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