How to fix Error in `$<-.data.frame`(`*tmp*`, "Kingdom", value = character(0)) : replacement has 0 rows, data has 2407

Question

[arsilan324]

Hi all, I am stuck with this error.

Error in `$<-.data.frame`(`*tmp*`, "Kingdom", value = character(0)) : 
  replacement has 0 rows, data has 2407

This is what I get after running this command

amp_rabund(data = physeqP,
           tax.aggregate = "Genus",
           tax.add = "Phylum",
           scale.seq = 100)

This is how my phyloseq object (data) looks like

> physeqP
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 2407 taxa and 73 samples ]
sample_data() Sample Data:       [ 73 samples by 3 sample variables ]
tax_table()   Taxonomy Table:    [ 2407 taxa by 6 taxonomic ranks ]

I have tried to do it on data subset as well but it fails every time. I am not even able to understand what problem it is. The instructions i am following are given in this link

http://madsalbertsen.github.io/ampvis/examples/ampvis_guide.html

I would be very thankful if you please help me fix the issue... Thanks in advance Arslan

[Devon Ryan]

You need to show the actual command producing this error and some context surrounding it.

[arsilan324]

Apologies. Here is the command.

amp_rabund(data = dsn,
           tax.aggregate = "Genus",
           tax.add = "Phylum",
           scale.seq = 100)

Answer 1

[arsilan324]

The new version ampvis2 worked perfectly. Thanks!