Vega Editor not working on Chrome or Safari

Technical Support
1

Cannot seem to load emperor qzv files into the Vega editor.

I get this output:

Invalid specification {"$schema":"https://vega.github.io/schema/vega/v5.json","axes":[{"orient":"bottom","scale":"xScale","title":"Axis 1 (27.12 %)"},{"orient":"left","scale":"yScale","title":"Axis 2 (6.047 %)"}],"background":"#ffffff","config":{"axis":{"labelColor":"#000000","titleColor":"#000000"},"title":{"color":"#000000"}},"data":[{"name":"metadata","values":[{"Accession":"PRJNA763205","Age":"Adult","City":"Buenos Aires","Class":"Mammalia","Diet":"Omnivore","Disease":"Healthy","Family":"Homin ……

Does this happen when the emperor plots have too many samples? I think mine has ~10k samples.

Attaching the file as well:

Weird thing is I replicated the error with a small emperor file with only 20 samples or so. But then upon reloading it, it worked so it seems like there’s a limit to what Vega can handle?

Thanks!

humanallunweighted_unifrac_emperor.qzv (2.4 MB)

2

It's working for me in Chrome and Safri, but I'm running an M1 mac... So I'm not sure I'm much help here.
Chrome v141.0.7390.67

What version of Chrome are you running? What other clues have you discovered?

3

Just reupdated to same version as you. So strange! Because I also have an M1 and a remote M4 mini and both give the same error. Tried disabling adblocker extensions and going incognito.

Here is an error I output I get sometimes (other times its just blank)

image
image1570×1252 418 KB

Will keep messing around and update here if I find anything

1 Like
4

Hi @Sam_Degregori,

I am also getting this issue on Firefox and Safari on multiple qiime2 qzv. (example: Moving Picture tutorial PCOA)

So I think I know why its erroring but I have no solution. I found this warning at the bottom of the moving picture tutorial viz. Its also at the bottom of your viz but the spec is so long that it takes a while of scrolling to get to it.

[Warning] The specification expects Vega-Lite v5 but the editor uses v6.2.0.

From this error I understand that QIIME 2 is using a vega v5 spec and the editor only uses v6.2.0 making the spec rendered by QIIME 2 completely useless in the vega online editor. I will discuss this with our software team and let you know what our path forward is regarding this bug.

Hope this helps!

2 Likes
5

@cherman2 this is great (i guess also bad) news! thought I was going crazy for a sec.

Thanks!

1 Like
6

@yoshiki, have you run into this? I'm wondering updating the vega spec version number from 5 to 6 here would fix this.

8

Hi @Sam_Degregori,
Can you try this again? Yesterday, I went to troubleshoot how to fix this issue and I can't recreate it today.

I think vega did something on their end to fix this? Hopefully its fixed!

1 Like
9

Oddly, I was still able reproduce this error. Although as @gregcaporaso pointed out changing the $schema from v5 to v6 fixed the issue. However, after reloading a couple of times the I can’t reproduce the error anymore. :melting_face:

3 Likes
10

Hi @cherman2 @yoshiki, after changing $schema to v6 it works!! thank you!

When i try a bigger file (attached) I get a blank screen but I imagine this is because Vega has an upper limit on how many samples it can show? If not, I can open a new post for this.

Thanks again for help!

Luis_gg2_unweighted_unifrac_emperor.qzv (4.2 MB)

11

Yeah, this display works fine for me. I suppose this is a good time to check on your physical hardware and software stack?

image
image1920×1094 166 KB

12

Hi @colinbrislawn,

Just to confirm it works for you when taking it into vega experimental?

13

No, I don't think I did that. This is just whatever is on http://view.qiime2.org/

(if this is not helpful, I can leave it to the JS devs to sort it out!)

14

Encountered same problem.

Changed schema to v6, as suggested here Vega Editor not working on Chrome or Safari - #6 by gregcaporaso , and it worked. I have 537 samples.

It is interesting. Changing v5.json to V6.json was required for first .qzv file. Change was not required for subsequent .qzv files. They open fine with v5.json.

1 Like
15

Yeah i think the blank screen problem happens when you get to multiple thousands

1 Like