the coordinates are flipped

[Lena926]

Hello, thank you for creating such a useful tool, I am very happy to use it in my data, but when I draw a graph with tg.plot_cell_annotation_sc, I find that the coordinates are flipped, how can I solve it?

when I use scanpy I got this:

But tg.plot_cell_annotation_sc

Thanks a lot!

[giovp]

Hi @Lena926 ,

the reason for the inconsistency is that in scanpy (or squidpy ) we enforce the origin (0, 0) to be on the top left, as is common convention with image data. You can recover this by flipping the coords in adata.obsm["spatial"] with np.flipud and np.fliplr

[Lena926]

Hi @Lena926 ,

the reason for the inconsistency is that in scanpy (or squidpy ) we enforce the origin (0, 0) to be on the top left, as is common convention with image data. You can recover this by flipping the coords in adata.obsm["spatial"] with np.flipud and np.fliplr

Thanks for your help, I'll give it a try