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Add cluster markers and heatmap to scRNASEQ #30

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ilan-gold opened this issue May 14, 2020 · 1 comment
Open
1 of 3 tasks

Add cluster markers and heatmap to scRNASEQ #30

ilan-gold opened this issue May 14, 2020 · 1 comment
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enhancement New feature or request

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@ilan-gold
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ilan-gold commented May 14, 2020

In the h5ad-to-arrow, we actually have much more data than we output. We could ouptut as well:

  • Cluster assignments form leiden clustering
  • Heatmap of cell x expression
  • Intermediate PCA/KNN visualization

This will need to be discussed as to what is visualized and what is not. For now the cluster assignments are a must.

@ilan-gold ilan-gold self-assigned this May 14, 2020
@ilan-gold ilan-gold added the enhancement New feature or request label May 14, 2020
@ngehlenborg
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We should aim to get the Leiden clusters in as soon as possible. The heatmap would be useful, too, but I think for large data sets it might get prohibitively large. It is worth testing it though.

@mruffalo would need to comment on how useful intermediate results from PCA/kNN are.

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