phsc.plot.most.likely.transmission.chain: Plot most likely transmission chain
In olli0601/phyloscan:

phsc.plot.most.likely.transmission.chain

R Documentation

Plot most likely transmission chain

Description

This function plots a most likely transmission chain, showing one edges with two labels: L indicates the proportion of deep-sequence phylogenies in whom the two individuals are phylogenetically close and adjacent. D indicates the proportion of deep-sequence phylogenies that support the indicated direction of transmission, out of all deep-sequence phylogenies that support either direction of transmission.

Usage

phsc.plot.most.likely.transmission.chain(
  df,
  di,
  point.size = 10,
  edge.gap = 0.04,
  edge.size = 0.4,
  curvature = -0.2,
  arrow = arrow(length = unit(0.04, "npc"), type = "open"),
  curv.shift = 0.08,
  label.size = 3,
  node.label = "ID",
  node.shape = NA_character_,
  node.fill = NA_character_,
  node.shape.values = NA_integer_,
  node.fill.values = NA_character_,
  threshold.linked = NA_real_,
  layout = NULL
)

Arguments

`df`	data.table with the following columns 'IDCLU','ID1', 'ID2', 'TYPE','KEFF','LKL_MAX','POSTERIOR_SCORE'
`di`	data.table with meta-data to customize the plot with columns ID, node.shape, node.label, node.fill
`point.size`	size of the individual points
`edge.gap`	value to adjust start / end points of edges
`edge.size`	multiplier by which the size of edges is shrunk/magnified
`curvature`	curvature of directed edges
`arrow`	type of arrow to be plotted
`curv.shift`	offset to place the label for directed edges
`label.size`	size of label
`node.label`	Text displayed on top of each node
`node.shape`	column name in di by which the shape of each node is drawn
`node.fill`	column name in di by which each node is coloured
`node.shape.values`	named vector associating shapes to the values in the node.shape column
`node.fill.values`	named vector associating colours to the values in the node.fill column
`threshold.linked`	treshold value between 0 and 1. Edges with weight above this treshold are shown in black.
`point.sizec.couple`	size of the outer ring around individuals in couples