creating a factor-based in dendrogram with R and ggplot2 - r

Question

This is not so much a coding as general approach call for help ;-) I prepared a table containing taxonomic information about organisms. But I want to use the "names" of these organisms, so no values or anything where you could compute a distance or clustering with (this is also all the information I have). I just want to use these factors to create a plot that shows the relationship. My data looks like this:
test2<-structure(list(genus = structure(c(4L, 2L, 7L, 8L, 6L, 1L, 3L,
5L, 5L), .Label = c("Aminobacter", "Bradyrhizobium", "Hoeflea",
"Hyphomonas", "Mesorhizobium", "Methylosinus", "Ochrobactrum",
"uncultured"), class = "factor"), family = structure(c(4L, 1L,
2L, 3L, 5L, 6L, 6L, 6L, 6L), .Label = c("Bradyrhizobiaceae",
"Brucellaceae", "Hyphomicrobiaceae", "Hyphomonadaceae", "Methylocystaceae",
"Phyllobacteriaceae"), class = "factor"), order = structure(c(1L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("Caulobacterales",
"Rhizobiales"), class = "factor"), class = structure(c(1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = "Alphaproteobacteria", class = "factor"),
phylum = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = "Proteobacteria", class = "factor")), .Names = c("genus",
"family", "order", "class", "phylum"), class = "data.frame", row.names = c(NA,
9L))
is it necessary to set up artificial values to describe a distance between the levels?

Answer 1

Here is an attempt using data.tree library
First create a string variable in the form:
Proteobacteria/Alphaproteobacteria/Caulobacterales/Hyphomonadaceae/Hyphomonas
library(data.tree)
test2$pathString <- with(test2,
paste(phylum,
class,
order,
family,
genus, sep = "/"))
tree_test2 = as.Node(test2)
plot(tree_test2)
many things can be done after like:
Interactive network:
library(networkD3)
test2_Network <- ToDataFrameNetwork(tree_test2, "name")
simpleNetwork(test2_Network)
or graph styled
library(igraph)
plot(as.igraph(tree_test2, directed = TRUE, direction = "climb"))
check out the vignette
using ggplot2:
library(ggraph)
graph = as.igraph(tree_test2, directed = TRUE, direction = "climb")
ggraph(graph, layout = 'kk') +
geom_node_text(aes(label = name))+
geom_edge_link(arrow = arrow(type = "closed", ends = "first",
length = unit(0.20, "inches"),
angle = 15)) +
geom_node_point() +
theme_graph()+
coord_cartesian(xlim = c(-3,3), expand = TRUE)
or perhaps:
ggraph(graph, layout = 'kk') +
geom_node_text(aes(label = name), repel = T)+
geom_edge_link(angle_calc = 'along',
end_cap = circle(3, 'mm'))+
geom_node_point(size = 5) +
theme_graph()+
coord_cartesian(xlim = c(-3,3), expand = TRUE)