Is it possible to run CCI in muti-sample?

BiomedicalMachineLearning / stLearn

A novel machine learning pipeline to analyse spatial transcriptomics data

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Is it possible to run CCI in muti-sample? #285

Closed yunbokai closed 3 months ago

yunbokai commented 4 months ago

Hi, I got an integrated ST data and I tried to use CCI function. When I ran stats = ['lr_scores', 'p_vals', 'p_adjs', '-log10(p_adjs)'] fig, axes = plt.subplots(ncols=len(stats), figsize=(16,6)) for i, stat in enumerate(stats): st.pl.lr_result_plot(adata, use_result=stat, use_lr=best_lr, show_color_bar=False, ax=axes[i]) axes[i].set_title(f'{best_lr} {stat}') It occured ERROR Found multiple possible libraries in `.uns['spatial']. Please specify. How to solve it? Thanks.

duypham2108 commented 3 months ago

Currently, we only support single library anndata only. You can create a new anndata object with a specific library and then run it again