Nothing
## ----global_options, include=FALSE--------------------------------------------
knitr::opts_chunk$set(fig.width=12, fig.height=8,
echo=TRUE, warning=FALSE, message=FALSE,
tidy=TRUE)
## -----------------------------------------------------------------------------
library(rhierbaps)
library(ggtree)
library(phytools)
library(ape)
set.seed(1234)
## -----------------------------------------------------------------------------
fasta.file.name <- system.file("extdata", "seqs.fa", package = "rhierbaps")
snp.matrix <- load_fasta(fasta.file.name)
## -----------------------------------------------------------------------------
data(woodmouse)
woodmouse.snp.matrix <- load_fasta(woodmouse)
## -----------------------------------------------------------------------------
hb.results <- hierBAPS(snp.matrix, max.depth=2, n.pops=20, quiet = TRUE)
head(hb.results$partition.df)
## ---- eval=FALSE--------------------------------------------------------------
# hb.results <- hierBAPS(snp.matrix, max.depth=2, n.pops=20, n.extra.rounds = Inf,
# quiet = TRUE)
## -----------------------------------------------------------------------------
system.time(hierBAPS(snp.matrix, max.depth=2, n.pops=20, quiet = TRUE))
## -----------------------------------------------------------------------------
newick.file.name <- system.file("extdata", "seqs.fa.treefile", package = "rhierbaps")
iqtree <- phytools::read.newick(newick.file.name)
## -----------------------------------------------------------------------------
gg <- ggtree(iqtree, layout="circular")
gg <- gg %<+% hb.results$partition.df
gg <- gg + geom_tippoint(aes(color=factor(`level 1`)))
gg
## -----------------------------------------------------------------------------
gg <- ggtree(iqtree, layout="circular", branch.length = "none")
gg <- gg %<+% hb.results$partition.df
gg <- gg + geom_tippoint(aes(color=factor(`level 1`)))
gg <- gg + theme(legend.position="right")
gg <- gg + geom_tiplab(aes(label = `level 2`), size = 1, offset = 1)
gg
## -----------------------------------------------------------------------------
plot_sub_cluster(hb.results, iqtree, level = 1, sub.cluster = 9)
## -----------------------------------------------------------------------------
hb.results$lml.list
## -----------------------------------------------------------------------------
hb.results.woodmouse <- hierBAPS(woodmouse.snp.matrix, max.depth=2, n.extra.rounds = Inf,
quiet = TRUE, assignment.probs = TRUE)
head(hb.results.woodmouse$cluster.assignment.prob[[1]])
## ---- eval=FALSE--------------------------------------------------------------
# write.csv(hb.results$partition.df, file=file.path(tempdir(), "hierbaps_partition.csv"),
# col.names = TRUE, row.names = FALSE)
#
# save_lml_logs(hb.results, file.path(tempdir(), "hierbaps_logML.txt"))
## -----------------------------------------------------------------------------
sessionInfo()
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