[QUESTION] How to change the initialContent of Suggest @blueprintjs/select to list full genes for Quick gene search.

[lijinbio]

Hi all,

I want to change the initalContent of Suggest to show full genes when clicking on the quick search box. Right now, it pops out a "Enter a gene" text box that is specified by initialContent. Is there a way to show all genes in scrolling box instead? Like below.

Could you please help suggest how could I change this behavior of cellxgene? Thanks.

[seve]

Hi, thanks for the inquiry! I believe we've already implemented a similar dropdown over on scExpression. Could you verify that the gene select on this page is the kind of functionality you're looking for?

[lijinbio]

Hi @seve, exactly, this is the function I am looking for. May I ask how could I change it for cellxgene? Thanks.

[lijinbio]

Hi @seve, thanks for your info. I understand the dropdown function on scExpression is using a self defined QuickSelect() module in https://github.com/chanzuckerberg/single-cell-data-portal. However, cellxgene is using the Suggest module of blueprintjs. Might be a naive question. May I ask how I could extend blueprintjs/Suggest to have the functionality as QuickSelect()? Thanks.

[MaximilianLombardo]

Hi @lijinbio - I wanted to jump in and ask a follow-up question. For your use case, what does the requested feature accomplish for your workflow?

[lijinbio]

Hi @MaximilianLombardo, thanks for follow up. I tried to use cellxgene to visualize a spatial data, from which the gene panel is quite small, e.g., < 300 genes. Users/biologists are very likely to explore this genes one by one, but it is hard to remember all of them and input them in the Quick search box. So, it will be super helpful if we can list the gene panel so that users can select them from the dropdown list.

[lijinbio]

Hi @MaximilianLombardo, thanks for follow up. I tried to use cellxgene to visualize a spatial data, from which the gene panel is quite small, e.g., < 300 genes. Users/biologists are very likely to explore this genes one by one, but it is hard to remember all of them and input them in the Quick search box. So, it will be super helpful if we can list the gene panel so that users can select them from the dropdown list.

Hi @MaximilianLombardo, I hope cellxgene might consider to add this dropdown list feature. Alternatively, could you please help suggest if blueprintjs/Suggest (used in cellxgene for quick search) could extend its function to show the dropdown list by setting some parameters? E.g., initialContent? Thank you so much.

[lijinbio]

Hi @seve and @MaximilianLombardo, may I ask any update on this? Thanks.

[MaximilianLombardo]

Hey @lijinbio!

I appreciate the follow-up and the context on how the change would benefit your use case. I think for the scenario where the list of genes is small, the change you suggested to cellxgene desktop explorer would be feasible/make sense. But in the more common scenario (i.e a regular scRNA-seq experiment) this list would be too long to be able to parse reasonably, and I expect that the gene list would need further organization (i.e. grouping by gene functionality, gene class, average expression or variable expression) in order to make it easier to navigate. I do think the point/request you brought up is a good one, and we will continue to evaluate the priority of this type of feature in relation to other items on the roadmap. Very happy to continue the discussion here if you have other points to add to the matter.

Alternatively, could you please help suggest if blueprintjs/Suggest (used in cellxgene for quick search) could extend its function to show the dropdown list by setting some parameters? E.g., initialContent? Thank you so much.

This looks like it is on the right track, @seve will be able to weigh in and confirm this

[lijinbio]

Hi @MaximilianLombardo, thank you so much for your nice reply. I don't have others to add to the matter. I am very happy to know that this feature is under your consideration.

Hi @seve, yes, please let me know if initContent or other parameters might do the trick. If so, could you please help show me some example code of the change? Thank you so much.

[lijinbio]

Hi @seve, may I ask any update on this? Thank you so much.

[lijinbio]

Hi @seve, may I ask if you might have any suggestions about this initContent of blueprintjs/Suggest to show the full gene list? Thank you so much for your help.