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
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!