Adding data

In this section, we look over ways of adding extra information or data to a plot.

Adding labels

To add labels on edges (or nodes), we need to know their numbers. We can use the showedgenumber = true option for this. (Use shownodenumber = true to see node numbers).

plot(net, showedgenumber=true);
plot(net, showedgenumber=true, edgenumbercolor="red4");

Edge numbers are shown in grey by default (to avoid mistaking them for edge lengths), but their color can be adjusted as shown above.

We then need to define a DataFrame with two columns of information: the number of the edge (or node), and the label that goes on it, like this:

After including the DataFrames package, we can define it as so:

julia> using DataFrames
julia> DataFrame(number=[1,2], label=["edge number 1","edge # 2"])2×2 DataFrame
 Row │ number  label
     │ Int64   String
─────┼───────────────────────
   1 │      1  edge number 1
   2 │      2  edge # 2

Using this data frame as input to the edgelabel option (nodelabel for nodes) puts the text on the correct edges:

plot(net, edgelabel=DataFrame(number = [1,2],
                              label = ["edge number 1", "edge # 2"]),
          edgelabelcolor="orangered", edgecex=[0.9,1.1]);

Adding other annotations using R

We can use the return values of plot to get information on the coordinates of different elements of the plot. Using this, we can add any other information we want.

The plot function returns the following tuple:

(xmin, xmax, ymin, ymax,
 node_x, node_y, node_yB, node_yE,
 edge_xB, edge_xE, edge_yB, edge_yE,
 nodedataframe, edgedataframe)

See the documentation for descriptions of these elements: plot

Side clade bars example

Here's example code that adds bars to denote clades in the margin:

net = readTopology("(((((((1,2),3),4),5),(6,7)),(8,9)),10);");
plot(net, xlim=(1,10))
using RCall # to send any R command, to make further plot modifications
R"segments"([9, 9, 9], [0.8, 7.8, 9.8], [9, 9, 9], [7.2, 9.2, 10.2])
R"text"([9.5, 9.5, 9.5], [4, 8.5, 10], ["C", "B", "A"])

Let's break this down step by step. First, we read the topology, and plot the graph normally. plot actually returns a value, from which we can get useful information. Below, we store the plot output in res, then check its first two values because they contain the default range of the x axis; xmin and xmax.

res = plot(net);
res[1:2]

(0.29999999999999993, 8.77)

Looking at xmin and xmax returned by default, we can see that the x range is about (0.3, 9). To give us extra space to work with, we can set xlim to (0.3,10), forcing the range to be wider on the right, for annotations. We can also see that in this case there is some extra white space on the left, so that we can increase xmin a little bit, finally settling on xlim=(1,10).

plot(net, xlim=(1, 10));

Knowing the coordinates, we can now add more information to the plot through RCall. For this, I use the R functions segments and text to add side bars with text on them.

using RCall # add (install) the RCall package prior to 'using' it
R"segments"([9, 9, 9], [0.8, 7.8, 9.8], [9, 9, 9], [7.2, 9.2, 10.2])
R"text"([9.5, 9.5, 9.5], [4, 8.5, 10], ["C", "B", "A"])