Using additional fields from annData objects

[pinin4fjords]

Hi Max,

We'd like for CellBrowser to pick up ALL of the cell-wise metadata from Scanpy annData objects. But cbScanpyImport() seems to ignore anything it's not expecting. So e.g. we can color by Louvain clusters, but not any of the biological covariates that are already in objects we're using. Is there a way to have it pull all of the metadata so you can use it to color points?

Thanks,

Jon

[maximilianh]

Ok, if both you are having the same problem, then I'll fix this. Let me look...

On Fri, Mar 8, 2019 at 12:47 PM Jonathan Manning notifications@github.com wrote:

Hi Max,

We'd like for CellBrowser to pick up ALL of the cell-wise metadata from Scanpy annData objects. But cbScanpyImport() seems to ignore anything it's not expecting. So e.g. we can color by Louvain clusters, but not any of the biological covariates that are already in objects we're using. Is there a way to have it pull all of the metadata so you can use it to color points?

Thanks,

Jon

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[maximilianh]

I'll work towards exporting all meta data fields by default. @mspeir also asked for this.

On Fri, Mar 8, 2019 at 1:19 PM Maximilian Haeussler maximilianh@gmail.com wrote:

Ok, if both you are having the same problem, then I'll fix this. Let me look...

On Fri, Mar 8, 2019 at 12:47 PM Jonathan Manning notifications@github.com wrote:

Hi Max,

We'd like for CellBrowser to pick up ALL of the cell-wise metadata from Scanpy annData objects. But cbScanpyImport() seems to ignore anything it's not expecting. So e.g. we can color by Louvain clusters, but not any of the biological covariates that are already in objects we're using. Is there a way to have it pull all of the metadata so you can use it to color points?

Thanks,

Jon

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[pinin4fjords]

Okay cool, thanks- apologies I didn't realise this was a duplicate issue.

[maximilianh]

OK this should be good now. The default now is to export all meta data from the scanpy object in scanpyToCellbrowser().

this affects cbScanpy in the sense that if you load a file that already has meta data, like loom or a5hd, it'll get passed through.

On Fri, Mar 8, 2019 at 4:36 PM Jonathan Manning notifications@github.com wrote:

Okay cool, thanks- apologies I didn't realise this was a duplicate issue.

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[maximilianh]

release 0.4.52

On Mon, Mar 11, 2019 at 5:24 PM Maximilian Haeussler maximilianh@gmail.com wrote:

OK this should be good now. The default now is to export all meta data from the scanpy object in scanpyToCellbrowser().

this affects cbScanpy in the sense that if you load a file that already has meta data, like loom or a5hd, it'll get passed through.

On Fri, Mar 8, 2019 at 4:36 PM Jonathan Manning notifications@github.com wrote:

Okay cool, thanks- apologies I didn't realise this was a duplicate issue.

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[maximilianh]

Can you give this a try and check it? It seems to work for me on the loom file that @mspeir posted in the other ticket, with cbScanpy.

[pinin4fjords]

Awesome, thanks Max, we'll try it as soon as we can.