cophyloplot(x, y, assoc = NULL, use.edge.length = FALSE, space = 0,
length.line = 1, gap = 2, type = "phylogram", rotate = FALSE,
col = par("fg"), lwd = par("lwd"), lty = par("lty"),
show.tip.label = TRUE, font = 3, ...)
"phylo"
.The association matrix used to draw the links has to be a matrix with two columns containing the names of the tips. One line in the matrix represents one link on the plot. The first column of the matrix has to contain tip labels of the first tree (phy1
) and the second column of the matrix, tip labels of the second tree (phy2
). There is no limit (low or high) for the number of lines in the matrix. A matrix with two colums and one line will give a plot with one link.
Arguments gap
, length.line
and space
have to be changed to get a nice plot of the two phylogenies. Note that the function takes into account the length of the character strings corresponding to the names at the tips, so that the lines do not overwrite those names.
The rotate
argument can be used to transform both phylogenies in order to get the more readable plot (typically by decreasing the number of crossing lines). This can be done by clicking on the nodes. The escape button or right click take back to the console.
plot.phylo
, rotate
, rotateConstr
#two random trees
tree1 <- rtree(40)
tree2 <- rtree(20)
#creation of the association matrix:
association <- cbind(tree2$tip.label, tree2$tip.label)
cophyloplot(tree1, tree2, assoc = association,
length.line = 4, space = 28, gap = 3)
#plot with rotations
cophyloplot(tree1, tree2, assoc=association, length.line=4, space=28, gap=3, rotate=TRUE)
Run the code above in your browser using DataLab