Exporting Results
ProtSpace allows you to export publication-ready figures, raw data, and protein IDs.
Export Button
Click Export in the control bar to see available formats:
| Format | Description |
|---|---|
| PNG | Raster image of the current view with legend |
| PDF document of the current view with legend | |
| Protein IDs | Text file with newline-separated identifiers |
| Parquet | .parquetbundle file with all data and optional settings |
Image Export (PNG / PDF)
When PNG or PDF is selected, you have two export paths:
Figure Editor (Recommended)
Click Figure Editor to open a full-screen editor with live preview. This is the primary workflow for creating publication-quality figures. See the Figure Editor guide for full documentation.
Key features:
- Journal presets for Nature, Science, Cell, PNAS, PLOS, and presentations
- Photoshop-style Dimensions panel, Width/Height/DPI, unit toggle (px/mm/in/cm), Resample on/off, aspect-lock chain
- Overlays, circles, arrows, and text labels to annotate your figure
- Zoom insets, true geometric magnification with a per-inset Dot size slider
- Legend customization, position, font size in pt or px, columns, free-floating placement
- Click-to-select + Delete/Backspace, click an overlay or inset (canvas or sidebar) and press Delete to remove it
- Persistent settings, your layout is saved to localStorage and optionally embedded in
.parquetbundlefiles - Print-correct output, PNG includes pHYs DPI metadata; PDF page size is mm-accurate
Quick Export
Click Quick Export to download an image immediately, with no preview. It always uses fixed defaults, a 2048 × 1024 px image with the legend on the right, and keeps your current zoom and pan; it does not use Figure Editor settings. For another size or layout, or for the full plot, use the Figure Editor.
Dot size in images
Dots grow as you zoom in. Quick Export keeps your current zoom, so its dots match the size you see on screen. The Figure Editor always renders the full view, so its dots are drawn at their unzoomed size.
Contours are not exported yet
Contours are not drawn in exported images: Quick Export PNG and PDF, the Figure Editor and its zoom insets show the points only. The Figure Editor preview shows exactly what will be exported. Tracked in #498.
Parquet Export
Export a .parquetbundle file that can be loaded back into ProtSpace or shared.
- Include legend settings: Saves your current legend customizations (colors, shapes, ordering, visibility, palette, and the shape size if you picked one) inside the file. Anyone who loads it will see the same visual configuration. The Contours mode is not saved in the file; it lives in the page URL.
- Figure editor settings: When legend settings are included, the Figure Editor state (dimensions, DPI, legend layout, overlays, insets) is also saved. This lets you reopen the Figure Editor exactly where you left off.
If the bundle you loaded carried statistics (prepared with protspace ... --stats), the export re-emits them byte for byte, even with Include legend settings off. See Separation Scores for what those scores drive.
Export fails on a reserved value
Export stops with an error, rather than writing a corrupt file, if any annotation value or category name contains the literal text ---PARQUET_DELIMITER---. That string separates the bundle's parts, so it cannot appear inside one.
Protein IDs Export
Exports a plain text file with one protein ID per line. Useful for downstream analysis.
What Gets Exported
| State | Exported Data |
|---|---|
| Proteins isolated | Only isolated proteins |
| No isolation | All proteins |
Use isolation to export specific subsets.
A subset export drops the statistics: the scores were computed over the whole dataset, so keeping them in a slice would make them read as describing that slice.
Next Steps
- Figure Editor - Full guide to the publication figure editor
- FAQ - Common questions
- Data Format Reference - Understanding the file format