Saad khan comments

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                                            Saad khan

Error when running python commandline.

Thanks Huidong, Another bug I found is that if cell labels have spaces in them e.g. 'CD34+ LMPP' , 'CD34+ Lymphoid UNK', 'CD34+ MDP-1' etc the marker found step throws...

Error when running python commandline.

Cool software btw!

Increase the line size in STREAM plot

Is it something that can be changed by changing seaborn configuration settings in STREAM. I can try make changes to the code to achieve what I want if you can...

Idents in Featureplot in Seurat outputs Idents name on top of the if Label is set to true. How do we see labels on top of scanpy UMAP plots.

Nope what I am looking for is Featureplot functionality of Seurat in scanpy where you can label the UMAP by Idents like shown in the attached figure. ![umap 50 0...

Idents in Featureplot in Seurat outputs Idents name on top of the if Label is set to true. How do we see labels on top of scanpy UMAP plots.

Here the Ident is set to be a particular clustering resolution and we are visualizing nCount on the UMAP. So basically what I am looking for is "Color by Key"...

I keep getting error when running spatialdm_local AttributeError: 'NoneType' object has no attribute 'to_adata'

Thank you that fixed it but now I am getting a new error when I am trying to save anndata object using `adata.write`. Here is the error. ``` File "h5py/_objects.pyx",...

I keep getting error when running spatialdm_local AttributeError: 'NoneType' object has no attribute 'to_adata'

Do I have to remove all the adata.uns objects. I have not looked at your code in detail but a cursory glance indicates that following uns data might have to...

I keep getting error when running spatialdm_local AttributeError: 'NoneType' object has no attribute 'to_adata'

I understand why some of unstructured data may not work when writing anndata file. What I don't understand is why I would run into errors when doing pickle dump of...

Working with st_make_grid on spatial transcriptomics data

And this cellsize is the polygon size (in the grid) I am assuming. In that case why are the two hexagons plots so different from each other may I ask?

Working with st_make_grid on spatial transcriptomics data

Is there a way to control the no. of `celltrek_points` (or cells) that occur in each polygon?