Nothing
## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----import_tree, message=FALSE-----------------------------------------------
library(sitePath)
tree_file <- system.file("extdata", "ZIKV.newick", package = "sitePath")
tree <- read.tree(tree_file)
## ----bad_tree_example, echo=FALSE---------------------------------------------
bad_tree <- read.tree(system.file("extdata", "WNV.newick", package = "sitePath"))
ggtree::ggtree(bad_tree)
## ----add_alignment, message=FALSE---------------------------------------------
alignment_file <- system.file("extdata", "ZIKV.fasta", package = "sitePath")
tree <- addMSA(tree, alignment_file, "fasta")
## ----sneakPeek_plot-----------------------------------------------------------
preassessment <- sneakPeek(tree, makePlot = TRUE)
## ----get_lineagePath----------------------------------------------------------
paths <- lineagePath(preassessment, similarity = 0.05)
paths
## ----plot_paths---------------------------------------------------------------
plot(paths)
## ----min_entropy--------------------------------------------------------------
minEntropy <- sitesMinEntropy(paths)
## ----find_fixations-----------------------------------------------------------
fixations <- fixationSites(minEntropy)
fixations
## -----------------------------------------------------------------------------
allSites <- allSitesName(fixations)
allSites
## ----get_sitePath-------------------------------------------------------------
sp <- extractSite(fixations, 139)
## ----get_tipNames-------------------------------------------------------------
extractTips(fixations, 139)
## ----plot_sitePath------------------------------------------------------------
plot(sp)
plotSingleSite(fixations, 139)
## ----plot_fixations-----------------------------------------------------------
plot(fixations)
## -----------------------------------------------------------------------------
paraSites <- parallelSites(minEntropy, mutMode = "exact")
paraSites
## -----------------------------------------------------------------------------
plotSingleSite(paraSites, 105)
## ----plot_sites---------------------------------------------------------------
plotSingleSite(paths, 139)
plotSingleSite(paths, 763)
## ----find_SNP-----------------------------------------------------------------
snps <- SNPsites(tree)
plotMutSites(snps)
plotSingleSite(paths, snps[4])
plotSingleSite(paths, snps[5])
## ----session_info-------------------------------------------------------------
sessionInfo()
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