trackClonotype function for tracking clonotypes.
Speed up Morisita-Horn index computation for up to 3 times.
Add the incremental overlap function
inc_overlap, available from
Add the downsampling option to incremental overlaps.
Add visualisations for incvremental overlaps.
prop_sample function completely.
Move all downsampling, resampling and sampling procedures to the
Add normalisation to rarafection.
Remove the .dup argument from
repOverlap, all equal clonotypes are now always merged and their counts summed up.
Remove .quant from
repOverlap, the column is now automatically detected.
Add an argument .add.layer to
vis_hist to add any additional ggplot2 layers to the plots in the output grid.
Add grouping in
vis_hist if data is grouped and
.grid is T.
Update MiXCR parser (yet again) to read MiXCR files from the May 2019 release.
.target argument to visualisation of incremental overlaps.
Add more MiXCR file variants parsing.
repLoad returns sorted by “Clones” data frames now.
geneUsage when the first two columns with gene usages were swapped.
repExplore doesn’t work with a single repertoire.
vis_heatmap doesn’t work with
Fix a bug in computation of Morisita-Horn index.
vis_box doesn’t work with numeric grouping variables.
repOverlap failing when working on data tables with
repOverlap failing to work with data tables on
repLoad failing when parsing MiXCR files with zero clonotypes.
Fix a bug in incorrect grouping in visualisations.
Fix a bug when clonal homeostasis and clonotype tracking don’t work properly with filtered coding.
Fix D50, “top” and “clonal.prop” from repClonality returns wrong values when the input data frame is not sorted.
Remove the “wei” option from
geneUsage becase it’s useless.
ggseqlogo for visualising of seq-logo plots.
repOverlap default .col value is “aa” for comfortable usage.
Remove “fill” aesthetics warnings from
Remove warnings “In parse_fun(.path[i]) : NAs introduced by coercion” when parsing MiXCR files.
A lot or minor fixing and documentation improving to prepare for the CRAN release.
Remove short function names.
Parser for ArcherDX.
Update a parser for MiXCR to make it work with the “targetSequences” column format.
Update the coding function family to make it work with CDR3 amino acid sequences only.
Replace all “unresolved” genes in ImmunoSEQ parsed files with NAs.
Add an argument for the color palette to
.grid=F by default in
vis_hist for gene usage analysis.
Fix parsing functions to not remove strings after dots in filenames.
Update the post-parsing processing subroutine to remove all characters except for amino acid alphabet,
~ for compatability with all
Remove MonetDBLite from dependencies because it got removed from CRAN.
Boxplots and barplots are now support statistical tests via the
Add parsers for old VDJtools formats.
Update docs and vignettes with statistical tests information.
Add a note for list names to vignettes.
Documentation for clustering.
Documentation for dimension reduction.
Minor fix for
fixVis now supports the following legends: size, shape, color, fill, linetype.
fixVis can plot figures to R console / RStudio “Plots” tab.
fixVis now supports the number of columns in legends.
Support for the AIRR file format.
Experimental support for the 10xGenomics format.
Save and load
immunarch format via
Save and load VDJtools format via