# Creates the figures for the rOpenSci blog post
# E.g. https://github.com/ropensci/roweb2/pull/415
setwd("/home/richel/GitHubs/roweb2/themes/ropensci/static/img/blog-images/2019-01-06-babette")
library(babette)
phylogeny <- ape::read.tree(text = "(((1:1,2:1):1, 3:2):1, 4:3);")
png(filename = "phylogeny.png", width = 400, height = 300)
ape::plot.phylo(phylogeny, cex = 2.0, edge.width = 2.0)
dev.off()
fasta_filename <- "alignment.fasta"
# Simulate an alignment
pirouette::sim_alignment_file(
phylogeny = phylogeny,
alignment_params = pirouette::create_alignment_params(
root_sequence = pirouette::create_blocked_dna(length = 40),
mutation_rate = 0.5 * 1.0 / 3.0
),
fasta_filename = fasta_filename
)
png(filename = "alignment.png", width = 800, height = 300)
ape::image.DNAbin(ape::read.FASTA(
file = fasta_filename),
grid = TRUE,
show.bases = FALSE,
legend = FALSE,
cex.lab = 2.0,
cex.axis = 2.0
)
dev.off()
output <- babette::bbt_run(fasta_filename = fasta_filename, overwrite = TRUE)
png(filename = "densitree.png", width = 1000, height = 800)
babette::plot_densitree(
output$alignment_trees, library = "phangorn",
alpha = 0.01,
consensus = as.character(c(1:4)),
cex = 2.0,
scaleX = TRUE,
scale.bar = FALSE
)
dev.off()
babette::plot_densitree(posterior_trees[501:1001], width = 1, alpha = 0.01)
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