All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
- 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
cell_contact_embedding_zoom
toembedding_zoom
and abstracted functionality
- Removed volcano plot function
- 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
- Renamed arguments to
mb.calc.neighborhood_profile
for better understanding
mb.calc.neighborhood_profile
can take in a number of nearest neighbors to consider instead of radius
mb.plot.cell_contact_heatmap
sorts categories
mb.calc.shortest_distances
now returns a DataFrame for easier indexingmb.plot.cell_transcript_proximity
uses predetermined colors if previously added by Scanpy
- Fixed calculation in shortest distance statistical test
- Basis customization to functions using coordinates
- This changelog
- Neighborhood profile function
- Plotting function legends now better located
load_merscope
maintains transcript ids
- Enhancements to plotting functions with better labels/legends
- Shortest distances permutation test now includes pseudocount
- Removed unnecessary columns from
detected_transcripts.csv
when usingload_merscope
- Tutorial notebook added to documentation
- Kernel density with multiple groups are scaled individually
- Kernel density plot bug with multiple displays
- Docstring return descriptions
- Address issue from v0.3.2 (now yanked)
- Cell contact counting function
- Default
show = True
for plotting functions for consistency with scverse ecosystem
- FOV column added to
adata.obs
when usingload_merscope
- Plotting cell contact embedding now requires a
group
argument
- Various bug fixes in cell contact, cell-transcript proximity, and shortest distances
- FOV column added to
adata.obs
when usingload_merscope
- Updated kernel density documentation
- Integration with cookiecutter-scverse
- Option to subset by coordinates in
subset_cells
- Better documentation for cell contact calculation
- Add basis argument to cell contact embedding plot
- Cell contact count removes duplicate contacts from the dictionary
- Cell contact statistical method no longer uses z-test
- Cell contact counts returning 0 due to inaccurate comparison
- Cell contact statistical method only returns p-values if
split_groups = True
- Cell contact statistical method uses updated counting method
- Cell contact statistical test array initialization bug
- Volcano plots
- Cell contact embedding, heatmap, and histplot separated functions
- Cell contact unified plotting function
load_merscope
can use a cached object in a few different ways
- Utility function for loading an AnnData object from MERSCOPE data
- Functions for investigating cell-transcript proximity
- Initial functions for cell contact, kernel density, and shortest distances
- Utility function for subsetting cells