Issues using qiime2R


(Kaylee Arnold) #22

Hi!!

I am also having issues using qiime2R.

phyloseq <- qza_to_phyloseq(features = “table.qza”, tree = “rooted-tree.qza”, taxonomy = “taxonomy.qza”, metadata = “Updated_metadata.tsv”)

My physoseq object looks like this:

And when I try to create a bar plot

bar_plot <- plot_bar(phyloseq, fill = “Phylum”)

I get the error:

Error in FUN(X[[i]], …) : object ‘Phylum’ not found


(Jordan Bisanz) #23

Hi Kaylee,

I see why this has happened. The taxonomy string is not stored in a fixed-width format inside the artifact and was getting an arbitrary column title (ta1->ta7). A quick work around that should work now is plot_bar(phyloseq, fill="ta2").

I just pushed an update that should more carefully import the taxonomy and explicitly name the columns such that plot_bar(phyloseq, fill="Phylum") should work. Just reinstall using devtools::install_github("jbisanz/MicrobeR") to get the newest version.

Jordan


(Kaylee Arnold) #24

Wonderful! It is working now. Thank you so much for your quick reply.