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Issue with selecting cell types in the STREAM #135

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Pawan291 opened this issue Jan 13, 2022 · 2 comments
Open

Issue with selecting cell types in the STREAM #135

Pawan291 opened this issue Jan 13, 2022 · 2 comments

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@Pawan291
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Pawan291 commented Jan 13, 2022

Hello,

I have already annotated object from SCANPY that I am trying to use in the stream. But I can't select and visualize cell types from my data while making stream plots, flat tree plots, subway map plots, and so on. Could anyone please help me with this?

@huidongchen
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I am not sure I understand the problem here. As illustrated in STREAM tutorial notebooks, it should be quite straightforward to visualize whatever annotations you use.

@Pawan291
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Pawan291 commented Jan 17, 2022

Hello,

Sorry for the late reply. Let me elaborate.
I am using scanpy for the analysis of my datasets. I have already annotated Louvain clusters with cell types in the scanpy. To study specific population from my datasets, I have subset them from main datasets and employed the stream for further analysis. But while making different plots in the stream, I can't select different parameters such as cell types, Louvain, etc. (details are in the attachment).

Thanks
Stream

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