Add cluster markers and heatmap to scRNASEQ

hubmapconsortium / portal-containers

Docker containers to pre-process data for visualization in the portal

MIT License

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Add cluster markers and heatmap to scRNASEQ #30

Open ilan-gold opened 4 years ago

ilan-gold commented 4 years ago

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

[x] 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.

ngehlenborg commented 4 years ago

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.