Monkeybread

Changed

- Major refactoring and revamping of the functionality from Verion 0 to 1
- Refactored pipeline for computing cellular niches
- Ability to run more exact kernel density estimation in addition to the grid approximation
- New visualization tools for exploring cell type enrichment in cellular niches
- New visualization tools for visualizing ligand-receptor co-expression in neighboring cells
- Ability to download ligand-receptor pairs from OmniPath
- Removal of many functions deemed reduntant
- New tutorial notebook

Changed

- Changed `cell_contact_embedding_zoom` to `embedding_zoom` and abstracted functionality

Removed

- Removed volcano plot function

Added

- Added ligand-receptor interaction calculation, statistical, and plotting functions
- Added cell contact zoom plot for more finely focused examination of cell contacts
- Added embedding filter plot for highlighting only certain groups while coloring by another metric

Changed

- Renamed arguments to `mb.calc.neighborhood_profile` for better understanding

Added

- `mb.calc.neighborhood_profile` can take in a number of nearest neighbors to consider instead of radius

Changed

- `mb.plot.cell_contact_heatmap` sorts categories

Changed

- `mb.calc.shortest_distances` now returns a DataFrame for easier indexing
- `mb.plot.cell_transcript_proximity` uses predetermined colors if previously added by Scanpy

Fixed

- Fixed calculation in shortest distance statistical test