Issue is plotting output from estimateAbundance function using ExampleDb dataset

[Akshaya Ramesh]

Hello,

I’m a new user to immcantation, and have been exploring alakazam to plot diversity and abundance. I’ve been following the code from https://alakazam.readthedocs.io/en/stable/vignettes/Diversity-Vignette/, and notice the following error in the ExampleDb dataset. I tried this code on my dataset as well, and get the same error.

Code I am using:

mysample <- estimateAbundance(ExampleDb, group="SAMPLE", ci=0.95, nboot=200)
plot(mysample)

Error:

Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In data.matrix(x) : NAs introduced by coercion
2: In data.matrix(x) : NAs introduced by coercion
3: In min(x) : no non-missing arguments to min; returning Inf
4: In max(x) : no non-missing arguments to max; returning -Inf
5: In min(x) : no non-missing arguments to min; returning Inf
6: In max(x) : no non-missing arguments to max; returning -Inf

I have tried changing the columns to make sure they are recognized as numbers using as.numeric, but haven’t had any luck in getting it to work. Is anyone else facing this issue/is able to help me with this?

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Thank you.

[ssnn]

Hi! What version of alakazam are you using? Maybe we have fixed that issue in a recent version? I have tried with alakazam_0.3.0.999 and I don’t get the error.

library(alakazam)
data(ExampleDb)
# note: I use sample and not SAMPLE because we changed ExampleDB to use AIRR formatted column names
mysample <- estimateAbundance(ExampleDb, group="sample", ci=0.95, nboot=200)
plot(mysample)

[Akshaya Ramesh]

Hello,

Thanks for the quick response! I was using version alakazam_0.2.8, just updated version, and it works great,

Thank you.