public documentation

plot(net::HybridNetwork; ...)

Plot a network with edges going from left to right and taxa (leaves) placed on the right, using R graphics. Optional arguments are listed below.

lines forming the network:

• useedgelength = false: if true, the tree edges and major hybrid edges are drawn proportionally to their length. Minor hybrid edges are not, however. Note that edge lengths in coalescent units may scale very poorly with time.
• style = :fulltree: symbol indicating the style of the diagram
  • :majortree will simply draw minor edges onto the major tree.
  • :fulltree will draw minor edges as their own branches in the tree, in the same style used by icytree. This is useful for overlapping or confusing networks.
• arrowlen: the length of the arrow tips in the full tree style. The default is 0.1 if style = :fulltree, and 0 if style = :majortree (making the arrows appear as segments).
• minorlinetype: type of lines used for minor edges, represented by arrows. Default is "solid" under the major-tree style, and "longdash" under the full tree style.
• edgewidth=1: width of horizontal (not diagonal) edges. To vary them, use a dictionary to map the number of each edge to its desired width.
• xlim, ylim: array of 2 values, to determine the axes limits.

tip annotations:

• showtiplabel = true: if true, taxon labels (names) are shown.
• tipoffset = 0: to offset tip labels.
• tipcex = 1: character expansion for tip and internal node names.

nodes & edges annotations:

• shownodelabel = false: if true, internal nodes are labelled with their names. Useful for hybrid nodes, which have labels such as "H1".
• shownodenumber = false: if true, nodes are labelled with the number used internally.
• showedgenumber = false: if true, edges are labelled with the number used internally.
• showedgelength = false: if true, edges are labelled with their length (above).
• showgamma = false: if true, hybrid edges are labelled with their heritability (below).
• edgelabel = DataFrame(): dataframe with two columns: the first with edge numbers, the second with labels (like bootstrap values) to annotate edges. empty by default.
• nodelabel = DataFrame(): dataframe with two columns: the first with node numbers, the second with labels (like bootstrap values for hybrid relationships) to annotate nodes. empty by default.
• nodecex = 1 and edgecex = 1: character expansion for labels in the nodelabel and edgelabel data frames.
• nodelabeladj = 1 and edgelabeladj = [.5,0]: position adjustment to place the labels from edgelabel and nodelabel data frames.

colors:

• edgecolor = "black": color for tree edges if a single color is given. To vary edge colors, use a dictionary to map the number of each edge to its desired color. In that case, unmapped edges are given the defaultedgecolor.
• majorhybridedgecolor = "deepskyblue4": color for major hybrid edges. minorhybridedgecolor = "deepskyblue": color for minor hybrid edges. Both are ignored if edgecolor is a dictionary.
• defaultedgecolor: default is "black" if edgecolor is a dictionary, or edgecolor otherwise. Used to draw the segments representing each node.
• edgenumbercolor = "grey": color for edge numbers.
• edgelabelcolor = "black": color for labels in the edgelabel data frame.
• nodelabelcolor = "black": color for labels in the nodelabel data frame.

Output the following named tuple, that can be used for downstream annotations with RCall:

(xmin, xmax, ymin, ymax,
 node_x,     node_y,     node_y_lo, node_y_hi,
 edge_x_lo,  edge_x_hi,  edge_y_lo,  edge_y_hi,
 arrow_x_lo, arrow_x_hi, arrow_y_lo, arrow_y_hi,
 node_data, edge_data)

1. :xmin: minimum x value of the plot
2. :xmax: maximum x value of the plot
3. :ymin: minimum y value of the plot
4. :ymax: maximum y value of the plot
5. :node_x: x values of the nodes in net.node in their respective order
6. :node_y: y values of the nodes
7. :node_y_lo: y value of the beginning of the vertical bar representing the clade at each node
8. :node_y_hi: y value of the end of the vertical bar
9. :edge_x_lo: x value of the beginning of the edges in net.edge in their respective order. An edge (or branch) in the network is represented by 2 segments if it is a minor edge under the :fulltree style. :edge_* give the coordinates of the first (horizontal) segment for these minor edges, and the coordinates of the unique (horizontal) segment for major edges (tree of major hybrid edges).
10. :edge_x_hi: x value of the end of the edges
11. :edge_y_lo: y value of the beginning of the edges
12. :edge_y_hi: y value of the end of the edges
13. :arrow_x_lo: x value for the beginning of the arrows, for minor hybrid edges, listed in the same order as in filter(e -> !e.ismajor, net.edge).
14. :arrow_x_hi: same, but for the end of arrows
15. :arrow_y_lo: y values for the beginning of arrows
16. :arrow_y_hi: same, but for the end of arrows
17. :node_data: node data frame: see section Adding labels for more
18. :edge_data: edge data frame

Note that plot actually modifies some (minor) attributes of the network, as it calls PhyloNetworks.directedges! and PhyloNetworks.preorder! (unless with option preorder = false, which is not recommended).

If hybrid edges cross tree and major edges, you may choose to rotate some tree edges to eliminate crossing edges, using PhyloNetworks.rotate!.

Alternative: a tree or network can be exported with sexp and then displayed with R's "plot" and all its options.

function sexp(net::HybridNetwork)

Export a HybridNework object to the R language as either phylo or evonet object (depending on degree of hybridization) recognized by the R package ape. Used by the $object syntax and by @rput to use a Julia object in R: see the examples below. Makes it easy to plot a Julia tree or network using plotting facilities in R.

Examples

julia> using RCall
julia> using PhyloNetworks
julia> net = readnewick("(((A:.2,(B:.1)#H1:.1::0.9):.1,(C:.11,#H1:.01::0.1):.19):.1,D:.4);");
R> library(ape); # type $ to switch from julia to R
R> $net

    Evolutionary network with 1 reticulation

               --- Base tree ---
Phylogenetic tree with 4 tips and 5 internal nodes.

Tip labels:
  A, B, C, D

Rooted; includes branch lengths.

julia> @rput net; # press the delete key to switch from R back to julia

R> net

    Evolutionary network with 1 reticulation

               --- Base tree ---
Phylogenetic tree with 4 tips and 5 internal nodes.

Tip labels:
  A, B, C, D

Rooted; includes branch lengths.

R> str(net)
List of 7
 $ edge               : int [1:8, 1:2] 5 5 6 6 7 8 8 9 6 4 ...
 $ reticulation.length: num 0.01
 $ Nnode              : int 5
 $ edge.length        : num [1:8] 0.1 0.4 0.1 0.19 0.11 0.2 0.1 0.1
 $ reticulation       : int [1, 1:2] 7 9
 $ reticulation.gamma : num 0.1
 $ tip.label          : chr [1:4] "A" "B" "C" "D"
 - attr(*, "class")= chr [1:2] "evonet" "phylo"

R> plot(net)