plotFilteredGD: plot the gd result corrected by filter_GD_by_coverage and...
In Chien-Hsun/rePhylo: Re-investigating and Improving Phylogenies

plotFilteredGD plot a tree with node labels as the corrected values (both count and percent). Only nodes both shown in both gd and deno have node labels. Only nodes with deno > 0 are shown.

plotFilteredGD(
  tree,
  gd,
  deno,
  type = "percent",
  thres_node,
  thres_count = 100,
  thres_percent = 5,
  color = c("red", "yellow"),
  tip.offset = NULL,
  node.cex = 1,
  plot.margin = c(6, 140, 6, 6),
  xlim = NULL
)

`tree`	the species tree used to do tree reconciliation.
`gd`	the summary table of `filter_GD_by_coverage`.
`deno`	the result of `denominator`.
`type`	can be one of "percent", "count", or "both", determines the type of threshod value used for node color. Defaults to `"percent"`.
`thres_node`	optional. A numeric specify which node (in ape id) are used as threshold to give colors on node labels.
`thres_count`	nodes with counts above this threshold will be plotted as red. Defaults to `100`
`thres_percent`	nodes with percent above this threshold will be plotted as red. Defaults to `5`
`color`	two characters specify the colors for node labels. The first is for node above the threshold, and the second is for those below.
`tip.offset`	offset of tip labels in `ggtree`. Defaults to `NULL`.
`node.cex`	size of node labels.
`plot.margin`	four numeric indicate plot margin. Defaults to `c(6, 140, 6, 6)`.
`xlim`	used as the x scale in `ggtree`.