Changes requested by Justin Cook

[innovate-invent]

Globe Analysis Page

• [x] Can “upload data to visualize” say “upload csv” to make it clear that is the file format we’re expecting?

• [ ] Window for picking colours (the window with the different presents, slider, colour palette and RGB specifier) won’t go away unless you click on something else. It doesn’t turn off based on hovering.

• [ ] Export key was a little glitchy, he clicked it and none of the image format options showed up

• [ ] The Black Band Problem #20

General Observations/comments

• [ ] Domain movement was pretty smooth around the outside of the globe, didn’t see the accidental click on/ click off issues
• [ ] Side bar seemed a little trigger happy with the hover
• [ ] When hovering over a domain and all the bands within that domain show up, he was expecting some kind of summary statistic such as the actual number of bands in that domain to show up. Instead, we just get a random correlation value showing up.
• [ ] Since he can click domains on/off he would expect to also be able to click on specific correlation ribbons and turn those on/off as well.
• [x] Saying “document order” wasn’t super clear, he thinks “Order in File” may be a better way to label that option.
• [ ] For quick settings, was expecting a ‘token system’ for saving the globes instead of what we have now.
• [x] Would expect clicking on the GlobeCorr Icon in the upper left to bring you to home page, it didn’t for him.

Looking at the homepage, the description of the website felt too general. It was hard to figure out just from that what kind of data you were supposed to be using. The concepts of variable within domains was not familiar. But he also said he imagined that people coming to this site would have a better idea of what they were looking for and know whether or not their data would fit into this structure.

[cookersjs]

@innovate-invent I toggled the 'Windows for picking colours' checkbox, which is why it shows I edited the message (I hadn't seen it like that in a PR so I was curious - didn't realize it would edit, sorry about that!) - I put it back to unchecked

[github-actions[bot]]

Pull request has been successfully built and is ready for review at https://cooked-579608958-globecorr.stage.brinkmanlab.ca/

[innovate-invent]

I meant to follow up on the unchecked items.

The color palettes do not disappear until they lose focus rather than mouse hover because they are able to appear without the mouse over them. This can potentially cause them to immediately disappear. I can enable this functionality if you feel it is important though.

I can't reproduce the issue with the export key.

I am waiting on Mariam to reply to the black band problem.

I am not sure what is meant about the sidebar being trigger happy. Adding a delay before it appears could be annoying to people trying to flip back and forth changing settings rapidly.

All visualization functionality changes would be best requested from Mariam.

I am not sure what is meant by a "token system" for saving the settings. This may be a misunderstanding that there is a server backing this website when it is actually static.

[cookersjs]

Hi @innovate-invent, some responses from me:

I can't reproduce the issue with the export key.

My memory is a little fuzzy on this one, but I think it was a very minor thing that happened. I think it just took multiple clicks the very first time to get the filetypes to appear - I can revisit the site and see if I can reproduce myself

I am not sure what is meant about the sidebar being trigger happy. Adding a delay before it appears could be annoying to people trying to flip back and forth changing settings rapidly.

I think what I meant by that wasn't the 'quickness' with which it appeared/hid but rather the element area that seems to activate hiding/appearing. I think I meant more that the sidebar would appear/hide with my mouse further away than expected. I can revisit the site to nail down exactly what I mean.

I am not sure what is meant by a "token system" for saving the settings. This may be a misunderstanding that there is a server backing this website when it is actually static.

This was more of an offhand comment based on my previous experience at Reactome - not anything I actually expected. I was just in 'say what I'm thinking while I'm using the website' mode. You might find it interesting though, so here is what I meant, briefly:

1. Go to https://reactome.org/ and click on 'Analyze Data'. This should bring you to https://reactome.org/PathwayBrowser/#TOOL=AT.
2. Click one of the items in the 'Some examples' list (such as UniProt accession list) and click Continue, and then Analyse! in the next window.
3. After a second or two you should see the Pathway Browser get yellow highlighting - this just represents UniProt accession ID coverage in the Reactome database (not important).
4. At the top of that page after the analysis has been run, the URL will look like https://reactome.org/PathwayBrowser/#/DTAB=AN&ANALYSIS=MjAyMTAxMjUxNTE4MjRfMw%253D%253D&FILTER=resource:UNIPROT. That MjAyMTAxMjUxNTE4MjRfMw%253D%253D part is what I refer to when I say 'token' - it just Reactome's way of storing analysis results, either for yourself or for you to share. So, not a request, just something I was familiar with

If you'd like, I'd be happy to run through the website again if it would be useful for you. Just let me know!

[innovate-invent]

If you and @esgarlock are happy with leaving the unchecked issues unchecked then we can move forward with merging. Otherwise I would appreciate expanding on them a bit more.

I see what you mean with the token system, that would require a server to store the session. There is no server backing GlobeCorr.