## $matching ## [1] 1 2 NA 4 5 3 ## +## $matchedSplits +## [1] "A B | C D E F G H I => A B | C D E F G H I" +## [2] "C D E | A B F G H I => C D E I | A B F G H" +## [3] "F G H I | A B C D E => F G H | A B C D E I" +## [4] "G H I | A B C D E F => G H | A B C D E F I" +## [5] "H I | A B C D E F G .. E I | A B C D F G H" +## +## $matchedScores +## [1] 3.700440 3.252981 NA 3.252981 2.115477 0.000000 +## ## $pairScores ## [,1] [,2] [,3] [,4] [,5] ## [1,] 3.7004397 0.8930848 0.2410081 0.5305147 0.2410081 @@ -330,14 +340,7 @@ Constructing a matching## [3,] 0.2410081 1.3785116 0.0000000 0.5305147 0.2410081 ## [4,] 0.8930848 0.0000000 0.0000000 3.2529807 1.3785116 ## [5,] 0.5305147 0.0000000 0.0000000 0.0000000 2.1154772 -## [6,] 0.2410081 0.0000000 0.0000000 0.0000000 0.0000000 -## -## $matchedSplits -## [1] "A B | C D E F G H I => A B | C D E F G H I" -## [2] "C D E | A B F G H I => C D E I | A B F G H" -## [3] "F G H I | A B C D E => F G H | A B C D E I" -## [4] "G H I | A B C D E F => G H | A B C D E F I" -## [5] "H I | A B C D E F G .. E I | A B C D F G H"
.. denotes that the fifth matching contributes zero to similarity score; an alternative optimal matching would leave these splits unpaired.
..
## [1] 6.960578 ## attr(,"matching") ## [1] 1 2 3 5 6 4 +## attr(,"matchedSplits") +## [1] "B C D E | A F G H I => B C D H I | A E F G" +## [2] "C D E | A B F G H I => C D H I | A B E F G" +## [3] "D E | A B C F G H I => D H I | A B C E F G" +## [4] "F G H I | A B C D E => E F G | A B C D H I" +## [5] "F G | A B C D E H I => F G | A B C D E H I" +## [6] "H I | A B C D E F G => H I | A B C D E F G" +## attr(,"matchedScores") +## [1] 0.09109101 0.07278023 0.02475761 0.07278023 0.76420451 0.76420451 ## attr(,"pairScores") ## [,1] [,2] [,3] [,4] [,5] [,6] ## [1,] 0.091091008 0.007214618 0.01831078 0.22478751 0.01831078 0.22478751 @@ -185,14 +194,7 @@ Visualizing a matching## [3,] 0.002565287 0.002565287 0.02475761 0.09288851 0.02475761 0.09288851 ## [4,] 0.007214618 0.007214618 0.07278023 0.31976006 0.07278023 0.31976006 ## [5,] 0.319760062 0.224787510 0.15200728 0.09288851 0.45810590 0.76420451 -## [6,] 0.224787510 0.319760062 0.45810590 0.76420451 0.15200728 0.09288851 -## attr(,"matchedSplits") -## [1] "B C D E | A F G H I => B C D H I | A E F G" -## [2] "C D E | A B F G H I => C D H I | A B E F G" -## [3] "D E | A B C F G H I => D H I | A B C E F G" -## [4] "F G H I | A B C D E => E F G | A B C D H I" -## [5] "F G | A B C D E H I => F G | A B C D E H I" -## [6] "H I | A B C D E F G => H I | A B C D E F G"
Here, the pairScores attribute lists the score of each possible matching of splits.
pairScores
We can identify the splits with:
(Use the mouse to reorient)
Smith, M.R. (2020b). TreeDist: Distances between Phylogenetic Trees. R package version 2.8.0.9000. Comprehensive R Archive Network. doi:10.5281/zenodo.3528124
Smith, M.R. (2020b). TreeDist: Distances between Phylogenetic Trees. R package version 2.8.0.9001. Comprehensive R Archive Network. doi:10.5281/zenodo.3528124
@Manual{TreeDist, - title = {TreeDist: Distances between Phylogenetic Trees. R package version 2.8.0.9000}, + title = {TreeDist: Distances between Phylogenetic Trees. R package version 2.8.0.9001}, author = {Martin R. Smith}, doi = {10.5281/zenodo.3528124}, journal = {Comprehensive R Archive Network}, diff --git a/dev/index.html b/dev/index.html index 3fcff9f12..a226174e1 100644 --- a/dev/index.html +++ b/dev/index.html @@ -30,7 +30,7 @@ TreeDist - 2.8.0.9000 + 2.8.0.9001 diff --git a/dev/news/index.html b/dev/news/index.html index db8860078..93be366d5 100644 --- a/dev/news/index.html +++ b/dev/news/index.html @@ -13,7 +13,7 @@ TreeDist - 2.8.0.9000 + 2.8.0.9001 @@ -59,8 +59,10 @@ Changelog
VisualizeMatching()
SpectralEigens()
nEig
reportMatching = TRUE
matching: which split in splits2 is optimally matched to each split in split1 (NA if not matched);
matching
splits2
split1
NA
pairScores: Calculated scores for each possible matching of each split.
matchedSplits: Textual representation of each match
matchedSplits
matchedScores: Scores for matched split.
matchedScores
R/VisualizeMatching.R
VisualizeMatching.Rd
Character expansion for edge labels. +If FALSE, suppress edge labels.
FALSE
Character expansion for values on edge labels. +If FALSE, values are not displayed.
Character specifying the kind of frame to be printed around +the text of the edge labels. Choose an abbreviation of "rect", "circle", +or "none".
"rect"
"circle"
"none"
Additional parameters to send to Plot().
Plot()
VisualizeMatching() invisibly returns the matching of splits +between tree1 and tree2 (i.e. +Func(tree1, tree2, reportMatching = TRUE))
tree1
tree2
Func(tree1, tree2, reportMatching = TRUE)
Note that when visualizing a Robinson–Foulds distance (using @@ -148,8 +173,27 @@