View source: R/phyloscan.fun.plotting.R
phsc.plot.transmission.network | R Documentation |
This function plots a phylogenetic transmission network, showing three types of edges: two directed edges respectively in the 1->2 and 2->1 direction, and an undirected edge that represents phylogenetic support of close and adjacent individuals without evidence into the direction transmission.
phsc.plot.transmission.network(
df,
di,
point.size = 10,
point.size.couple = point.size * 1.4,
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_
)
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 |
ggplot object
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