Dear all,
I have a question for you. I generated a beta diversity emperor in two different environments: in QIIME2 (2024.2) and in R. Despite for Bray-Curtis, Jaccard and Weighted Unifrac the plot is basically the same, there is a strange result for Unweighted Unifrac using R. I want to ask you for any suggestions what can be a cause of that.
unweighted_unifrac_emperor.qzv (980.5 KB)
Here is a script for R:
ps <- qza_to_phyloseq(
features = paste0('/../../../analysis/',project_name,'/processing_data/qiime2_analysis/nb_classifier/filtered-table.qza'),
tree = paste0('/../../../analysis/',project_name,'/processing_data/qiime2_analysis/diversity/phylogeny/rooted-tree.qza'),
metadata = paste0('/../../../analysis/',project_name,'/manifest_metadata/metadata.tsv'),
taxonomy = paste0('/../../../analysis/',project_name,'/processing_data/qiime2_analysis/nb_classifier/classified-rep-seqs.qza'))
ord = ordinate(ps, method="PCoA", distance = "uunifrac")
uunifrac <- plot_ordination(ps, ord, color = condition) +
geom_point(size = 4) +
stat_ellipse(aes_string(group = condition)) +
ggtitle("Unweighted Unifrac") +
scale_color_manual(values = allGroupsColors) +
theme_classic(20) +
theme(plot.title = element_text(color = "black",
size = 25,
hjust = 0.5,
face = "bold"))
Do you have any ideas ?
Thank you very much!