Default interface simplification?

[robertamezquita]

Working with several biological collaborators using iSEE, a few things came up as must-haves to make iSEE a part of their regular routine. One issue that came up was the default interface was a bit intimidating with the sheer number of panels that came up.

Most of the biological collaborators come from using 10X's software, the Loupe Browser (https://support.10xgenomics.com/single-cell-gene-expression/software/visualization/latest/what-is-loupe-cell-browser), which presents a single panel on start-up. I could see a similar tact here with one of the dimreds being loaded (anything matching TSNE/UMAP since thats always the first go to, or the first dimred otherwise).

Maybe this would also help slightly with the long load time as well if only one panel is loaded at start-up?

[LTLA]

Just configure it yourself, I assume you're using a server instance.

[federicomarini]

For this purpose, we have a full set of mode functions coming up from iSEEu, also with the beauty of having some external contributors (Charlotte and I coordinated a session at the recent Developer Day at #EuroBioc2019)

You can find some pointers here:

• mode empty, "build up as you go": https://github.com/isee-developers/iSEEu/blob/master/R/modeEmpty.R
• mode "gating", i.e. with linked multiple feature assay plots https://github.com/isee-developers/iSEEu/blob/master/R/modeGating.R
• some more ideas dropped in GROUP: Expanding the collection of iSEE modes Bioconductor/EuroBioc2019#4

Hope this helps to set up your config 😉
(and more than happy to get a PR in iSEEu with modeHutch)

[robertamezquita]

Great to see this functionality here! Thanks for the pointer to modeEmpty and mode "gating" in particular, those look like what I'm looking for :)

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On Mon, Jan 13, 2020 at 11:39 AM Federico Marini ***@***.***> wrote: For this purpose, we have a full set of mode functions coming up from iSEEu, also with the beauty of having some external contributors (Charlotte and I coordinated a session at the recent Developer Day at #EuroBioc2019) You can find some pointers here: - mode empty, "build up as you go": https://github.com/isee-developers/iSEEu/blob/master/R/modeEmpty.R - mode "gating", i.e. with linked multiple feature assay plots https://github.com/isee-developers/iSEEu/blob/master/R/modeGating.R - some more ideas dropped in Bioconductor/EuroBioc2019#4 <Bioconductor/EuroBioc2019#4> Hope this helps to set up your config 😉 (and more than happy to get a PR in iSEEu with modeHutch) — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <https://github.com/isee-developers/iSEE/issues/339?email_source=notifications&email_token=AASTMLLL43HER75GTHSIHXDQ5S7NZA5CNFSM4KGFYQE2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEI2AKEY#issuecomment-573834515>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AASTMLKOTS3AIDG2B5YLJ4TQ5S7NZANCNFSM4KGFYQEQ> .

[federicomarini]

Glad it helped.

Keep an eye on the contributed mode objects as well, @mbstadler had a cool redDim comparison idea, @plger something to embez Gviz visualizations, @fionarhuang a novel TreeSummarizedExperiment viewer (thank you all!). We hope the API rewriting will make it possible to have such custom panels and modes in an even more straightforward way!

[LTLA]

I'm going to move this to iSEEu because that's where all the modes are going to live.

[kevinrue]

Seems like this was answered above