Added newick import/export

[Jason Vander Heiden]

Using the data.tree package seems the easiest path from igraph to newick format:

library(igraph)
library(data.tree)
tree <- FromDataFrameNetwork(as_data_frame(graph))
ToNewick(tree, heightAttribute=NULL)

Not sure what you want to do with the heightAttribute, but you could base it of the "weight" column instead of excluding it.

[ssnn]

Using the data.tree package seems the easiest path from igraph to newick format:

library(igraph)
library(data.tree)
tree <- FromDataFrameNetwork(as_data_frame(graph))
ToNewick(tree, heightAttribute=NULL)

Not sure what you want to do with the heightAttribute, but you could base it of the "weight" column instead of excluding it.

[Kenneth Hoehn]

I wrote a function for converting from R phylo objects to igraph to work with igphyml trees. I can add a more general function to do this though.

[Kenneth Hoehn]

Added phyloToGraph and graphToPhylo to allow for interconversion between phylo, igraph, and newick formats. Example:

‌

library(ape)
library(igraph)
library(phangorn)
library(alakazam)
library(shazam)
library(dplyr)

clone <- makeChangeoClone(subset(ExampleDb,CLONE == 3163))

graph <- buildPhylipLineage(clone,
    "/home/kenneth/Programs/phylip-3.697/exe/dnapars",
    rm_temp=TRUE)

#plot lineage tree
plot(graph,layout=layout_as_tree)

# convert to phylo
phylo = graphToPhylo(graph)

#plot using ape
plot(phylo,show.node.label=TRUE)

#store as newick tree
write.tree(phylo,file="3163.newick")

#read in tree
phylo_r = read.tree("3163.newick")

#convert to igraph
graph_r = phyloToGraph(phylo_r,germline="Germline")

#plot converted form - same as before
plot(graph_r,layout=layout_as_tree)

#convert back to phylo
phylo_rr = graphToPhylo(graph_r)

#tree topologies are the same
phangorn::RF.dist(phylo,phylo_rr)

[Jason Vander Heiden]

Awesome. Thanks. How do you feel about polishing this example a little and dropping into the end of the lineage vignette (vignettes/Lineage-Vignette.Rmd)?

[Kenneth Hoehn]

Sure - what do you think should be changed?

[Jason Vander Heiden]

Not much.

Put some short section header text in explaining the point. Style fixes. Consistency with the rest of vignette (eg, there’s already an example of running phylip in the vignette, so no need to repeat). Make sure it passes check when in the vignette.

Just make it jive with the rest of the vignette.

[Kenneth Hoehn]

Sounds good - just pushed it.

[Jason Vander Heiden]

Coolness. Thanks!

[ssnn]

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