pathway activity by cluster
Exploring pathway activity over clusters would be a great way to identify and compare what cell types are doing. A function should be implemented that creates a heatmap showing summarized gene expression for pathways vs. cell types. Similar to this:
To achieve this we need to:
- get a database to assign genes to pathways (e.g. gene ontology)
- summarize gene expression by cluster (pseudobulk)
- further, summarize gene expression by pathway
As, summarizing the data could lead to loss of information. Another option should be to do a dotplot, where dot size is based on % cells expressing a gene or % pathway associated genes active.