## ----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) + ggplot2::ggtitle("Do not use a tree like this") ## ----add_alignment, message=FALSE--------------------------------------------- alignment_file <- system.file("extdata", "ZIKV.fasta", package = "sitePath") options(list("cl.cores" = 1)) # Set this bigger than 1 to use multiprocessing paths <- addMSA(tree, msaPath = alignment_file, msaFormat = "fasta") ## ----sneakPeek_plot----------------------------------------------------------- preassessment <- sneakPeek(paths, makePlot = TRUE) ## ----get_lineagePath---------------------------------------------------------- paths <- lineagePath(preassessment, 18) 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, minSNP = 1, mutMode = "exact") paraSites ## ----------------------------------------------------------------------------- plotSingleSite(paraSites, 105) ## ----plot_parallel------------------------------------------------------------ plot(paraSites) ## ----plot_sites--------------------------------------------------------------- plotSingleSite(paths, 139) plotSingleSite(paths, 763) ## ----find_SNP----------------------------------------------------------------- snps <- SNPsites(paths) plotMutSites(snps) plotSingleSite(paths, snps[4]) plotSingleSite(paths, snps[5]) ## ----session_info------------------------------------------------------------- sessionInfo()