v0.17.0

[0.17.0] - 2024-05-23

Added

• Add rate_diff_transformation function with rate-diff alias as an alternative option for transforming marker counts before colocalization calculation.
• Add local_g function to compute spatial autocorrelation of marker counts per node.
• Add compute_transition_probabilities function to compute transition probabilities for k-step random walks for node pairs in a graph.
• Add QC plot showing UMIs per UPIA vs Tau.
• Add plot functions showing edge rank and cell counts.
• Add 2D and 3D graph plot functions.
• Add heatmap plot functions showing colocalization and differential colocalization.
• Add volcano plot (value difference vs log p-value) function for differential colocalization.
• Add a function to calculate the differential colocalization between two conditions.
• Performance improvements and reduced bundle size in QC report.
• Improved console output in verbose mode.
• Improved logging from multiprocessing jobs.
• Improved runtime for graph creation.
• Added PMDS layout algorithm.
• Add --sample_name option to single-cell amplicon to overwrite the name derived from the input filename.
• Add --skip-input-checks option to single-cell amplicon to make input filename checks warnings instead of errors.
• PixelDataset instances are now written to disk without creating intermediate files on-disk.
• A nice string representation for the Graph class, to let you know how many nodes and edges there are in the current graph object instance.
• Metric to collect molecules (edges) in cells with outlier distributions of antibodies (aggregates).
• Provide typed interfaces for all per-stage report files using pydantic.
• Centralize pixelator intermediate file lookup and access.
• Add a precomputed_layouts property to PixelDataset to allow for loading precomputed layouts.
• Add pixelator single-cell layout stage to pixelator, which allows users to compute layouts for a PXL file that can then be used to visualize the graph in 2D or 3D downstream.
• Add minimum marker count polarization_min_marker_count parameter to calculate Polarity Score.
• Add "log1p" as an alternative for PolarizationNormalizationTypes.
• Add convert_indices_to_integers option when creating graphs.
• Add a feature flag module to aid in the development of new features.

Changed

• Change name and description of Avg. Reads per Cell and Avg. Reads Usable per Cell in QC report.
• The output name of the .pxl file from the annotate step is now *.annotated.dataset.pxl.
• The output name of the .pxl file from the analysis step is now *.analysis.dataset.pxl.
• The term edges in metrics and adata is now replaced with molecules.
• Renaming of variables in per-stage JSON reports.
• Changed name of TCRb to TCRVb5 antibody in human-immunology-panel file and bumped to version 0.5.0.
• Renaming of component metrics in adata.
• Use MPX graph compatible permutation strategy when calculating Moran's I related statistics.
• Marker filtering is now done after count transformation in polarization score calculation.
• Use the input read count at the annotate stage for the fraction_antibody_reads_in_outliers metric denominator instead of the total raw input reads.
• Use common analysis engine to orchestrate running different "per component" analyses, like polarization and colocalization analysis (yielding a roughly 3x speed-up over the previous approach).
• The default transformation for the calculation of the polarity score is now log1p instead of clr.

Fixed

• Fix a bug in how discarded UMIs are calculated and reported.
• Fix deflated counts in the edgelist after collapse.
• Fix a bug where an r1 or r2 in the directory part of a read file would break file name sanity checks.
• Fix a bug where the wrong r1 or r2 in the filename would be removed when multiple matches are present.
• Logging would cause deadlocks in multiprocessing scenarios, this has been resolved by switching to a server/client-based logging system.
• Fix a bug in the amplicon stage where read suffixes were not correctly recognized.
• Ensure deterministic results from pmds_layout (given a set seed).
• Fix an issue with the fraction_antibody_reads_usable_per_cell metric where the denominator read count was not correctly averaged with the cell count.

Removed

• Remove multi-sample processing from all single-cell subcommands.
• Remove --input1_pattern and --input2_pattern from single-cell amplicon command.
• Self-correlations, e.g. CD8 vs CD8 are no longer part of the colocalization results, as these values will always be undefined.
• Remove umi_unique_count and upi_unique_count from edgelist.
• Remove umi and median_umi_degree from component metrics.
• Remove normalized_rel and denoised from obsm in anndata.
• Remove the denoise function.
• Remove cell type selector in QC report for UMAP colored by molecule count plots.
• Remove clr as a transformation option in pixelator analysis.