Some problems in Visualization of UMAP plots

[lightoorange]

Dear Professor,

Thank you for your explanation and patience! I would like to know why, when running the “Plot UMAP of STitch3D’s learned representations” section, the generated images appear as shown below rather than resembling those in the Tutorials.

Also, When executing the following code:

sc.tl.louvain(adata_all, resolution=0.8)
colours = ['#8c564b', '#ff7f0e', '#2ca02c', '#17becf', '#9467bd', '#1f77b4', '#e377c2', '#7f7f7f', '#bcbd22', '#d62728', '#aec7e8']
sc.pl.umap(adata_all, color="louvain", palette={str(i): colours[i] for i in range(11)})

I encountered an error

After modifying the code to: "sc.pl.umap(adata_all, color="louvain", palette=colours)", it showes:

Best regards

[gefeiwang]

Hi there,

Please check you umap and scanpy versions, as in https://github.com/YangLabHKUST/STitch3D/issues/18.

Best, Gefei