Importing Newick trees in Cytoscape by conversion to igraph via RCy3

Question

[elliskidsjunkemail]

I am trying to import a Newick format tree into Cystoscape using vinette in Bioconductor. (https://bioconductor.org/packages/release/bioc/vignettes/RCy3/inst/doc/Phylogenetic-trees.html)

This works well until I get to this call in the vinette....

tree <- phytools::read.newick(system.file("extdata","C:/Users/chuck/Desktop/tree.newick", package="RCy3"))

I keep getting this error…

"Argument text is missing with no default"

Does anyone know what I could be missing?

Answer 1

[xanderpico]

It looks like you've changed the line. The original is:

tree <- phytools::read.newick(system.file("extdata","phylotree.newick", package="RCy3"))

Which is grabbing an example newick file provided by the RCy3 package. You've replaced with filename with a local path, which obviously is not a part of the RCy3 package. So, here are two fixes, depending on your intent:

1. Restore the original line in order to run the example data
2. Replace the entire example file call with your local file, like so:

.

tree <- phytools::read.newick("C:/Users/chuck/Desktop/tree.newick")

Answer 2

[elliskidsjunkemail]

Many thanks Xanderpico that got me a bit further down the workflow.

Now it works well until I get to this call in the vinette....

createNetworkFromIgraph(ig, title="phylotree", collection = "phylotree")

I then get the following error.. . RCy3::commandsPOST, HTTP Error Code: 500 url=http://localhost:1234/v1/commands/vizmap/apply body={ "styles": "default" } Error in commandsPOST("vizmap apply styles=\"default\"", base.url = base.url) : No network views selected.

Thanks again!