Hello everyone,
I have a rookie question but unfortunately I am unable to find an answer myself. I would like to generate a cladrogram using ggtree package based on the taxonomy of my strains.
As I know the taxonomic classification of he strains I thought that I could use that to generate a tree in Newick format, for that I used the makeNewick function from the Taxonomizr package.
setwd("D:/R/phylogeny/Jemime_collection")
taxofile<-"cladotest.tab"
Taxo <- read.table (taxofile, check.names = FALSE, header = TRUE, dec = ".", sep = "\t", comment.char = "")
which got me this, so far so good:
Taxo
family genus species
1 Actinomycetaceae Actinobaculum Actinobaculum_sp_oral_taxon_183
2 Actinomycetaceae Actinomyces Actinomyces_bouchesdurhonensis
3 Actinomycetaceae Actinomyces Actinomyces_dentalis
4 Actinomycetaceae Actinomyces Actinomyces_gerencseriae
5 Actinomycetaceae Actinomyces Actinomyces_graevenitzii
6 Actinomycetaceae Actinomyces Actinomyces_israelii
7 Actinomycetaceae Actinomyces Actinomyces_johnsonii
8 Actinomycetaceae Actinomyces Actinomyces_massiliensis
9 Actinomycetaceae Actinomyces Actinomyces_naeslundii
10 Actinomycetaceae Actinomyces Actinomyces_oris
11 Actinomycetaceae Actinomyces Actinomyces_SGB17154
12 Actinomycetaceae Actinomyces Actinomyces_SGB17168
13 Actinomycetaceae Actinomyces Actinomyces_sp_ICM47
After that I tried to generate a newick tree from this using the makenewick function, which seemed to work :
tree <- makeNewick(Taxo)
tree
[1] "(((Actinobaculum_sp_oral_taxon_183)Actinobaculum,(Actinomyces_bouchesdurhonensis,Actinomyces_dentalis,Actinomyces_gerencseriae,Actinomyces_graevenitzii,Actinomyces_israelii,Actinomyces_johnsonii,Actinomyces_massiliensis,Actinomyces_naeslundii,Actinomyces_oris,Actinomyces_SGB17154,Actinomyces_SGB17168,Actinomyces_sp_ICM47)Actinomyces)Actinomycetaceae);"
However, when I tried to use this newick tree to generate the tree I got an error message:
ggtree(tree)
> Error in `fortify()`:
! `data` must be a <data.frame>, or an object coercible by `fortify()`, not the string "(((Actinobaculum_sp_oral_ta...".
Run `rlang::last_trace()` to see where the error occurred.
I ran line indicated and got this:
<error/rlang_error>
Error in `fortify()`:
! `data` must be a <data.frame>, or an object coercible by `fortify()`, not the string "(((Actinobaculum_sp_oral_ta...".
---
Backtrace:
Run rlang::last_trace(drop = FALSE) to see 2 hidden frames.
Which did not help me understand how and why my tree was not data.frame and how to convert it into a data.frame.
Has anyone an idea on how to solve this problem?
1 answer
The output of makeNewick() is a character string. It needs to be a data.frame or phylo class to work with ggtree. You have some options:
# Option 1: convert string to phylo within R
tree_string <- "(((Actinobaculum_sp_oral_taxon_183)Actinobaculum,(Actinomyces_bouchesdurhonensis,Actinomyces_dentalis,Actinomyces_gerencseriae,Actinomyces_graevenitzii,Actinomyces_israelii,Actinomyces_johnsonii,Actinomyces_massiliensis,Actinomyces_naeslundii,Actinomyces_oris,Actinomyces_SGB17154,Actinomyces_SGB17168,Actinomyces_sp_ICM47)Actinomyces)Actinomycetaceae);"
phylo_tree <- ape::read.tree(text = tree_string)
ggtree(phylo_tree)
# Option 2: write string to file, read in as tree
tree_string <- "(((Actinobaculum_sp_oral_taxon_183)Actinobaculum,(Actinomyces_bouchesdurhonensis,Actinomyces_dentalis,Actinomyces_gerencseriae,Actinomyces_graevenitzii,Actinomyces_israelii,Actinomyces_johnsonii,Actinomyces_massiliensis,Actinomyces_naeslundii,Actinomyces_oris,Actinomyces_SGB17154,Actinomyces_SGB17168,Actinomyces_sp_ICM47)Actinomyces)Actinomycetaceae);"
writeLines(tree_string, "tree.nwk")
tree_in <- treeio::read.newick("tree.nwk")
ggtree(tree_in)
Log in to answer this question.
Please use the formatting bar (especially the
codeoption) to present your post better. You can use backticks for inline code (`text` becomestext), or use one of (a) the option highlighted in the image below/ (b) fenced code blocks for multi-line code. Fenced code blocks are useful in syntax highlighting. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted. I've done it for you this time.Thank you, my apologies for the improper formating.