How to stretch an nLTT timepoints matrix

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Richel Bilderbeek

2023-08-21

An nLTT plot consists out of points that denote a number of (normalized) lineages in (normalized) time. For nLTT plots with only a few points, stretch_nltt_matrix inserts timepoints.

Examples

For all examples, the following R code must be run:

library(ape)
library(nLTT) # nolint
library(testit)

Example: Easy tree

Create an easy tree:

newick <- "((A:1,B:1):1,C:2);"
phylogeny <- ape::read.tree(text = newick)
plot(phylogeny)
ape::add.scale.bar() #nolint

From this tree, we can create an nLTT plot:

nltt_plot(phylogeny)

We can extract the timepoints of the nLTT plot using the get_phylogeny_nltt_matrix function.

nltt <- nLTT::get_phylogeny_nltt_matrix(phylogeny)
print(nltt)

##      time         N
## [1,]  0.0 0.3333333
## [2,]  0.5 0.6666667
## [3,]  1.0 1.0000000

The timepoints are plotted in red over the nLTT plot:

nltt_plot(phylogeny)
points(nltt, pch = 19, col = "red")

The function stretch_nltt_matrix inserts timepoints, as shown in this table:

nltt <- nLTT::get_phylogeny_nltt_matrix(phylogeny)
stretch_matrix <- nLTT::stretch_nltt_matrix(
  nltt, dt = 0.25, step_type = "upper"
)
print(stretch_matrix)

##      [,1]      [,2]
## [1,] 0.00 0.6666667
## [2,] 0.25 0.6666667
## [3,] 0.50 1.0000000
## [4,] 0.75 1.0000000
## [5,] 1.00 1.0000000

Plotting these as blue points between the red points:

nltt_plot(phylogeny)
points(nltt, pch = 19, col = "red")
points(stretch_matrix, pch = 19, col = "blue")

A good result is when all blue points fall on the line.

Example: Tree that has two branching events at the same time

Create an easy tree:

newick <- "((A:1,B:1):1,(C:1,D:1):1);"
phylogeny <- ape::read.tree(text = newick)
plot(phylogeny)
ape::add.scale.bar() #nolint

From this tree, we can create an nLTT plot:

nltt_plot(phylogeny)

We can extract the timepoints of the nLTT plot using the get_phylogeny_nltt_matrix function.

nltt <- nLTT::get_phylogeny_nltt_matrix(phylogeny)
print(nltt)

##      time    N
## [1,]  0.0 0.25
## [2,]  0.5 0.50
## [3,]  0.5 0.75
## [4,]  1.0 1.00

The timepoints are plotted in red over the nLTT plot:

nltt_plot(phylogeny)
points(nltt, pch = 19, col = "red")

The function stretch_nltt_matrix inserts timepoints, as shown in this table:

nltt <- nLTT::get_phylogeny_nltt_matrix(phylogeny)
stretch_matrix <- nLTT::stretch_nltt_matrix(
  nltt, dt = 0.25, step_type = "upper"
)
print(stretch_matrix)

##      [,1] [,2]
## [1,] 0.00  0.5
## [2,] 0.25  0.5
## [3,] 0.50  1.0
## [4,] 0.75  1.0
## [5,] 1.00  1.0

Plotting these as blue points between the red points:

nltt_plot(phylogeny)
points(nltt, pch = 19, col = "red")
points(stretch_matrix, pch = 19, col = "blue")

A good result is when all blue points fall on the line.

Example: Complex tree

Create a complex tree:

newick <- paste0("((((XD:1,ZD:1):1,CE:2):1,(FE:2,EE:2):1):4,((AE:1,BE:1):1,",
  "(WD:1,YD:1):1):5);"
)
phylogeny <- ape::read.tree(text = newick)
plot(phylogeny)
ape::add.scale.bar() #nolint

From this tree, we can create an nLTT plot:

nltt_plot(phylogeny)

We can extract the timepoints of the nLTT plot using the get_phylogeny_nltt_matrix function.

nltt <- nLTT::get_phylogeny_nltt_matrix(phylogeny)
print(nltt)

##            time         N
##  [1,] 0.0000000 0.1111111
##  [2,] 0.5714286 0.2222222
##  [3,] 0.7142857 0.3333333
##  [4,] 0.7142857 0.4444444
##  [5,] 0.7142857 0.5555556
##  [6,] 0.8571429 0.6666667
##  [7,] 0.8571429 0.7777778
##  [8,] 0.8571429 0.8888889
##  [9,] 1.0000000 1.0000000

The timepoints are plotted in red over the nLTT plot:

nltt_plot(phylogeny)
points(nltt, pch = 19, col = "red")

The function stretch_nltt_matrix inserts blue points between these red points:

nltt <- nLTT::get_phylogeny_nltt_matrix(phylogeny)
nltt_plot(phylogeny)
stretch_matrix <- nLTT::stretch_nltt_matrix(
  nltt, dt = 0.05, step_type = "upper"
)
points(nltt, pch = 19, col = "red")
points(stretch_matrix, pch = 19, col = "blue")

A good result is when all blue points fall on the line.

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