I’ve just figured out how to run a build with nextstrian pipeline and got a pretty good view in auspice. I want to export that result as an image and use it as a figure in my paper. How can I do that? Or is there any other easy ways to use another tool to do so? I’m using WSL btw.
Hi @xchen,
These instructions to export a screenshot in SVG format were written for nextstrain.org, but you can use them for any view in Auspice.
Let me know if that doesn’t work for you!
– Victor
Thanks for your reply. I can download the image now! However, this brought up another problem. The radial tree does not look complete. Like the date displayed at the bottom… Is there any way to zoom out a bit?
I think this is a bug with Auspice, but you should be able to work around it by editing the SVG file directly. Can you upload your SVG file as an attachment? I can try to fix it for you, and that will also help me understand the bug better.
Sure. I appreciate your help. Here’s the file. And also, there’s a weird small circle in the middle.
Weird. I can’t attach it. I uploaded it to my onedrive. Here’s the link. Hope it works. https://1drv.ms/u/s!ApPu7dEx34YYhzonkY4-1qN_ySP-?e=ncucgu
@xchen Here’s a fixed version, hosted at nextstrain_ncov_mybuild1.svg (github.com).
Detailed changes
% git log --pretty=format:"---%n%n%B"
---
Fix centering of smallest major grid circle
---
Increase tree SVG height by 200
This way all grid lines are shown.
---
Remove tree SVG clipping
This is not suitable for the radial view¹.
¹https://github.com/nextstrain/auspice/commit/ca4c4176795b6a903239469111920fc6e1294f46
---
I hope this helps!
Looks perfect. May I ask how you edited the SVG file? What tool did you use?
For this I used a text editor. You can clone the GitHub Gist to see the changes in detail:
git clone https://gist.github.com/victorlin/a2d397fb7f89eff4346126f29939b3e2 svg-fix
cd svg-fix
# View changes with git log, git show, etc.
For bigger changes, you can look into using visual SVG editors. For that, I personally use Graphic on macOS.
Sounds great! Thanks!