GGRaSP failing on tree dataset

[FilipeMatteoli]

Hello,
I've been trying to use ggrasp to deal with a 10k NJ tree with no success.
Can I access all command line options through R console (or Rstudio) or only in terminal?

I tried to create a .rank file assigning 1 to all Ids present in my tree. Looks like this (tree.ranks):
"000018085 1
000163595 1
000176835 1
000186485 1"

tree.file <- system.file("extdata", "outtree.tree", package = "ggrasp")
summary(tree.file)
Length Class Mode
1 character character
rank.file.in <- system.file("extdata", "tree.ranks", package = "ggrasp")
Enter.tree.in <- ggrasp.load(tree.file, file.format = "tree", rank.file = rank.file.in)
complete
Error in names(rank.lst) <- rank.list$V1 :
attempt to set an attribute on NULL

No object is created. I also tried using the downloader script (LOCUST) but I already have the tree and the typer.pl code issued several warnings and failed.

Best,

[thclarke]

I think that this can be solved by removing the "extdata" from the system.file command. This forces the system to load the files from the package examples data as opposed to your own data. If you want to use your own data, you can just load it into the ggrasp.load directly:

Enter.tree.in <- ggrasp.load("outtree.tree", file.format = "tree", rank.file = "tree.ranks")
assuming that the R current directory contains the outtree.tree and tree.ranks file.

Cheers-

Thomas Clarke