Q2R PCOA Plot Problem

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1

Hi all, I have followed QIIME2R integration tutorial (Tutorial: Integrating QIIME2 and R for data visualization and analysis using qiime2R). I am trying to create PCOA plot with my bray curtis artifact distance matrix generated by QIIME2. Below is my code. I keep getting error "Error in bray$data$Vectors : $ operator is invalid for atomic vectors". Strangely, if I run is.atomic(bray) I get FALSE. Not sure what is happening here but appreciate help very much!!

bray$data$Vectors %>%

  • select(SampleID, PC1, PC2) %>%
  • left_join(metadata) %>%
  • left_join(shannon) %>%
  • ggplot(aes(x=PC1, y=PC2, color=genotype, shape=gender, size=shannon)) +
  • geom_point(alpha=0.5) + alpha controls transparency and helps when points are overlapping
  • theme_q2r() +
  • scale_shape_manual(values=c(16,1), name="gender") + #see http://www.sthda.com/sthda/RDoc/figure/graphs/r-plot-pch-symbols-points-in-r.png for numeric shape codes
  • scale_size_continuous(name="shannon") +
  • scale_color_discrete(name="genotype")
    Error in bray$data$Vectors : $ operator is invalid for atomic vectors
2

Hi everyone, I figured this out. I was using the wrong input file. While I should have been using the bray_curtis_pcoa_results.qza file, I was using the bray_curtis_distance_matrix.qza file. Hope this helps anyone who has this problem in the future! Please mark this problem as completed.

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