Multiomics partitions

Question

• [x] Additional function parameters / changed functionality / changed defaults?
• [ ] New analysis tool: A simple analysis tool you have been using and are missing in sc.tools?
• [ ] New plotting function: A kind of plot you would like to seein sc.pl?
• [ ] External tools: Do you know an existing package that should go into sc.external.*?
• [ ] Other?

As more and more technologies allow multimodal characterization of single cells it could be useful to exploit some functionalities of scanpy's toolkit to perform, at least, some rough integrative analysis. Assuming we have to modalities on different layers (say RNA and ATAC), one could create two knn graphs for both layers and use leidenalg.find_partition_multiplex to perform a joint call of partitions handling the two (or more) graphs as a multiplex. I have tested myself this approach, described in leidenalg documentation, it works and it is highly configurable. We can take care of the implementation of enhancement (as leiden_multiplex() function?), I just want to be sure that it is not already on the development roadmap and that it is ok to have it into scanpy and not as an external tool.

该提问来源于开源项目：theislab/scanpy

Answer 1

I realize that I'm working on a specific dataset that fits into layer specification (i.e. same obs, same var), while in general this is not true (e.g. scRNA + scATAC). Still, multiplex could be analyzed from 2+ AnnData objects when adata.uns['neighbors'] is present