First time working on a network in R, and I was looking into some possible packages/libraries to do so. There is this guide using ggraph that seems pretty complete and has some nice features I'm interested in.
I have some plots did in the past using ggtree based on PHYLO objects as inputs, so I tried to figure out whether there were ways to convert one into the other e.g. phylo -> igraph similar to what the guide is using.
I generated my PHYLO objects starting from a distance matrix with the upgma function from phangorn (see below), some issues were suggesting it is possible to convert phylo -> igraph with:
<network> <- as.igraph(<phylo>)
which is what I did. However, when following along the guide trying to subselect for a specific list to plot I'm getting the following error
Error in
geom_edge_elbow0(): ! Problem while computing aesthetics. ℹ Error occurred in the 1st layer. Caused by error: ! object 'direction' not found Runrlang::last_trace()to see where the error occurred.
MWE
library(ape)
library(igraph)
library(ggraph)
library(network)
library(phangorn)
network <- as.igraph(phylo)
autograph(phylo)
networkS2 <- network[[2]]
autograph(networkS2) #this is giving the error above
dput() phylo
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"SRR17658415"), Nnode = 303L), class = "phylo", order = "postorder")
As the discussion in the comments has brought to light, OP followed the tutorial too closely and, in doing so, overlooked that network (OP's data) is a single igraph object while got (from tutorial) is a list of seven igraph objects.
> devtools::install_github('schochastics/networkdata')
> library(networkdata)
> class(got)
[1] "list"
> sapply(got, class)
[1] "igraph" "igraph" "igraph" "igraph" "igraph" "igraph" "igraph"
> # lapply(got, igraph::plot.igraph)
>
> network = ape::as.igraph.phylo(phylo)
> class(network)
[1] "igraph"
> # plot(network)
i.e.
# str(network)
network[[2]]
returns a list-formatted piece of network
$SRR17658386
+ 0/607 vertices, named, from e933f34:
which cannot be plotted while
> class(got[[2]])
[1] "igraph"
is an igraph object for which plotting methods exists. The tutorial's intro could have been more explicit.