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If you want to contribute here, adding plots of the UMAP representations of the integrations to the report would be a good starting point. UMAP creation currently happens in this module, more specifically in this script. After this line, the X_umap obsm field will contain the proper representation that can directly used for plotting.
Plotting itself should not be much of a problem. Make sure to use ${prefix}.png as the plot file name. In order to properly add the plots to the multiQC report, some additional steps are required:
Change the output definition of the UMAP process so that the png and json are emitted properly (example)
Add a new channel to the CLUSTER subworkflow called ch_multiqc_files like here. Make sure to mix in the json outputs and emit the channel in the end of the CLUSTER subworkflow
Mix the subworkflow ch_multiqc_files into the global one like here
If necessary, adjust the multiQC config. General information on MultiQC can be found in the docs.
PS:
Because of the way the CLUSTER subworkflow is structured, you can be sure that the neighborhood graph that is used as a base for UMAP creation is based on the correct embeddings.
Description of feature
Example reporting has already been implemented here. scFlow had really nice reports that should be used as inspiration (can be viewed here).
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