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Question about dyn.pl.umap

See original GitHub issue

Hi, I try to run “Zebrafish pigmentation” tutorial as follows:

adata=dyn.read('zebrafish.h5ad')
dyn.pp.recipe_monocle(adata)
dyn.tl.dynamics(adata, model='stochastic', cores=10)
dyn.tl.reduceDimension(adata)
dyn.pl.umap(adata, color='Cell_type',pointsize=0.5, alpha = 0.7,save_show_or_return='save')

The output feels strange:

dyna

The file comes from #116: https://www.dropbox.com/s/5wk3q2xhgqai2xq/zebrafish.h5ad?dl=1

Issue Analytics

State:
Created 2 years ago
Comments:5

Top GitHub Comments

1reaction

Xiaojieqiucommented, Feb 22, 2022

Dear @lh12565, thanks for reporting this.

For your first question:

The API to this function has been changes. please set return_df = True instead of output_values and the adata are also saved in the adata so that is why you can still plot it

@dummyindex can you please update the corresponding notebook

0reactions

Xiaojieqiucommented, Feb 22, 2022

these could be just numerical instability, as many steps may be not fully deterministic such as dimension reduction, vector field reconstruction, etc. – I would not worry about this too much if the overall conclusion is the same