## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----import_tree, message=FALSE----------------------------------------------- library(ape) tree <- read.tree(system.file("extdata", "ZIKV.newick", package = "sitePath")) ## ----add_alignment, message=FALSE--------------------------------------------- library(sitePath) alignment_file <- system.file("extdata", "ZIKV.fasta", package = "sitePath") tree <- addMSA(tree, alignment_file, "fasta") ## ----sneakPeek_plot----------------------------------------------------------- preassessment <- sneakPeek(tree) plot(preassessment$similarity, preassessment$pathNum) ## ----get_lineagePath---------------------------------------------------------- paths <- lineagePath(tree) paths ## ----plot_paths--------------------------------------------------------------- plot(paths, no.margin = TRUE) ## ----find_fixations----------------------------------------------------------- fixations <- fixationSites(paths) fixations ## ----get_sitePath------------------------------------------------------------- extractSite(fixations, 139) ## ----get_tipNames------------------------------------------------------------- extractTips(fixations, 139) ## ----plot_fixations----------------------------------------------------------- plotSingleSite(fixations, 139) ## ----plot_sites--------------------------------------------------------------- plotSingleSite(paths, 139) plotSingleSite(paths, 763) ## ----find_SNP----------------------------------------------------------------- snps <- SNPsites(tree) plotSingleSite(paths, snps[4]) plotSingleSite(paths, snps[5]) ## ----group_tips--------------------------------------------------------------- grouping <- groupTips(tree) grouping ## ----session_info------------------------------------------------------------- sessionInfo()