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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.
For all examples, the following R code must be run:
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:
We can extract the timepoints of the nLTT plot using the
get_phylogeny_nltt_matrix
function.
## 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:
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.
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:
We can extract the timepoints of the nLTT plot using the
get_phylogeny_nltt_matrix
function.
## 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:
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.
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:
We can extract the timepoints of the nLTT plot using the
get_phylogeny_nltt_matrix
function.
## 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:
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.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.