R/phyloscan.fun.plotting.R
phsc.plot.most.likely.transmission.chain.Rd
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.
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)
df | data.table with the following columns 'IDCLU','ID1', 'ID2', 'TYPE','KEFF','LKL_MAX','POSTERIOR_SCORE' |
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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