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immunomind / immunarch

🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
https://immunarch.com
Apache License 2.0
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Clonotypes across timepoints - why does it merge more than one clone? #162

Open venchi9 opened 2 years ago

venchi9 commented 2 years ago

Hi,

When I use this command: tc2 <- trackClonotypes(immdata$data, list("mydatanames", 10), .col = "aa+v")

I get this warning:

In melt.data.table(.data) : id.vars and measure.vars are internally guessed when both are 'NULL'. All non-numeric/integer/logical type columns are considered id.vars, which in this case are columns [CDR3.aa, V.name]. Consider providing at least one of 'id' or 'measure' vars in future.

However, it generates a plot but it looks like it is combining more than one clonotype ID (picture attached). Not sure why?

Thank you.

test.pdf

vadimnazarov commented 2 years ago

Hi @venchi9 ,

Thank you for using our package! Could you share please what type of data you work with? It seems like you have a mix of single-cell and bulk data in the repertoires, so that's why some clonotypes are "merged" and some are not.

venchi9 commented 2 years ago

Hi @venchi9 ,

Thank you for using our package! Could you share please what type of data you work with? It seems like you have a mix of single-cell and bulk data in the repertoires, so that's why some clonotypes are "merged" and some are not.

venchi9 commented 2 years ago

Sorry, accidentally closed the issue! It is just single cell data - there is no bulk data in this dataset. Here is the result when I put in top(immdata$data[[1]]) The sample has both immune and cancer cells, so not all cells contain a VDJ region.

data.xlsx