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xiaoyeye / TFvelo

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not show velocity very well #7

Open haoqing12 opened 6 months ago

haoqing12 commented 6 months ago

I am impressed by the described in your paper and am eager to explore the applications of the TFvelo in my research.

However, it doesn't show velocity very well in my adata, what parameters can be adjusted the result.

Any information you can provide would be greatly appreciated.

lijc0804 commented 4 months ago

If the pseudotime inferred by TFvelo is inconsistent with your expectation, we suggest checking the phase portrait fitting, especially for key genes known to be critical for the biological processes. Phase portrait fitting shows the performance of dynamic modeling on each individual gene, which is the basis for downstream pseudotime inference and sreamplot visualization. To visulize the phase portrait of a list of genes, e.g. genes=['AA', 'BB', ...], you can use TFv.pl.velocity(adata, genes). If the phase portrait fitting on most genes is not satisfactory, maybe you can try larger WX_thres. This could help improve the model's fitting capabilities.