About summarize_taxa (qiime2R)

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1

Hello,

I used summarize_taxa to give me the sum of the counts, but the function returned the wrong sum by placing the results in column P168.
The data is attached.

Would you happen to have any suggestions to fix this issue?

The code used is:

taxonomy <- read_qza ("taxonomy.qza")$data %>% parse_taxonomy()
SVs<-read_qza("table.qza")$data
abundance <- summarize_taxa(SVs, taxonomy)$Genus
view(abundance)

taxonomy.qza (192.9 KB)
table.qza (107.7 KB)

Thanks.

2

Is there any suggestion on how to address this issue?

Thanks.

3

I'm not sure I can replicate your issue. A quick check would suggest this worked as expected where the correct number of reads were retained per sample:

library(tidyverse)
library(qiime2R)

asvs<-read_qza("~/Downloads/table.qza")$data
tax<-read_qza("~/Downloads/taxonomy.qza")$data

tax<-tax %>% parse_taxonomy()

sums<-summarize_taxa(asvs, tax)

colSums(asvs)==colSums(sums$Genus)

P148 P149 P152 P153 P155 P156 P158 P159 P160 P161 P164 P165 P166 P167 P168 P169 P170 P172 P174 P175 P177 P178 TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE

Probably not want you want to hear, but while I was looking at this I noticed your data looks rather odd. I don't know what your experiment is, but all but one sample exclusively contains ASVs unassigned to a phylum... or even kingdom! If this was not expected, you may want to trace back through the analysis for potential issues.

4

Thanks, Jordan, for your time to give me an input on this issue.

Yes - I will get back to the data and check.

Something must be wrong with the .qza files.

Kind regards.