Issue with selecting cell types in the STREAM

[Pawan291]

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]

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]

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