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 to embedding_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 indexing

  • mb.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 using load_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 using load_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 using load_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