How to export high dpi pictures with export_image and cytoscape v3.10?

[matthiaskoenig]

How can one generate high dpi images with the export_image function? It states in the doc string:

resolution (int): The resolution of the exported image, in DPI. Valid only for bitmap formats, when the selected width and height 'units' is inches. The possible values are: 72 (default), 100, 150, 300, 600. [DEPRECATED as of Cytoscape v3.10]

I have a high DPI monitor and require high dpi images (also for publication). Everything looks blurry with 72 dpi.

• The SVG export changes the figure too much (especially text and transparency).
• The only way I see is to export a high zoom version and than create a higher dpi version by downsizing & increasing dpi manually/via a script afterwards. Or is there another way? Why is there no resolution/dpi option anymore?

[bdemchak]

Hi, Matthias --

The situation with the export_image() parameters is pretty difficult. It comes from an overhaul of image exporting features starting in Cytoscape v3.10, and is compounded by not creating a new function (e.g., export_image_10()) when the parameters changed so drastically.

The quickest and easiest way to answer your question would be for you to use Cytoscape manually to create an example of the image you'd like to generate, and then send us a screenshot of the Export Network As Image dialog (from File | Export network to image...). We can derive the equivalent export_image() parameters from there.

Here's an example of that dialog box:

[matthiaskoenig]

Thanks. I saw how to set all these settings in the function. I just thought there is an option to set the dpi, but the zoom will work.

I am just used to save things for publication/PDF in high dpi. But I can just export with a larger zoom and set the dpi of the image afterwards.

[bdemchak]

Thanks ... you're probably right. I don't recall the specific rationale of the Cytoscape developers at the time, but your idea rings a bell.