I am trying to build a phylogenetic tree with iTol. I downloaded all the necessary .qza files and got a very heavy tree of 1243 leaves.
Question: how to reduce the number of leaves and nodes so that everything works more or less quickly.
And how to upload metadata so can see the result of the meta-analysis
Hello, Colin! Thank you for your attention!
I filtered my sequences - it turned about 700
And tried to reduce with help "auto collapse’, but
I am not sure, that it done: system wrote: “please provide average branch”
And I deleted branches, but didn’t get faster.
Fortunately, I familiar with R. I try now to do tree with
results<-results %>% mutate(Significant=if_else(we.eBH<0.1,"*", ""))
tree<-drop.tip(tree, tree$tip.label[!tree$tip.label %in% results$Feature.ID]) # remove all the features from the tree we do not have data for
ggtree(tree, layout="circular") %<+% results +
geom_tippoint(aes(fill=diff.btw), shape=21, color="grey50") +
geom_tiplab2(aes(label=Significant), size=10) +
scale_fill_gradient2(low="darkblue",high="darkred", midpoint = 0, mid="white", name="log2(fold-change") +
ggsave("tree.pdf", height=10, width=10, device="pdf", useDingbats=F)
But what is ```
differentials.qza - is problem
Might there is another way to construct tree with R ?