How to specify groups order?

[makarov-ccf]

Hello,

Any plot I make where I need to compare samples by group, the groups are always listed alphabetically. Is it a way to position them in specified order? Example is attached. I wanted to plot in order: Pre, Post, but unless I added xPost, the order was always Post, Pre (i.e. alphabetically)

Thank you

repertoire_diversity_status.pdf

[linqy-immune]

Hi, I also encountered this problem, and I found one post with relevant content in this website. It would be useful to add a column to define the data by the order you want like "A, B, C" in the metadata.txt and then analyze by .by=new_column. This seems a littile funny, but actually solve my problem. Best wishes!

[makarov-ccf]

That's very helpful, thank you for sharing

[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