XLSX export requires taxonomy character matrix which is not necessarily present at import

[chrysn]

The write.xlsx function fails with "Error: Taxonomy map must be a character matrix." when importing a minimal BIOM file, rather than simply not outputting data that is not present in the object.

To reproduce, use this as test.txt (careful, there are tabs in it):

#OTU ID sample1 sample2
obs1    1.0 0.0
obs2    0.0 2.0

and run

$ biom convert -i test.txt -o test.biom --to-hdf5
$ R
> library('rbiom')
> b <- read.biom('test.biom', tree=FALSE)
> write.xlsx(b, 'test.xlsx')
Error: Taxonomy map must be a character matrix.

As a workaround, I'm running

> b$taxonomy[1,] = c("a")

What is particularly weird is that the taxonomy data injected here is not even emitted in the XLSX -- but then again, maybe I'm not putting it in the right way.

Please consider updating the error handling so that any loaded file can also be saved to XLSX.

[dansmith01]

Thanks for pointing that out! Fixed!