VisualizeMatching {TreeDist} | R Documentation |
Visualize a matching
Description
Depict the splits that are matched between two trees using a specified Generalized Robinson–Foulds similarity measure.
Usage
VisualizeMatching(
Func,
tree1,
tree2,
setPar = TRUE,
precision = 3L,
Plot = plot.phylo,
matchZeros = TRUE,
plainEdges = FALSE,
edge.cex = par("cex"),
value.cex = edge.cex * 0.8,
edge.frame = "rect",
edge.width = 1,
edge.color = "black",
...
)
Arguments
Func |
Function used to construct tree similarity. |
tree1 , tree2 |
Trees of class |
setPar |
Logical specifying whether graphical parameters should be set to display trees side by side. |
precision |
Integer specifying number of significant figures to display when reporting matching scores. |
Plot |
Function to use to plot trees. |
matchZeros |
Logical specifying whether to pair splits with zero
similarity ( |
plainEdges |
Logical specifying whether to plot edges with a uniform
width and colour ( |
edge.cex |
Character expansion for edge labels.
If |
value.cex |
Character expansion for values on edge labels.
If |
edge.frame |
Character specifying the kind of frame to be printed around
the text of the edge labels. Choose an abbreviation of |
edge.width , edge.color , ... |
Additional parameters to send to |
Details
Note that when visualizing a Robinson–Foulds distance (using
Func = RobinsonFouldsMatching
), matched splits are assigned a similarity
score of 1, which is deducted from the total number of splits to calculate
the Robinson–Foulds distance. Unmatched splits thus contribute one to
total tree distance.
Value
VisualizeMatching()
invisibly returns the matching of splits
between tree1
and tree2
(i.e.
Func(tree1, tree2, reportMatching = TRUE)
)
Author(s)
Martin R. Smith (martin.smith@durham.ac.uk)
Examples
tree1 <- TreeTools::BalancedTree(6)
tree2 <- TreeTools::PectinateTree(6)
VisualizeMatching(RobinsonFouldsMatching, tree1, tree2)
matching <- VisualizeMatching(SharedPhylogeneticInfo, tree1, tree2,
matchZeros = FALSE)
attributes(matching)