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maximilianh / cellBrowser

main repo: https://github.com/ucscGenomeBrowser/cellBrowser/ - Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org
https://github.com/ucscGenomeBrowser/cellBrowser/
GNU General Public License v3.0
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'Find Cells' doesn't work #63

Closed matthewspeir closed 5 years ago

matthewspeir commented 5 years ago

@maximilianh When I open the 'Find Cells' pop-up from the 'Edit' drop-down, I can't seem to actually find any cells after selecting a field and entering a filter value. If I hit 'enter' on my keyboard or click 'OK' nothing happens. The pop-up doesn't close and no filter is applied.

Steps to reproduce:

maximilianh commented 5 years ago

I've fixed this now for gene expression values. Still working on it. Will take some more time.

maximilianh commented 5 years ago

I've added a LOT of code for find cells, You can now remove fields and the current status is written to the URL and also the dialog is recreated with your current filtering options.

But... I still haven't fixed this issue with numeric fields. Will do tomorrow.

matthewspeir commented 5 years ago

Awesome! Those were actually things I was going to suggest in some new tickets, but you've already added them! :)

Thanks!

matthewspeir commented 5 years ago

Any update on fixing 'Find Cells' for numerical values? Thanks!

maximilianh commented 5 years ago

Haven't gotten to that yet... sorry...

On Tue, Mar 5, 2019 at 10:28 PM Matt Speir notifications@github.com wrote:

Any update on fixing 'Find Cells' for numerical values? Thanks!

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matthewspeir commented 5 years ago

No problem. Was just wondering if there were any updates. :)

maximilianh commented 5 years ago

Update before you think I'm not doing anything on this: I think I've spent two full days on this now in total. Still ongoing. It moves the assignment of bins to numbers from Python into Javascript. Somehow I'm too stupid to do the discretization of the numbers in javascript even though I had it all working in Python before.

On Wed, Mar 6, 2019 at 9:01 PM Matt Speir notifications@github.com wrote:

No problem. Was just wondering if there were any updates. :)

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maximilianh commented 5 years ago

Given Hiram's Wiggle experience, I should have known that storing numbers in bins instead of the original numbers (which is what I used to do with meta fields that are numbers), is a really bad idea....

On Thu, Mar 14, 2019 at 5:23 PM Maximilian Haeussler maximilianh@gmail.com wrote:

Update before you think I'm not doing anything on this: I think I've spent two full days on this now in total. Still ongoing. It moves the assignment of bins to numbers from Python into Javascript. Somehow I'm too stupid to do the discretization of the numbers in javascript even though I had it all working in Python before.

On Wed, Mar 6, 2019 at 9:01 PM Matt Speir notifications@github.com wrote:

No problem. Was just wondering if there were any updates. :)

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maximilianh commented 5 years ago

OK, after three long days, this should be working now. you can try it on cells.ucsc.edu/dev, I've only tested with the cortex-dev dataset yet.

cortex-dev.cells.ucsc.edu/dev

Let me know what else I should fix. Here are a few ideas:

1) when you come back to Find - cells, shouldn't you find the same state as last time again? I find it annoying I always have to reclick everything 2) the input box should be cleared when you change the field 3) I wonder if there should be some way to select if the criteria are ANDed or ORed, when it searches for these cells.

I wonder if it should have some sort of command line, so you can type a query instead of this clicking business, but that's a feature for another day.

maximilianh commented 5 years ago

The changes to number meta data fields have not been committed yet, I'm worried that I've broken something fundamental.

Oh and by the way multi-selecting cells now is working again, it shows reasonable stuff when you mouse over the field. The histogram is fixed, too.

On Fri, Mar 15, 2019 at 6:13 PM Maximilian Haeussler maximilianh@gmail.com wrote:

OK, after three long days, this should be working now. you can try it on cells.ucsc.edu/dev, I've only tested with the cortex-dev dataset yet.

cortex-dev.cells.ucsc.edu/dev

Let me know what else I should fix. Here are a few ideas:

1) when you come back to Find - cells, shouldn't you find the same state as last time again? I find it annoying I always have to reclick everything 2) the input box should be cleared when you change the field 3) I wonder if there should be some way to select if the criteria are ANDed or ORed, when it searches for these cells.

I wonder if it should have some sort of command line, so you can type a query instead of this clicking business, but that's a feature for another day.

matthewspeir commented 5 years ago

Thanks, Max!

Few things:

  1. Doesn't look like settings are saved in the 'Find Cells' pop-up. If I apply a set of filters and then come back, the fields I chose are still there, but the values are not.
  2. Related to (1), it looks like if the first cell annotation field selected in 'Find Cells' is a numerical field, then field name is never saved upon applying the filter and reopening the pop-up. It could be that this applies to all numerical fields, but the issue in (3) is preventing me from seeing the other numerical fields in the 'Find Cells' pop-up.
  3. It looks like if there are over 22 'cell annotation' fields (such as in https://hgwdev.gi.ucsc.edu/~mspeir/cb_GSE84465/?ds=Quake_Glioblastoma_GSE84465, where I think I have 35 -40) then only the first 22 are shown in the 'Find Cells' drop-down menu.
maximilianh commented 5 years ago

Doesn't look like settings are saved in the 'Find Cells' pop-up. If I apply a set of filters and then come back, the fields I chose are still there, but the values are not. I think I fixed this in today's release.

Related to (1), it looks like if the first cell annotation field selected in 'Find Cells' is a numerical field, then field name is never saved upon applying the filter and reopening the pop-up. It could be that this applies to all numerical fields, but the issue in (3) is preventing me from seeing the other numerical fields in the 'Find Cells' pop-up. Should be OK.

It looks like if there are over 22 'cell annotation' fields (such as in https://hgwdev.gi.ucsc.edu/~mspeir/cb_GSE84465/?ds=Quake_Glioblastoma_GSE84465, where I think I have 35 -40) then only the first 22 are shown in the 'Find Cells' drop-down menu. this I hope had something to do with this broken meta data file which was due to the bug in metaCat. It seems to be fixed now.

Can you update and re-run cbBuild and let me know if this is indeed all fine?

It's incredible how slow I am with fixing these things compared to writing them. It took a day to write this dialog and probably give to fix the edge cases. Sigh. I guess that's always the same with software.

matthewspeir commented 5 years ago

Everything looks to be fixed in the latest, 0.4.63.

maximilianh commented 5 years ago

I meant to write “three days” not “give”. Wow now I’m making typos as autocorrect was on, even though I type on the laptop.

Thanks Matt for helping me getting these things fixed!

On Tue 19 Mar 2019 at 19:19, Matt Speir notifications@github.com wrote:

Closed #63 https://github.com/maximilianh/cellBrowser/issues/63.

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