Error in check_edgelist(x) : Cannot find root. network is not a tree!

YuLab-SMU / treeio

:seedling: Base Classes and Functions for Phylogenetic Tree Input and Output

https://yulab-smu.top/treedata-book/

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Error in check_edgelist(x) : Cannot find root. network is not a tree! #80

Closed acpaulo closed 1 year ago

acpaulo commented 2 years ago

Describe you issue

[ ] I import a nkw file as read.newick(".nwk")
[ ] I construct this file with PopPUNK to habe GPSC
[ ] I don't want to plot the references jusst my query sequences
[ ] I run tree.df.2018 <- tree.2018 %>% as_tibble() %>% as.data.frame() # to trsaform to data.frame
[ ] Then I run tree.df2.2018 <- tree.df.2018[grepl("PT",tree.df.2018$label),] #to keep only sequnces starting with PT
[ ] tree.df2.2018 %>% as.phylo() # gives the error Error in check_edgelist(x) : Cannot find root. network is not a tree!

Is there a way to subset the nwk file without transform it to a data.frame or to pass a data.fram to a phylo object again ?

Thank you in advance

brj1 commented 2 years ago

You should use the ape library to manipulate phylo objects. It is a dependency of treeio so should already have it installed. ape's keep.tip function subsets tips.

library(ape)
tree.2018.subset <- keep.tip(tree.2018, grep("PT", tree.2018$tip.label))

Note that keep.tip uses tip/node numbers not a boolean filter so you need to use grep instead of grepl.

acpaulo commented 2 years ago

Thank you Brad, it did solve the problem.