Release 0.19.0

[ambarrio]

[0.19.0] - 2024-12-10

Changed

• Name components using UPI hashes.
• Run multiple iterations of multiplet recovery during the graph stage specified using --max-refinement-recursion-depth.
• Specify maximum number of edges that can be removed between two sub-components during multiplet recovery using --max-edges-to-split.
• Support for MultiGraphs in pmds_layout
• Support multiple targets in plot_colocalization_diff_volcano and plot_colocalization_diff_heatmap.
• If demultiplexing has a success rate lower than 50% the command will exit with a status of 1. This prevents further pipeline stages to be run on
  what is probably bad data.
• Clarify that --min-size and --max-size in the annotate stage should not be used at the same time as --dynamic-filter.
• Setting a lower threshold of 300 edges when --dynamic-filter is used in the annotate stage, components smaller than that will always
  be filtered. Note that this can still be overridden by setting --min-size explicitly.
• Clarify error message when all components are filtered out in the annotate stage.

Added

• Add depth column to discarded_edgelist.parquet output of the graph stage that indicates at which refinement iteration the edge is removed.
• Add edges_removed_in_multiplet_recovery_first_iteration, edges_removed_in_multiplet_recovery_refinement and fraction_edges_removed_in_refinement to graph report.json.
• Add is_potential_doublet and n_edges_to_split_doublet columns to adata.obs.
• Add fraction_potential_doublets and n_edges_to_split_potential_doublets to annotate report.json.
• Add --max-edges-to-split option to graph to specify the maximum number of edges that can be removed between two sub-components during multiplet recovery.
• Add abundance_colocalization_plot function to make scatter plots of selected marker-pairs' abundance.
• Add plot_polarity_diff_volcano to make statistical comparison plots of selected component groups.
• Add get_differential_polarity to statistically compare polarity scores of selected component groups.

Removed

• Remove the components_recovered.csv output from the graph stage.

Fixed

• Improved error message when the number of nodes is lower than the number of requested dimensions in pmds_layout.