v0.18.3

[0.18.3] - 2024-09-26

Fixed

• Improved memory usage when aggregating PXL files with precomputed layouts.

Full Changelog: v0.18.2...v0.18.3

v0.17.3

[0.17.3] - 2024-08-29

Fixed

• A bug in compute_transition_probabilities when k>1 where the weight matrix was not computed correctly. This bug also affected the results from local_g when k>1 which results in invalid Z scores.

Full Changelog: v0.17.2...v0.17.3

v0.16.3

[0.16.3] - 2024-07-29

Fixed

• Pin scipy version to be compatible with triu function used in the 0.16 series

Full Changelog: v0.16.2...v0.16.3

v0.18.2

[0.18.2] - 2024-07-16

Changed

• Bump polars to stable 1.x series

Fixed

• Fix a qc report crash issue when the layout stage is run in a pipeline due to an unsupported parameter type.

v0.18.1

[0.18.1] - 2024-07-12

Changed

• Bump umi_tools version requirements

v0.17.2

[0.17.2] - 2024-07-12

• Bump umi_tools version requirements
• Fix a bug in aggregating files with precomputed layouts, where the lazy-loading of the layouts was not working correctly.

Full Changelog: v0.17.1...v0.17.2

v0.18.0

[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.

v0.17.1

[0.17.1] - 2024-05-27

Fixed

• Poor performance when writing many small layouts to pxl file (~45x speed-up). This should almost only
  impact test scenarios, since most real components should be large enough for this not to be an issue.

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.

v0.16.2

[0.16.2] - 2024-03-19

Fixed

• Uninitialized value for --polarization-n-permutations