Changelog
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.
[1.0.0] - 2023-08-23
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
[0.6.0] - 2022-12-16
Changed
Changed
cell_contact_embedding_zoom
toembedding_zoom
and abstracted functionality
Removed
Removed volcano plot function
[0.5.0] - 2022-12-13
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
[0.4.4] - 2022-11-29
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
[0.4.3] - 2022-11-28
Changed
mb.calc.shortest_distances
now returns a DataFrame for easier indexingmb.plot.cell_transcript_proximity
uses predetermined colors if previously added by Scanpy
[0.4.2] - 2022-11-23
Fixed
Fixed calculation in shortest distance statistical test
[0.4.1] - 2022-11-22
Added
Basis customization to functions using coordinates
[0.4.0] - 2022-11-21
Added
This changelog
Neighborhood profile function
Fixed
Plotting function legends now better located
load_merscope
maintains transcript ids
[0.3.5] - 2022-11-21
Added
Enhancements to plotting functions with better labels/legends
Fixed
Shortest distances permutation test now includes pseudocount
Removed
Removed unnecessary columns from
detected_transcripts.csv
when usingload_merscope
[0.3.4] - 2022-11-14
Added
Tutorial notebook added to documentation
Changed
Kernel density with multiple groups are scaled individually
Fixed
Kernel density plot bug with multiple displays
Docstring return descriptions
[0.3.3] - 2022-11-11
Fixed
Address issue from v0.3.2 (now yanked)
[0.3.1] - 2022-11-09
Added
Cell contact counting function
Changed
Default
show = True
for plotting functions for consistency with scverse ecosystem
[0.3.0] - 2022-11-08
Added
FOV column added to
adata.obs
when usingload_merscope
Changed
Plotting cell contact embedding now requires a
group
argument
Fixed
Various bug fixes in cell contact, cell-transcript proximity, and shortest distances
[0.2.2] - 2022-11-03
Added
FOV column added to
adata.obs
when usingload_merscope
[0.2.1] - 2022-11-02
Fixed
Updated kernel density documentation
[0.2.0] - 2022-11-01
Added
Integration with cookiecutter-scverse
[0.1.7] - 2022-10-31
Added
Option to subset by coordinates in
subset_cells
Better documentation for cell contact calculation
Add basis argument to cell contact embedding plot
[0.1.6] - 2022-10-28
Changed
Cell contact count removes duplicate contacts from the dictionary
[0.1.5] - 2022-10-26
Changed
Cell contact statistical method no longer uses z-test
[0.1.4] - 2022-10-25
Fixed
Cell contact counts returning 0 due to inaccurate comparison
[0.1.3] - 2022-10-25
Changed
Cell contact statistical method only returns p-values if
split_groups = True
[0.1.2] - 2022-10-25
Changed
Cell contact statistical method uses updated counting method
[0.1.1] - 2022-10-25
Fixed
Cell contact statistical test array initialization bug
[0.1.0] - 2022-10-25
Added
Volcano plots
Cell contact embedding, heatmap, and histplot separated functions
Removed
Cell contact unified plotting function
[0.0.3] - 2022-10-25
Changed
load_merscope
can use a cached object in a few different ways
[0.0.2] - 2022-09-06
Added
Utility function for loading an AnnData object from MERSCOPE data
Functions for investigating cell-transcript proximity
[0.0.1] - 2022-08-25
Added
Initial functions for cell contact, kernel density, and shortest distances
Utility function for subsetting cells