Release 0.18.0

[ambarrio]

[0.18.0] - 2024-07-11

Added

• Add minimum marker count colocalization_min_marker_count parameter to calculate colocalization score.
• Add density_scatter_plot function to make two-marker abundance scatter plots with pseudo-density coloring.
• Add wpmds option in pmds_layout to compute edge weighted layouts. This is now set as the default layout algorithm.
• Add dsb_normalization function for normalization of marker abundance.
• Add a Fraction of Outlier Cells metric to the QC report.
• Add a Panel Version metadata field to the QC report.
• Add support for datasets generated using the human-sc-immunology-spatial-proteomics-2 panel.

Changed

• The default value for normalize_counts in local_g is now False instead of True.
• The default transformation for the calculation of the colocalization score is now rate-diff instead of log1p.
• Rename edge_rank_plot function to molecule_rank_plot.

Fixed

• Fix a bug in compute_transition_probabilities when k>1 where the stochastic matrix was not correctly row-normalized.
• Fix a bug in local_g when use_weights=False where the adjacency matrix was not correctly expended if k>1.
• Fix a bug where a_pixels_per_b_pixel summary statistics where equal to the b_pixels_per_a_pixel statistics.
• collapse will return exit code 137 when one of the child processes is killed by the system (e.g. because it is
  to much memory). This allows e.g. Nextflow to retry the process with more memory automatically.
• Hide the Sample Description metadata field in the QC report when no value is available.
• Fix an issue where boolean parameters were formatted as integers in the Parameters section of the QC report.
• Fix a bug in aggregating files with precomputed layouts, where the lazy-loading of the layouts was not working correctly.

Removed

• Remove the Pixel Version metadata field from the QC report.

[codecov]

Codecov Report

Attention: Patch coverage is 85.51020% with 71 lines in your changes missing coverage. Please review.

Project coverage is 81.78%. Comparing base (6c1b0c9) to head (948efb8).

Files	Patch %	Lines
src/pixelator/cli/collapse.py	10.00%	18 Missing ⚠️
src/pixelator/plot/layout_plots.py	92.45%	12 Missing ⚠️
src/pixelator/plot/__init__.py	85.13%	11 Missing ⚠️
src/pixelator/plot/spatial_analysis_plots.py	86.74%	11 Missing ⚠️
...elator/graph/backends/implementations/_networkx.py	77.77%	10 Missing ⚠️
src/pixelator/graph/node_metrics.py	44.44%	5 Missing ⚠️
src/pixelator/analysis/normalization/__init__.py	94.59%	2 Missing ⚠️
src/pixelator/logging.py	50.00%	1 Missing ⚠️
src/pixelator/report/models/annotate.py	80.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #166      +/-   ##
==========================================
- Coverage   81.80%   81.78%   -0.03%     
==========================================
  Files         118      121       +3     
  Lines        6568     6795     +227     
==========================================
+ Hits         5373     5557     +184     
- Misses       1195     1238      +43     

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