detect_closest_out_for_GD: Detect the existence of the closest outgroups for each gd
In Chien-Hsun/rePhylo: Re-investigating and Improving Phylogenies

Description Usage Arguments Details Examples

View source: R/detect_closest_out_for_GD.R

detect_closest_out_for_GD is to find out whether each gd has tips of its sister clade as the closest outgroup, in order to verify the support of gd. The returning object contains a simple summary for the number and percent of gd that has the closest outgroup. This function will also produce pdf files plotting subclade of each gd, with tips colored, for easier manual investigation when required.

detect_closest_out_for_GD(
  phyto,
  node,
  trees,
  gdtable,
  sptree,
  split,
  tree_id_tab,
  up_one_node = FALSE,
  pdfwid = 10,
  pdflen = 30,
  mc.cores = 4
)

`phyto`	the phyto id for the analysis.
`node`	a numeric indicating the target node id as in `ape`. An alternative arg of `phyto`.
`trees`	a list of objects of class "`phylo`". A list of gene trees to be examined. Can be unrooted.
`gdtable`	a `data.frame` of the gd table file provided by Tree2GD.
`sptree`	the species tree used to do tree reconciliation.
`split`	a character. The symbol used to separate species name and the sequence number in the gene family trees.
`tree_id_tab`	a table for the tree id during Tree2GD and the name of the corresponding tree file. The first column is the id, and the second column is the tree names.
`up_one_node`	logical. Whether to choose tips of one node deeper as the closest outgroup, as a second step of investigation. Default `FALSE`.
`pdfwid`	the width of pdf file for subtrees. Default `10`.
`pdflen`	the length of pdf file for subtrees. Default `30`.
`mc.cores`	the number of cores used for mclapply. Defaults to `4`.

For each gd, detect whether there are closest outgroups exactly next to the duplicated node, that can actually define the gd at the indicated node. Otherwise, gd will be possible to be at other (deeper) nodes as well.

## Not run: 
res<-
detect_closest_out_of_GD(
phyto,trees = trees,gdtable = gdtable,
sptree = sptree,split=".",tree_id_tab = tree_id_tab,
up_one_node=FALSE,pdfwid = 20,pdflen = 100)

res

## End(Not run)