Release Notes¶

Version 0.1.5: September 11, 2023¶

General:

Updated some reports’ text to be more concise and clear.
In the define clones report, added the option to focus the convergence analysis on a particular V gene by setting convergence_vgene. Added the option to specify a threshold for the convergence analysis (convergence_threshold). Added a step to remove light chain only cells after createGermlines.
Updated the updated single cell qc report to remove cells with duplicated sequences, not just the sequences.
Added additional parameters to the dowser lineages report: num_fields, chain, cell, heavy, collapse, and columns. In the same report, added additional validation steps to check that the fields passed to dowser functions have data. Updated the example input data and the default values of some parameters ( traits: from c_call to day, tips: from c_call to day). Fixed the default value of outname, from define-clones to dowser.

General:

Aesthetic adjusments to figures and tables.
Added conditional evaluation logic to some chucks that don’t need to be evaluated always.

Bug fixes:

In find threshold report, updated output path used to save the final tables to use the parameter outname. Changed the output file suffix threshold_summary to threshold-summary.

General:

Find threshold report. Parametrized distance and threshold subsampling.
Define clones project. Added example data, available from url. Made singlecell optional, with default value NULL. species can be set to auto to auto detect from the field species.

Bug fixes:

The convergence UpSet was not showing in the report because it was missing a grid.draw statement.
Updated the logic in the find threshold report to show the distance to nearest plot only if it is not NULL.
Define clones project. Run chucks that require the tissue field only if it exists.
Updated figures widths and heights.

General:

Lineage report. Added parameters: tips, traits. All trees are saved to a .pdf and exported in graphml format.
Find threshold report. Added parameters: findthreshold_method, findthreshold_model, findthreshold_edge, findthreshold_cutoff, findthreshold_spc.
Define clones report. Limit the size of UpSet plots to 31 sets. 31 is the largest size allowed by ComplexHeatmap::make_comb_mat.
Create single page, self contained reports.

Bug fixes:

Fixed bug in collapse duplicates that caused the function to fail when all values in d_call were NA.
In the define clones report. Added conditional chunk evaluation to chunks of code that don’t need to be executed if only light chain data is available.
In the find threshold report. Skip distance plots and findThreshold if all distance values are NA and show a message.

Bug fixes:

Added the field cell_id to the set of selected columns used to subset the input repertoire in the find threshold report.

General:

Bug fixes:

Fixed a bug in collapse duplicates report, where it was trying to select columns that sometimes did not exist.

Breaks:

General: