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pinellolab / STREAM

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
http://stream.pinellolab.org
GNU Affero General Public License v3.0
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Issue with selecting cell types in the STREAM #135

Open Pawan291 opened 2 years ago

Pawan291 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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