Giovanni Palla
Giovanni Palla
hi @jamesMo84 > but how does one then use squidpy.gr.nhood_enrichment, sq.gr.interaction_matrix, sq.gr.centrality_scores functions to generate ‘per sample’ statistics to compare between samples. to do this, unfortunately you'd have to iterate...
hi @HelloWorldLTY , which example? thanks
hi @georgezakinih , apologies for very late reply, and thank you for your interest in squidpy. > In this case, the spatial coordinates can't be combined together in the annData...
Hi @SaskiaFreytag , thank you for the interest in squidpy. Could you please clarify the issue by providing a reprex (reproducible example) or attaching a piece of code that could...
I believe this issue is that you need to pass the `library_key` to the `spatial_neighbor` function in order to compute neighbors graph only on points belonging to the same fov....
unfortunately it's not possible but we are working on a solution in spatialdata. I will keep this opena and try to remember to link to the appropriate example here.
I would suggest you to take a look at the spatialdata-plot static plotting library https://github.com/scverse/spatialdata-plot
hey @andrewjkwok , thanks for reporting this, I'm afraid it's a bit tricky to help out without the data available. Could you share the data download so we can test...
@andrewjkwok any chance you could point us to some public data? for example, some data shared by vizgen?
hi @andrewjkwok I am unfortunately unable to look into this in the next two weeks, thanks for sharing the data, I'll get back to you soon