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.

[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