filter_GD_by_coverage: filters the GD counts by the species coverage of each of the...
In Chien-Hsun/rePhylo: Re-investigating and Improving Phylogenies

filter_GD_by_coverage is to identify for each gd whether the two duplicated subclades contains species number more than a given level.

filter_GD_by_coverage(
  phyto,
  node,
  trees,
  gdtable,
  sptree,
  split,
  tree_id_tab,
  sub_coverage = NULL,
  max.tip = NULL,
  up_one_node = FALSE,
  plot = 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.
`sub_coverage`	a numeric specify the species coverage level. If <= 1, treated as percentage. If > 1, treated as number of species.
`max.tip`	an integer specifying the max number of tips for the coverage filtering. Applied only when sub_coverage is set as percent (<= 1). Used as a cutoff for coverage as N tips as for deep nodes having large clades.
`up_one_node`	logical. Whether to choose tips of one node deeper as the closest outgroup, as a second step of investigation. Defaults to `FALSE`.
`plot`	whether to plot subclades. Defaults to `FALSE`.
`pdfwid`	the width of pdf file for subtrees. Defaults to `10`.
`pdflen`	the length of pdf file for subtrees. Defaults to `30`.
`mc.cores`	the number of cores used for mclapply. Defaults to `4`.

returns a pdf plotting the gd clades, with gd pairs in red and other species in the same clade in sptree in green. A file with prefix "Include_or_not_" indicates for each tree and gd the requirement is fulfilled or not. A file with prefix "Trees_have_basal_tips_" shows the page number the tree fulfilled the requirement in the pdf file.

Chien-Hsun/rePhylo documentation built on May 19, 2020, 3:15 a.m.