CDR3 length as proportion instead of clonotype number

[Hammer-Q]

Hi all, thanks for the great package, I'm enjoying it a lot! It might be a quite naive question: is there a possibility to analyze CDR3 lengths as a proportion/frequency instead as clonotype number? I have a set of samples with varying clone numbers and different clonotype proportions (some highly expanded clonotypes) and think that it could be useful to display the y-axis as proportion. Is this possible?

Small edit: I guess what I am trying to generate is a CDR3 length distribution plot that is weighted for clonotype size, i.e. that highly expanded clonotypes contribute more to the distribution compared to clonotypes of small proportion. Does that make sense?

[linqy-immune]

Hello! I am also trying to analyze CDR3 lengths as a proportion/frequency, but I didn't find my way. Have you already solved this problem? Could you please give me some advice? Thank you very much. Thanks and best regards, Linqy

[vadimnazarov]

Hello, I'm closing this issue because immunarch is moving to version 1.0.0, and many things have changed since this issue was opened.

The new version of immunarch is already available. Install it via:

1. pak (recommended)

# Install pak
install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))
# Install or update immunarch pre-1.0
pak::pkg_install("immunomind/immunarch")

2. CRAN

install.packages("immunarch")

What changed (in short):

• Some old functions were removed, moved or will be moved to other packages.
• The new interface is more lightweight and easier to understand.
• The package now uses the ImmunData format (from the immundata package) that supports out-of-memory datasets, both single- and paired-chain receptors, and allows flexible annotation of receptors with multi-modal information, such as information about cell clusters or gene expression from scRNAseq data.
• The focus is gradually shifting towards biomarker discovery, patient stratification, and other use cases for immunotherapy and vaccine development.

For smooth migration, please check:

• Migration guide: https://immunomind.github.io/docs/tutorials/migration
• Single-cell AIRR tutorial: https://immunomind.github.io/docs/tutorials/single_cell
• Updates on the transition to 1.0: https://github.com/immunomind/immunarch/issues/432

If you have any questions or issues with the new immunarch, please open a new issue. Thank you!

— Vadim