Cell Type Annotation Tutorial - Added UMAP of Embeddings

[ManuelSokolov]

Summary of Changes

• Altered the code to obtain cell embeddings for comparative analysis.

Why This Is Important

• These embeddings can help evaluate whether they offer a more accurate and meaningful representation of cell types compared to traditional gene expression data.

Key Considerations

• By analyzing the embeddings, we aim to determine if certain cell types that are close in biological function or structure are also represented closely in the embedding space. This could highlight potential similarities between the cell types and might explain instances of misclassification.

• From a visual inspection of the embedding plots, the embeddings appear to better represent the data, revealing separations between cell types that were not observed in the initial gene expression data.

Potential Impact

• This analysis could help us understand misclassifications between closely related cell types and improve model performance in distinguishing between them.
• The improved visualization of cell type separations could lead to better clustering and understanding of complex cell relationships.