Description Usage Arguments Value Examples
View source: R/Pipeline.SpeciesNetworkDistances.ScaleAllBranches.R
This function returns a matrix containing the 5 distance metics (3 probabilistic + Robinson-Foulds + BHV)
1 2 3 | Pipeline.SpeciesNetworkDistances.ScaleAllBranches(vector.ScaleFactor,
string.PathParentDir, string.PathHybridCoal,
handle.SpeciesNetwork.Model1, handle.SpeciesNetwork.Model2)
|
vector.ScaleFactor |
Vector to containing the values to scale the branches of the second species tree model |
string.PathParentDir |
Path to a parent directory that will be used for subdirectories |
string.PathHybridCoal |
Path to HYBRID-COAL executable |
handle.SpeciesTree.Model1 |
Species Tree Model 1 |
handle.SpeciesTree.Model2 |
Species Tree Model 2 |
XXX
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | library(phangorn)
library(PSTD)
library(distory)
string.SpeciesTree.1a <- "(((A:1,B:1):1,C:2):1,D:3);"
handle.SpeciesTree.1a <- read.tree(text = string.SpeciesTree.1a)
vector.Gamma <- seq(0.01, 10, 0.01)
handle.Figure1d <- Pipeline.SpeciesTreeDistances.ScaleAllBranches(vector.ScaleFactor = vector.Gamma,
string.PathParentDir = '~/Desktop/',
string.PathHybridCoal = '/Applications/hybrid-coal-v0.2.1-beta/hybrid-coal',
handle.SpeciesTree.Model1 = handle.SpeciesTree.1a,
handle.SpeciesTree.Model2 = handle.SpeciesTree.1a)
plot(handle.Figure1d[,1], ylim = c(0, 0.75), col = "darkblue", type = "l", xaxt='n', yaxt="n", lty = 1)
axis(1,at=seq(from = 0, to = 1000, by = 50),labels=seq(from = 0, to = 10, by = 0.50))
axis(2,at=seq(from = 0, to = 0.75, by = 0.10),labels=seq(from = 0, to = 0.75, by = 0.10))
lines(handle.Figure1d[,2], col = "blue", lty = 2)
lines(handle.Figure1d[,3], col = "lightblue", lty = 4)
lines(handle.Figure1d[,5]*0.025, col = "red", lty = 3)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.