qiime2R - qiime to phyloseq

Question

Im having a bit of trouble in qiime2R at the moment. I'm following the tutorial and getting stuck here:

unwunifrac <- read_qza("unweighted_unifrac_pcoa_results.qza")

         unwunifrac <- read_qza("unweighted_unifrac_pcoa_results.qza")

    unwunifrac$data$Vectors %>%
    select(SampleID, PC1, PC2) %>%
    left_join(metadata) %>%
    left_join(shannon)
    ggplot(aes(x=PC1, y=PC2, color=`SPT_No`, shape=`Geosmin`, size=shannon_entropy)) +
    geom_point(alpha=0.5) + 
    theme_q2r() +
   scale_shape_manual(values=c(16,1), name="Geosmin") +
   scale_size_continuous(name="Geosmin") +
   scale_color_discrete(name="Location")

It is because my sampleid is called sampleid in my metadata and shannon vector but its called SampleID in the unweighted unifrac qza file.

Has anyone experienced this issue? How do I resolve it? is it best to rename the columns?

Any help would be much appreciated.

Many thanks

Answer 1

This issue you are having is not clear. Can you please try to post something to reproduce whatever error message you are getting from q2R?