## ----style, echo=FALSE, results="asis", message=FALSE-------------------- knitr::opts_chunk$set(tidy = FALSE, message = FALSE) ## ----echo=FALSE, results="hide", message=FALSE--------------------------- library("ape") library("Biostrings") library("ggplot2") library("ggtree") ## ------------------------------------------------------------------------ file <- system.file("extdata/BEAST", "beast_mcc.tree", package="ggtree") beast <- read.beast(file) beast ## ------------------------------------------------------------------------ get.fields(beast) ## ----warning=FALSE, fig.width=10, fig.height=10-------------------------- ggtree(beast, ndigits=2, branch.length = 'none') + geom_text(aes(x=branch, label=length_0.95_HPD), vjust=-.5, color='firebrick') ## ----warning=FALSE, fig.width=10, fig.height=10-------------------------- ggtree(beast) + geom_range(range='length_0.95_HPD', color='red', alpha=.6, size=2) ## ----warning=FALSE, fig.width=10, fig.height=10-------------------------- ggtree(beast, branch.length = 'rate') + geom_range(range='rate_0.95_HPD', color='red', alpha=.6, size=2) ## ------------------------------------------------------------------------ beast_data <- fortify(beast) head(beast_data) ## ----fig.width=12, fig.height=10, warning=FALSE, fig.align="center"------ brstfile <- system.file("extdata/PAML_Baseml", "rst", package="ggtree") brst <- read.paml_rst(brstfile) brst p <- ggtree(brst) + geom_text(aes(x=branch, label=marginal_AA_subs), vjust=-.5, color='steelblue') + theme_tree2() print(p) ## ------------------------------------------------------------------------ crstfile <- system.file("extdata/PAML_Codeml", "rst", package="ggtree") crst <- read.paml_rst(crstfile) crst ## ----fig.width=12, fig.height=10, warning=FALSE, fig.align="center"------ p %<% crst ## ------------------------------------------------------------------------ mlcfile <- system.file("extdata/PAML_Codeml", "mlc", package="ggtree") mlc <- read.codeml_mlc(mlcfile) mlc ## ----fig.width=8, fig.height=8, warning=FALSE, fig.align="center"-------- ggtree(mlc) + geom_text(aes(x=branch, label=dN_vs_dS), color='blue', vjust=-.2) ## ------------------------------------------------------------------------ get.fields(mlc) ## ----fig.width=8, width=60, warning=FALSE, fig.align="center"------------ ggtree(mlc, branch.length = "dN_vs_dS", aes(color=dN_vs_dS)) + scale_color_continuous(name='dN/dS', limits=c(0, 1.5), oob=scales::squish, low="darkgreen", high="red")+ theme_tree2(legend.position=c(.9, .5)) ## ------------------------------------------------------------------------ ml <- read.codeml(crstfile, mlcfile) ml head(fortify(ml)) ## ----warning=FALSE------------------------------------------------------- nwk <- system.file("extdata/HYPHY", "labelledtree.tree", package="ggtree") ancseq <- system.file("extdata/HYPHY", "ancseq.nex", package="ggtree") tipfas <- system.file("extdata", "pa.fas", package="ggtree") hy <- read.hyphy(nwk, ancseq, tipfas) hy ## ----fig.width=16, fig.height=10, warning=FALSE, fig.align="center"------ ggtree(hy) + geom_text(aes(x=branch, label=AA_subs), vjust=-.5) ## ----fig.width=4, fig.height=6, width=60, warning=FALSE, fig.align="center"---- r8s <- read.r8s(system.file("extdata/r8s", "H3_r8s_output.log", package="ggtree")) ggtree(r8s, branch.length="TREE", mrsd="2014-01-01") + theme_tree2() ## ----fig.width=16, fig.height=10, width=60, warning=FALSE, fig.align="center"---- ggtree(get.tree(r8s), aes(color=.id)) + facet_wrap(~.id, scales="free_x") ## ----fig.width=12, fig.height=10, width=60, warning=FALSE, fig.align="center"---- raxml_file <- system.file("extdata/RAxML", "RAxML_bipartitionsBranchLabels.H3", package="ggtree") raxml <- read.raxml(raxml_file) ggtree(raxml) + geom_label(aes(label=bootstrap, fill=bootstrap)) + geom_tiplab() + scale_fill_continuous(low='darkgreen', high='red') + theme_tree2(legend.position='right') ## ------------------------------------------------------------------------ nhxfile <- system.file("extdata", "ADH.nhx", package="ggtree") nhx <- read.nhx(nhxfile) ggtree(nhx) + geom_tiplab() + geom_point(aes(color=S), size=5, alpha=.5) + theme(legend.position="right") + geom_text(aes(label=branch.length, x=branch), vjust=-.5) + xlim(NA, 0.3) ## ------------------------------------------------------------------------ phyfile <- system.file("extdata", "sample.phy", package="ggtree") phylip <- read.phylip(phyfile) phylip ggtree(phylip) + geom_tiplab() ## ----fig.width=10, fig.height=6------------------------------------------ msaplot(phylip, offset=1) ## ------------------------------------------------------------------------ jpf <- system.file("extdata/sample.jplace", package="ggtree") jp <- read.jplace(jpf) print(jp) ## ------------------------------------------------------------------------ ## get only best hit get.placements(jp, by="best") ## get all placement get.placements(jp, by="all") ## ------------------------------------------------------------------------ beast_file <- system.file("examples/MCC_FluA_H3.tree", package="ggtree") beast_tree <- read.beast(beast_file) rst_file <- system.file("examples/rst", package="ggtree") mlc_file <- system.file("examples/mlc", package="ggtree") codeml_tree <- read.codeml(rst_file, mlc_file) merged_tree <- merge_tree(beast_tree, codeml_tree) merged_tree head(fortify(merged_tree)) ## ----fig.width=20, fig.height=26, warning=FALSE-------------------------- ggtree(merged_tree, aes(color=dN_vs_dS), mrsd="2013-01-01", ndigits = 3) + geom_text(aes(label=posterior), vjust=.1, hjust=-.1, size=5, color="black") + scale_color_continuous(name='dN/dS', limits=c(0, 1.5), oob=scales::squish, low="green", high="red")+ theme_tree2(legend.position="right") ## ------------------------------------------------------------------------ tree <- system.file("extdata", "pa.nwk", package="ggtree") data <- read.csv(system.file("extdata", "pa_subs.csv", package="ggtree"), stringsAsFactor=FALSE) print(tree) head(data) ## ------------------------------------------------------------------------ outfile <- tempfile() write.jplace(tree, data, outfile) ## ------------------------------------------------------------------------ jp <- read.jplace(outfile) print(jp) ## ----fig.width=12, fig.height=12, warning=FALSE, fig.align="center"------ ggtree(jp) + geom_text(aes(x=branch, label=subs), color="purple", vjust=-1, size=3) + geom_text(aes(label=gc), color="steelblue", hjust=-.6, size=3) + geom_tiplab()