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
