comparing distribution of cell types per cohort per groups

[FADHLyemen]

• [ ] Additional function parameters / changed functionality / changed defaults?
• [x] New analysis tool: A simple analysis tool you have been using and are missing in sc.tools?
• [x] 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?

... I would like to see how to use scanpy to compare the cell types distribution per cohort per different condition. Imagine you have different disease state who have different drug exposure, so you need to compare different cell types in each cohort per each condition or drug exposure. so it id three dimension: cell types[Bcells and Tcells], disease status[CKD vs DKD] and drug exposure[absent vs non absent]

[ivirshup]

@mbuttner any thoughts on this? Perhaps this would fit better with the scCODA package?

[mbuttner]

@ivirshup changes in cell type composition can be analysed using scCODA, which builds upon scanpy. Please note that in order to analyse changes in composition, you will need at least three different cell types.