scRepertoire 2.7.3

BUG FIXES

• Fixed combineBCR() assigning the same group.by value to all cells instead of per-barcode values.
• Fixed clonalCluster() failing when group.by produces a single group by correcting the condition for adding the group column to the edge list.
• Fixed test for CTstrict clustering pattern to match the new default chain = "IGH" behavior in combineBCR().

v2.6.0

VERSION 2.6.0

BUG FIXES

• Fixed chain handling for BCR genes in percentGeneUsage() and propagates to wrappers: percentGenes, percentVJ and vizGenes
• Fixed passing group.by for combineBCR()
• Update unit tests for ggplot2 v4
• Fixed clonalProportion calculation to use grouping properly during combineExpression()
• Fixed immunarch support for exportClones() - TRA/Light chain column handling

NEW FUNCTIONALITY

• Added support for mouse genes in quietBCRgenes() and quietTCRgenes()
• Introduced pairwise calculations to StartracDiversity()
• Internal function conversion for clonalSizeDistribution() - remove cubature, truncdist and VGAM from dependencies.
• Increased speed of clonalSizeDistribution()

Tracked via issue #543

v2.5.0

UNDERLYING CHANGES

• Update/Improve code for loadContigs()
• Consolidated support for discrete AIRR formats under the umbrella of AIRR
• Added "tcrpheno" and immunarch to exportClones()
• Converted exportClones() to base R to reduce dependencies
• Added dandelionR vignette to pkgdown site
• Added tcrpheno vignette to pkgdown site
• percentAA() refactored to minimize dependencies and use immApex
  calculateFrequency()
• positionalEntropy() refactored to minimize dependencies and use immApex
  calculateEntropy()
• clonalDiversity() refactored for performance - it now calculates a
  single diversity metric at a time and includes new estimators like "gini",
  "d50", and supports hill numbers).
• percentKmer() refactored to use immApex calculateMotif for both aa and
  nt sequences. No longer calculates all possible motifs, but only motifs present.
• clonalCluster() now allows for dual-chain clustering, V/J filtering,
  normalized or straight edit distance calculations, and return of clusters,
  igraph objects or adjacency matrix
• combineBCR() offers single/dual chain clustering, aa or nt sequences, adaptive filtering of V and J genes and normalized or straight edit distance calculations
• percentGeneUsage() now is the underlying function for percentGenes(), percentVJ(),
  and vizGenes() and allows for percent, proportion and raw count quantification.
• Added common theme (internal .themeRepertoire()) to all plots and allow users to pass arguments to it

BUG FIXES

• clonalCompare() issue with plotting a 0 row data frame now errors with message
• clonalScatter() group.by/axes call now works for non-single-cell objects
• Fixed issue with NULL and "none" group.by in combineExpression()
• Allowing multi groupings via x.axis and group.by in clonalDiversity()

v2.3.4

scRepertoire VERSION 2.3.4

UNDERLYING CHANGES

• Update internal .parseContigs to function with more complex groupings
• Add annotateInvariant() functionality for mouse and human TCRs
• Add quietTCRgenes(), quietBCRgenes(), quietVDJgenes()
• Fixed issue with clonalCompare() assertthat statements
• Started integration with immApex API package
• Fixed issue with denominator in getCirclize()
• Fixing chain issue with clonalCompare() - expanded assertthat statement

v2.2.1

scRepertoire VERSION 2.2.1

NEW FEATURES

• Added getContigDoublets() experimental function to identify TCR and BCR doublets as a preprocessing step to combineExpression()
• Added proportion argument to clonalCompare() so that when set to FALSE, the comparison will be based on frequency normalized by per-sample repertoire diversity.

UNDERLYING CHANGES

• Fixed issue with single chain output for clonalLength()
• Removed unnecessary code remnant in clonalLength()
• Allow one sample to be plotted by percentVJ()
• Fixed issue with positionalProperty() and exportTable
• Fixed issue with loadContigs() edge case when TRUST4 data only has 1 row.
• convert documentation to use markdown (roxygen2md)
• import lifecycle, purrr, withr
• suppressed "using discrete variable for alpha is not recommended" warning in alluvialClones unit tests.
• Fixed issue with clonalCluster() and exportGraph = TRUE
• improve performance of combineBCR() by a constant factor with C++
• Restructured functions to exportTable before plotting
• Fixed issue with "group.by" in clonalOverlap()
• Fixed issue with "group.by" in clonalCompare()
• Fixed issue with custom column headers for clones

v2.0.5

scRepertoire VERSION 2.0.5

UNDERLYING CHANGES

• added type checks using assertthat
• updated conditional statements in constructConDFAndparseTCR.cpp
• Fixed issue in clonalQuant() and factor-based group.by variable
• Add error message for NULL results in clonalCluster() with export.graph = TRUE
• Fixed issue with "full.clones" missing in combineExpression() when using 1 chain

v2.0.4

scRepertoire VERSION 2.0.4

UNDERLYING CHANGE

• getCirclize() refactored to prevent assumptions and added include.self argument
• Added .count.clones() internal function for getCirclize() and clonalNetwork()
• Added order.by parameter to visualizations to specifically call order of plotting using a vector or can use "alphanumeric" to plot things in order
• Fix issue with clonalLength() and NA handling
• clonalCompare() now retains the original clonal info if using relabel.clones
• Add Dandelion support in to loadContigs() and testthat
• Fixed issue with positionalProperty() assumption that the clones will all have 20 amino acids.
• Fixed IGH/K/L mistaking gene issue in vizGenes()

v2.0.3

scRepertoire VERSION 2.0.3

UNDERLYING CHANGES

• Modified support for Omniscope format to allow for dual chains
• Added ParseBio support int loadContigs() and testthat
• Added support for productive variable to loadContigs() for BD, Omniscope, and Immcantation formats
• Replace numerical indexing with name indexing for loadContigs()
• combineBCR() and combineTCR() no allow for unproductive contig inclusions with new filterNonproductive parameter.
• combineBCR() will now prompt user if samples is not included instead of erroring.
• Added base threshold by length for internal .lvCompare()
• Ensured internal .lvcompare() only looks at first set of sequences in multi-sequence chain.
• Fixed bug in exporting graph for clonaCluster()
• Fixed conflict in functions between igraph and dplyr packages
• clonalOccupy() rewrite counting and NA handling (v2.0.2)
• clonalOverlay() arguments now cutpoint and use cut.category to select either clonalProportion or clonalFrequency v(2.0.1)

v2.0.0

NEW FEATURES

• Added percentAA()
• Added percentGenes()
• Added percentVJ()
• Added percentKmer()
• Added exportClones()
• Added positionalEntropy()
• Added positionalProperty()
• Changed compareClonotypes to clonalCompare()
• Changed clonotypeSizeDistribution to clonalSizeDistribution()
• Changed scatterClonotypes to clonalScatter()
• Changed quantContig to clonalQuant()
• Changed highlightClonotypes to highlightClones()
• Changed lengthContigs to clonalLength()
• Changed occupiedscRepertoire to clonalOccupy()
• Changed abundanceContig to clonalAbundance()
• Changed alluvialClonotypes to alluvialClones()
• Added features to clonalCompare() to allow for highlighting sequences, relabeling clonotypes.

UNDERLYING CHANGES

• Removed internal .quiet() function.
• .theCall() now allows for a custom header/variable and checks the colnames.
• Replaced data arguments to be more descriptive: df is now input.data, dir is now input, and sc is now sc.data
• Deep clean on the documentation for each function for increased consistency and explainability
• StartracDiversity() metric re-implemented to remove startrac-class object intermediary
• Implemented powerTCR locally to reduce dependencies and continue support
• Universalized underlying function language and intermediate variables
• License change to MIT
• group.by and split.by have been consolidated into single group.by parameter
• Added support for Immcantation pipeline, .json, Omniscope, and MiXCR formats for loadContigs()
• Made GitHub.io website for support/vignettes/FAQ
• Restructured NEWS Tracking
• Added testthat for all exported and internal functions
• Fixed issue with clonalQuant() for instance of scale = FALSE and group.by being set.
• clonalDiversity() no longer automatically orders samples.
• Remove order parameter from clonalQuant(), clonalLength(), and clonalAbundance()
• x.axis parameter in clonalDiversity() separated from group.by parameter
• filtering chains will not eliminate none matching chains.

DEPRECATED AND DEFUNCT

• Deprecate stripBarcodes()
• Deprecate expression2List() (now only an internal function).
• Deprecate checkContigs()