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()