayFig extracts a draft graph from your description; you review the relationships before opening the vector canvas. SVG and PNG exports are available, and a local JSON draft preserves your PathwayFig editing state.
Choose the AI-image workflow when you want to explore a composed illustration with cellular context and visual styling. The output is a raster image. Its individual labels, molecules, and arrows cannot be edited as vector objects. Keep your original prompt separately and generate a new draft if the image needs changes.
These workflows start from text. PathwayFig does not reconstruct an uploaded image as an editable graph, assemble plots from experimental datasets, or verify the literature for you.
Use a brief that a collaborator could also follow
Replace the bracketed fields below with your source-supported content. You can write your description in English or Chinese. Use your own concise notes rather than uploading confidential manuscript or patient information.
Figure purpose: explain [one result or proposed mechanism]. Biological context: [organism, cell type, condition]. Intervention: [treatment / knockout / stimulus]. Required labels: [exact molecule and readout names]. Supported relationships: [A activates B]; [C inhibits D]. Hypothesis: [proposed connection, explicitly labeled as hypothetical]. Observed readout: [what was measured, without invented values]. Compartments: [which structures matter to this mechanism]. Layout: [single pathway / two comparable panels]; keep labels readable. Do not add unlisted molecules, numerical data, or unsupported causal links.
Make the first draft in PathwayFig
- Open the workspace and choose the output you need. Start from a research example if it fits your question, then replace its description with your own scope.
- For an editable diagram, build the graph and inspect the relationship review. Correct names, arrow direction, direct versus indirect wording, and proposed steps before opening the editor.
- For an image draft, start at the default 1K resolution to review the composition. Open the advanced settings only when you need another aspect ratio or resolution. The selected credit cost is shown before submission.
- Inspect the result at its intended slide or document size. Simplify crowded branches and verify labels against your source notes before sharing.
Increasing resolution does not repair a wrong interaction or unreadable wording. Resolve the mechanism and composition before spending credits on a larger draft. Current packages and resolution costs are listed in the pricing facts.
Prepare a handoff someone can review
- Figure: export the selected draft with a descriptive versioned filename.
- Editable source: save the JSON draft for a vector figure. AI image history is a separate private library; it does not save later vector edits or the full original prompt.
- Evidence notes: keep the reference and experimental context for each relationship, plus a list of unverified assumptions.
- Caption notes: record the tools used, the purpose of the illustration, and your manual corrections. Follow the target venue’s disclosure requirements.
Check the destination before making a submission figure
A workflow called “scientific illustration” does not automatically make an AI output acceptable to a publisher. Elsevier’s policy distinguishes explanatory images from graphical abstracts and prohibits general-purpose generative AI image tools for graphical abstracts. Using PathwayFig’s interface does not remove the underlying image model from that rule.
Read the export and publication review guide, check the specific journal’s current instructions, and confirm your intended workflow before preparing a submission. A lab-meeting concept draft and a journal graphical abstract can have different requirements.