immunarch 0.4.0.9000

Work in progress

Kmers - analysis + plots, seqlogo / textlogo

pubRepStatistics function for computation of public clonotypes across groups and repertoires.

vis_public_frequencies, vis_public_clonotypes, vis_upset for public repertoire visualisations.

immunarch 0.4.0

Features

The trackClonotype function for tracking clonotypes.

Visualisations for trackClonotype.

Speed up Morisita-Horn index computation for up to 3 times.

Add the incremental overlap function inc_overlap, available from repOverlap.

Add the downsampling option to incremental overlaps.

Add visualisations for incvremental overlaps.

Remove the prop_sample function completely.

Move all downsampling, resampling and sampling procedures to the repSample function.

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.

Add .target argument to visualisation of incremental overlaps.

Add .clones to repExplore.

Add more MiXCR file variants parsing.

repLoad returns sorted by “Clones” data frames now.

Bug fixes

Fix geneUsage when the first two columns with gene usages were swapped.

Fix repExplore doesn’t work with a single repertoire.

Fix vis_heatmap doesn’t work with geneUsage output.

Fix a bug in computation of Morisita-Horn index.

Fix vis_bar and vis_box doesn’t work with numeric grouping variables.

Fix repOverlap failing when working on data tables with morisita.

Fix repOverlap failing to work with data tables on public, overlap, jaccard and tversky.

Fix 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.

Minor updates

Remove the “wei” option from geneUsage becase it’s useless.

New dependency ggseqlogo for visualising of seq-logo plots.

Add .transpose to vis_heatmap.

repOverlap default .col value is “aa” for comfortable usage.

Remove “fill” aesthetics warnings from vis_heatmap.

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.

immunarch 0.3.3

Features

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.

Minor updates

Replace all “unresolved” genes in ImmunoSEQ parsed files with NAs.

Add an argument for the color palette to vis_heatmap2.

Make .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, * and ~ for compatability with all immunarch’s functions.

Documentation

Add a documentation to the coding function family.

Update README.

immunarch 0.3.2

Remove MonetDBLite from dependencies because it got removed from CRAN.

Bug fixes

  • Fix a bug in MiXCR parser.

immunarch 0.3.1

Features

  • Boxplots and barplots are now support statistical tests via the .test argument.

  • Add parsers for old VDJtools formats.

Documentation

  • 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 repOverlap documentation.

Bug fixes

  • Fix a grouping bug in visualisations.

  • Fix statistical tests from ggpubr.

  • Fix for geneUsage with .type="family".

immunarch 0.3.0

Features

  • 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 repSave and repLoad.

  • Save and load VDJtools format via repSave and repLoad.

Bug fixes

  • .a and .b didn’t passed to Tversky index.

  • fixVis - fix a bug when users apply X/Y settings to the other axis.