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pinellolab / STREAM

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
http://stream.pinellolab.org
GNU Affero General Public License v3.0
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scATAC-seq using k-mers tutorial using v.0.4.1 #59

Closed carmenpetitjean closed 4 years ago

carmenpetitjean commented 4 years ago

Hi,

I am currently trying to follow the scATAC-seq using k-mers tutorial but have encountered difficulties reproducing your results (even using the same code), particularly for the dimension reduction plots and subway maps. I was wondering if these issues could be linked to the difference in STREAM versions used (your tutorial using v0.3.7 and I using v0.4.1) or if this could be due to any other reasons.

I've attached the plots that I have produced following the tutorial.

dimensionreductionplot1 dimensionreductionplot2 subwaymap

Thank you!

huidongchen commented 4 years ago

Hi ,

Thanks for trying STREAM. Indeed many changes including defaulting settings have been introduced since v0.4. So in order to exactly reproduce what is shown in the tutorial notebook, you might need to use the same version.

Nevertheless, for your current analysis with v0.4.1, the result actually is not bad except for the monocyte population. Can you try to increase the number of clusters to get a finer initial structure e.g.st.seed_elastic_principal_graph(adata,n_clusters=20) or increase the number of neighbors, e.g st.dimension_reduction(adata,n_neighbors=200,n_components=4) ? This should help improve the structure learning for the disconnected part.

carmenpetitjean commented 4 years ago

Increasing the number of clusters and the number of neighbours seemed to have improved analysis! Thank you!