select cells based on intersection of annotations

[Gibbsdavidl]

Is this possible? It's essentially making cell selections based on annotation set operations.

I want to select a set of cells within cluster A as background (param == 'X', cluster=='A'), and compare to the remaining cells within cluster A (param != 'X' and cluster =='A' or even param == 'Y').

Thanks!

[maximilianh]

Did you try Edit - Find Cells ?

On Mon, Sep 28, 2020 at 10:11 PM David L Gibbs notifications@github.com wrote:

Is this possible? It's essentially making cell selections based on annotation set operations.

I want to select a set of cells within cluster A as background (param == 'X', cluster=='A'), and compare to the remaining cells within cluster A (param != 'X' and cluster =='A' or even param == 'Y').

Thanks!

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[Gibbsdavidl]

Oh wow! Thanks. That's just what I was looking for.

-dave

[Gibbsdavidl]

One suggestion is to have a 'is not equal to' selection for enumerated types.

[maximilianh]

I'm glad you asked. It's very hard to get an idea for me which features people find useful...

On Tue, Sep 29, 2020 at 12:59 AM David L Gibbs notifications@github.com wrote:

One suggestion is to have a 'is not equal to' selection for enumerated types.

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[Gibbsdavidl]

Actually, this would be super useful feature for me... so I'm going to reopen the issue. :-) Hope that's OK.

I have a cluster where cells are annotated with 4 categories (A,B,C,D) and if you want to select category A, it's pretty easy (select cells: cluster == 1, category == A). But if you want to compare A vs others, it's more difficult (cluster == 1, category != A).

Thanks! -dave

[maximilianh]

Isn’t there a “is not equal” operator ? Oh... did I forget to add that ???

On Tue 29 Sep 2020 at 20:23, David L Gibbs notifications@github.com wrote:

Actually, this would be super useful feature for me... so I'm going to reopen the issue. :-) Hope that's OK.

I have a cluster where cells are annotated with 4 categories (A,B,C,D) and if you want to select category A,

it's pretty easy (select cells: cluster == 1, category == A). But if you want to compare A vs others, it's

more difficult (cluster == 1, category != A).

Thanks!

-dave

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[Gibbsdavidl]

Oh, uh, yes. There is not an "is not equal" (!=) operator.

-dave

[maximilianh]

Oops, sorry. I've added it now, you can find it on the Github develop branch and also on cells-test.gi.ucsc.edu. Is this for your own cell browser installation? Or for a dataset on cells.ucsc.edu ?

Also, I'd love to understand better the use case: is this for comparing two non-clusters?

@matthewspeir since we've covered it here, not sure, but maybe we need an internal redmine ticket for it, too? I don't remember what our plan was for handling Github issues w/r to releases.

[matthewspeir]

I believe this has made it into a release. Closing for now.