Description Usage Arguments Details
View source: R/filter_GD_by_coverage.R
filter_GD_by_coverage
is to identify for each gd whether the two
duplicated subclades contains species number more than a given level.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 |
phyto |
the phyto id for the analysis. |
node |
a numeric indicating the target node id as in |
trees |
a list of objects of class " |
gdtable |
a |
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 |
plot |
whether to plot subclades. Defaults to |
pdfwid |
the width of pdf file for subtrees. Defaults to |
pdflen |
the length of pdf file for subtrees. Defaults to |
mc.cores |
the number of cores used for mclapply. Defaults to |
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.
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