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@grst grst released this 28 Apr 12:54
v0.7.0
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This update features a

  • change of Scirpy's data structure to improve interoperability with the AIRR standard
  • a complete re-write of the clonotype definition module for improved performance.

This required several backwards-incompatible changes. Please read the release notes below and the updated tutorials.

Backwards-incompatible changes

Improve Interoperability by fully supporting the AIRR standard (#241)

Scirpy stores receptor information in adata.obs. In this release, we updated the column names to match the AIRR Rearrangement standard. Our data model is now much more flexible, allowing to import arbitrary immune-receptor (IR)-chain related information. Use scirpy.io.upgrade_schema() to update existing AnnData objects to the latest format.

Closed issues #240, #253, #258, #255, #242, #215.

This update includes the following changes:

  • IrCell is now replaced by AirrCell which has additional functionality
  • IrChain has been removed. Use a plain dictionary instead.
  • CDR3 information is now read from the junction and junction_aa columns instead of cdr3_nt and cdr3, respectively.
  • Clonotype assignments are now per default stored in the clone_id column.
  • expr and expr_raw are now duplicate_count and consensus_count.
  • {v,d,j,c}_gene is now {v,d,j,c}_call.
  • There's now an extra_chains column containing all IR-chains that don't fit into our receptor model. These chains are not used by scirpy, but can be re-exported to different formats.
  • merge_with_ir is now split up into merge_with_ir (to merge IR data with transcriptomics data) and merge_airr_chains (to merge several adatas with IR information, e.g. BCR and TCR data).
  • Tutorial and documentation updates, to reflect these changes
  • Sequences are not converted to upper case on import. Scirpy tools that consume the sequences convert them to upper case on-the-fly.
  • {to,from}_ir_objs has been renamed to {to,from}_airr_cells.

Refactor CDR3 network creation (#230)

Previously, pp.ir_neighbors constructed a cell x cell network based on clonotype similarity. This led to performance issues
with highly expanded clonotypes (i.e. thousands of cells with exactly the same receptor configuration). Such cells would
form dense blocks in the sparse adjacency matrix (see issue #217). Another downside was that expensive alignment-distances had
to be recomputed every time the parameters of ir_neighbors was changed.

The new implementation computes distances between all unique receptor configurations, only considering one instance of highly expanded clonotypes.

Closed issues #243, #217, #191, #192, #164.

This update includes the following changes:

  • pp.ir_neighbors has been replaced by pp.ir_dist.
  • The options receptor_arms and dual_ir have been moved from pp.ir_neighbors to tl.define_clonotypes and tl.define_clonotype_clusters.
  • The default key for clonotype clusters is now cc_{distance}_{metric} instead of ct_cluster_{distance}_{metric}.
  • same_v_gene now fully respects the options dual_ir and receptor_arms
  • v-genes and receptor types were previously simply appended to clonotype ids (when same_v_gene=True). Now clonotypes with different v-genes get assigned a different numeric id.
  • Distance metric classes have been moved from ir_dist to ir_dist.metrics.
  • Distances matrices generated by ir_dist are now square and symmetric instead of triangular.
  • The default value for dual_ir is now any instead of primary_only (Closes #164).
  • The API of clonotype_network has changed.
  • Clonotype network now visualizes cells with identical receptor configurations. The number of cells with identical receptor configurations is shown as point size (and optionally, as color). Clonotype network does not support plotting multiple colors at the same time any more.
Clonotype network (previous implementation) Clonotype network (now)
Each dot represents a cell. Cells with identical receptors form a fully connected subnetwork Each dot represents cells with identical receptors. The dot size refers to the number of cells
image image

Drop Support for Python 3.6

  • Support Python 3.9, drop support for Python 3.6, following the numpy guidelines. (#229)

Fixes

  • tl.clonal_expansion and tl.clonotype_convergence now respect cells with missing receptors and return nan for those cells. (#252)

Additions

  • util.graph.igraph_from_sparse_matrix allows to convert a sparse connectivity or distance matrix to an igraph object.
  • ir_dist.sequence_dist now also works sequence arrays that contain duplicate entries (#192)
  • from_dandelion and to_dandelion facilitate interaction with the Dandelion package (#240)
  • write_airr allows to write scirpy's adata.obs back to the AIRR Rearrangement format.
  • read_airr now tries to infer the locus from gene names, if no locus column is present.
  • ir.io.upgrade_schema allows to upgrade an existing scirpy anndata object to be compatible with the latest version of scirpy
  • define_clonotypes and define_clonotype_clusters now prints a logging message indicating where the results have been stored (#215)

Minor changes

  • tqdm now uses IPython widgets to display progress bars, if available
  • the process_map from tqdm is now used to display progress bars for parallel computations instead the custom implementation used previously f307c2b
  • matplotlibs "grid lines" are now suppressed by default in all plots.
  • Docs from the master branch are now deployed to icbi-lab.github.io/scirpy/develop instead of the main documentation website. The main website only gets updated on releases.
  • Refactored the _is_na function that checks if a string evaluates to None.
  • Fixed outdated documentation of the receptor_arms parameter (#264)
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