Trouble with qiime2R


(benjamin w.) #1

I just wanted to say thanks, I have been trouble shooting getting the export boom files into R and the import was the first to work correctly. Currently not sure wy I’m having trouble, but it may be something to do with the merging of the taxonomy + otu_table.

One quick comment though when I import it over, for some reason the row specified as titles/column titles does not import correctly:

[1] “V2” “V3” “V4” “V5” “V6” “V7” “V8” “V9” “V10” “V11” “V12” “V13” “V14” “V15” “V16” “V17” “V18” “V19” “V20” “V21” “V22” “V23”
[23] “V24” “V25” “V26” “V27” “V28”


Tutorial: Integrating QIIME2 and R for data visualization and analysis using qiime2R
(Jordan Bisanz) #2

Hi Ben, Could you send me a copy of the table and I can figure out what is going on?

Thanks,

Jordan


(benjamin w.) #3

Hi Jordan sure, which files do you need, the metadata table? Ben

Upload.assessment.txt (90.7 KB)

edit: I would like to add that the columns import correctly, it’s just the titles that do not, I was able to do analysis putting V# to send information to R to be able to select my samples.


(Jordan Bisanz) #4

Ahh, yes this was a bug on the import of the metadata table where the column names were becoming a row of the table. If you pull the latest version from github this should be fixed. Let me know if you still have problems.


(benjamin w.) #5

Great, will test it today, thank you again. Ben


(benjamin w.) #6

One quick recommendation, the column titles end up being:
rank_names(PHYLOSEQ.OBJECT)

[1] “ta1” “ta2” “ta3” “ta4” “ta5” “ta6” “ta7”

You can use this code to give your column titles:

colnames(tax_table(OBJECT.GOES.HERE))=c(“Domain”, “Phylum”, “Class”, “Order”, “Family”, “Genus”, “OTU”)