v0.16.0

[0.16.0] - 2024-01-12

This release introduces two major change in pixelator:

1. the Graph backend has been switched from using igraph to using networkx
2. the license has been changed from GLP2.0 to MIT

Added

• Experimental 3D heatmap plotting feature.
• Optional caching of layouts to speed up computations in some scenarios.
• experimental mark that can be added to functions that are not yet production ready.
• The underlying graph instance e.g. a networkx Graph instance is exposed as a property called raw from the pixelator Graph class.
• Monte Carlo permutations supported when calculating Moran's I (morans_z_sim) in polarization_scores.

Changed

• The default (and only) graph backend in pixelator is now based on networkx.
• mean_reads and median_reads in adata.obs to mean_reads_per_molecule and median_reads_per_molecule respectively.
• Drop support for python 3.8 and 3.9.
• Change output format of collapse from csv to parquet.
• Change input and output format of graph from csv to parquet.
• Change input format of annotate from csv to parquet.
• Rename the report to "qc report"
• Add a Reads per Molecule frequency figure to the sequencing section of the qc report.
• Remove placeholder warning of missing data for not yet implemented features.
• Change "Median antibody molecules per cell" to "Average antibody molecules per cell" in the qc report.
• Refactoring of the graph backend implementations module.
• Speeding up the amplicon step by roughly 3x.

Fixed

• Nicer error messages when there are no components valid for computing colocalization.
• A bunch of warnings.

Removed

• graph no longer outputs the raw edge list.
• igraph has been dropped as a graph backend for pixelator.