Question: How to fix Error in `$<-.data.frame`(`*tmp*`, "Kingdom", value = character(0)) : replacement has 0 rows, data has 2407
0
gravatar for arsilan324
2.2 years ago by
arsilan32480
arsilan32480 wrote:

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

phyloseq rank abundance • 6.8k views
ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by arsilan32480

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

ADD REPLYlink written 2.2 years ago by Devon Ryan96k

Apologies. Here is the command.

amp_rabund(data = dsn,
           tax.aggregate = "Genus",
           tax.add = "Phylum",
           scale.seq = 100)
ADD REPLYlink written 2.2 years ago by arsilan32480
0
gravatar for arsilan324
2.2 years ago by
arsilan32480
arsilan32480 wrote:

The new version ampvis2 worked perfectly. Thanks!

ADD COMMENTlink written 2.2 years ago by arsilan32480
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