## ----style, echo=FALSE, results="asis", message=FALSE--------------------
BiocStyle::markdown()
knitr::opts_chunk$set(tidy = FALSE,
		   message = FALSE)


## ----echo=FALSE, results="hide", message=FALSE---------------------------
library("colorspace")
library("Biostrings")
library("ape")
library("ggplot2")
library("gridExtra")
library("ggtree")


## ----fig.width=3, fig.height=3, fig.align="center"-----------------------
nwk <- system.file("extdata", "sample.nwk", package="ggtree")
x <- readLines(nwk)
cat(substring(x, 1, 56), "\n", substring(x, 57), "\n")

library("ggplot2")
library("ggtree")

tree <- read.tree(nwk)
ggplot(tree, aes(x, y)) + geom_tree() + theme_tree() + xlab("") + ylab("")


## ----fig.width=3, fig.height=3, fig.align="center"-----------------------
ggtree(tree, color="steelblue", size=0.5, linetype="dotted")


## ----fig.width=3, fig.height=3, fig.align="center"-----------------------
ggtree(tree, ladderize=FALSE)


## ----fig.width=3, fig.height=3, fig.align="center"-----------------------
ggtree(tree, branch.length="none")


## ----fig.width=6, fig.height=9, fig.align="center"-----------------------
library("gridExtra")
grid.arrange(ggtree(tree) + ggtitle("(Phylogram) rectangular layout"),
             ggtree(tree, branch.length='none') + ggtitle("(Cladogram) rectangular layout"),
	     ggtree(tree, layout="slanted") + ggtitle("(Phylogram) slanted layout"),
             ggtree(tree, layout="slanted", branch.length='none') + ggtitle("(Cladogram) slanted layout"),
	     ggtree(tree, layout="circular") + ggtitle("(Phylogram) circular layout"),
             ggtree(tree, layout="circular", branch.length="none") + ggtitle("(Cladogram) circular layout"),
	     ggtree(tree, layout="unrooted") + ggtitle("unrooted layout"),
	     ncol=2)


## ----fig.width=9, fig.height=4, fig.align="center"-----------------------
tree2d <- read.beast(system.file("extdata", "twoD.tree", package="ggtree"))
ggtree(tree2d, mrsd = "2014-05-01",
       yscale="NGS", yscale_mapping=c(N2=2, N3=3, N4=4, N5=5, N6=6, N7=7)) +
           theme_classic() + 
               theme(panel.grid.major=element_line(color="grey20", linetype="dotted", size=.3),
                     panel.grid.major.y=element_blank()) +
                         scale_y_continuous(labels=paste0("N", 2:7))


## ----fig.width=3, fig.height=3, fig.align="center"-----------------------
ggtree(tree) %>% add_legend()


## ----fig.width=3, fig.height=3, fig.align="center"-----------------------
ggtree(tree) + theme_tree2()


## ----fig.width=3, fig.height=3, fig.align="center"-----------------------
ggtree(tree)+geom_point(aes(shape=isTip, color=isTip), size=3)


## ----fig.width=3, fig.height=3, fig.align="center"-----------------------
p <- ggtree(tree) + geom_nodepoint(color="#b5e521", alpha=1/4, size=10)
p + geom_tippoint(color="#FDAC4F", shape=8, size=3)


## ----fig.width=3, fig.height=3, warning=FALSE, fig.align="center"--------
p + geom_text(aes(label=label), size=3, color="purple", hjust=-0.3)


## ----fig.width=6, fig.height=6, warning=FALSE, fig.align="center"--------
ggtree(tree, layout="circular") + geom_text(aes(label=label, angle=angle), size=3, color="purple", vjust=-0.3)


## ----fig.width=5, fig.height=3, warning=FALSE, fig.align="center"--------
p + geom_text(aes(x=branch, label=label), size=3, color="purple", vjust=-0.3)


## ----fig.width=6, fig.height=3, fig.align="center"-----------------------
grid.arrange(
	ggtree(rtree(30), color="red") + theme_tree("steelblue"),
	ggtree(rtree(20), color="white") + theme_tree("black"),
	ncol=2)


## ----fig.width=3, fig.height=3, fig.align="center"-----------------------
p %<% rtree(50)


## ----fig.width=18, fig.height=10, fig.align="center"---------------------
library("ape")
data(chiroptera)
library("ggtree")
gzoom(chiroptera, grep("Plecotus", chiroptera$tip.label))


## ----fig.width=5, fig.height=5-------------------------------------------
ggtree(tree, aes(color=branch.length)) +
    scale_color_continuous(low="green", high="red") +
        theme(legend.position="bottom")


## ----fig.width=5, fig.height=5, fig.align="center", warning=FALSE--------
ggtree(tree) + geom_text(aes(label=node))


## ----fig.width=5, fig.height=5-------------------------------------------
p <- ggtree(tree) + geom_tiplab()
annotation_clade(p, node=17, "selected clade", offset.text=2)


## ----fig.width=5, fig.height=5-------------------------------------------
annotation_clade2(p, "B", "E", "Clade X", offset.text=2) %>%
    annotation_clade2("G", "H", "Clade Y", bar.size=4, font.size=8, offset=5, offset.text=4, color="steelblue")


## ----fig.width=5, fig.height=5, fig.align="center", warning=FALSE--------
ggtree(tree) %>% hilight(node=21, fill="steelblue", alpha=.6) %>%
    hilight(node=17, fill="darkgreen", alpha=.6)


## ----fig.width=5, fig.height=5, fig.align="center", warning=FALSE--------
ggtree(tree, layout="fan") %>% hilight(node=21, fill="steelblue", alpha=.6) %>%
     hilight(node=23, fill="darkgreen", alpha=.6)


## ----fig.width=5, fig.height=5, fig.align="center", warning=FALSE--------
cp <- ggtree(tree) %>% collapse(node=21)
cp + geom_point(subset=.(node == 21), size=5, shape=23, fill="steelblue")


## ----fig.width=5, fig.height=5, fig.align="center", warning=FALSE--------
cp %>% expand(node=21)


## ----fig.width=20, fig.height=7, warning=FALSE---------------------------
set.seed(2015-06-30)
p1 <- ggtree(rtree(30)) + geom_text(aes(label=node))
p2 <- flip(p1, node1=45, node2=33)
p3 <- flip(p2, 32, 58)
grid.arrange(p1, p2, p3, ncol=3)


## ----fig.width=16, fig.height=8, warning=FALSE---------------------------
set.seed(2015-07-01)
p1 <- ggtree(rtree(30)) + geom_text(aes(label=node))
p1 <- hilight(p1, 33)
p2 <- rotate(p1, 33)
grid.arrange(p1, p2, ncol=2)


## ------------------------------------------------------------------------
tree <- groupOTU(tree, focus=c("A", "B", "C", "D", "E"))


## ----fig.width=5, fig.height=5, fig.align="center", warning=FALSE--------
ggtree(tree, aes(color=group)) + geom_tiplab()


## ----fig.width=5, fig.height=5, fig.align="center", warning=FALSE--------
cls <- list(c1=c("A", "B", "C", "D", "E"),
            c2=c("F", "G", "H"),
            c3=c("L", "K", "I", "J"),
            c4="M")

tree <- groupOTU(tree, cls)
library("colorspace")
ggtree(tree, aes(color=group, linetype=group)) + geom_text(aes(label=label),  hjust=-.25) +
     scale_color_manual(values=c("black", rainbow_hcl(4))) + theme(legend.position="right")


## ----fig.width=5, fig.height=5, fig.align="center", warning=FALSE--------
p <- ggtree(tree)
groupOTU(p, LETTERS[1:5]) + aes(color=group) + geom_tiplab() + scale_color_manual(values=c("black", "firebrick"))


## ----fig.width=20, fig.height=20, fig.align="center", warning=FALSE------
data(iris)
rn <- paste0(iris[,5], "_", 1:150)
rownames(iris) <- rn
d_iris <- dist(iris[,-5], method="man")

tree_iris <- bionj(d_iris)
tree_iris <- groupOTU(tree_iris, list(setosa    = rn[1:50],
				versicolor    = rn[51:100],
				virginica_145 = rn[101:150]))
cols <- rainbow_hcl(4)
ggtree(tree_iris, aes(color=group)) +
    geom_text(aes(label=label), hjust=-.1) +
        scale_color_manual(values=cols, breaks=1:3,
                           labels=c("Setosa", "Versicolor", "Virginica")) +
                               theme(legend.position="right")


## ----fig.width=5, fig.height=5, fig.align="center", warning=FALSE--------
tree <- groupClade(tree, node=21)
ggtree(tree, aes(color=group, linetype=group))


## ----fig.width=5, fig.height=5, fig.align="center", warning=FALSE--------
tree <- groupClade(tree, node=c(21, 17))
ggtree(tree, aes(color=group, linetype=group))


## ----fig.width=5, fig.height=5, fig.align="center", warning=FALSE--------
ggtree(tree, aes(color=group, linetype=group)) +
    geom_text(aes(label=label), subset=.(group==2), hjust = -.5) +
        geom_text(aes(label=label), subset=.(group==1), hjust = -.5, color="blue")


## ----fig.width=12, fig.height=6, warning=F-------------------------------
grid.arrange(ggtree(tree) %>% hilight(21, "steelblue"),
             ggtree(tree) %>% scaleClade(21, scale=0.3) %>% hilight(21, "steelblue"),
             ncol=2)


## ----fig.width=12, fig.height=6, warning=F-------------------------------
grid.arrange(ggtree(tree) %>% hilight(17, fill="steelblue") %>%
                 hilight(21, fill="darkgreen"),
             ggtree(tree) %>% scaleClade(17, scale=2) %>% scaleClade(21, scale=0.3) %>%
                 hilight(17, "steelblue") %>% hilight(21, fill="darkgreen"),
             ncol=2)


## ----fig.width=5, fig.height=5, fig.align="center", warning=FALSE, eval=FALSE----
## pp <- ggtree(tree) %>% phylopic("79ad5f09-cf21-4c89-8e7d-0c82a00ce728", color="steelblue", alpha = .3)
## print(pp)


## ----fig.width=5, fig.height=5, fig.align="center", warning=FALSE, eval=FALSE----
## pp %>% phylopic("67382184-5135-4faa-8e98-eadff02c3e8a", color="#86B875", alpha=.8, node=4) %>%
##      phylopic("d3563b54-780f-4711-a49a-7ea051e9dacc", color="darkcyan", alpha=.8, node=17, width=.2)


## ------------------------------------------------------------------------
file <- system.file("extdata/BEAST", "beast_mcc.tree", package="ggtree")
beast <- read.beast(file)
beast


## ----fig.width=8, width=60, warning=FALSE, fig.align="center"------------
plot(beast, annotation="length_0.95_HPD", branch.length="none") + theme_tree()


## ----fig.width=8, width=60, warning=FALSE, fig.align="center"------------
plot(beast, annotation="height", ndigits=3, annotation.color="red")


## ------------------------------------------------------------------------
rstfile <- system.file("extdata/PAML_Baseml", "rst", package="ggtree")
rst <- read.paml_rst(rstfile)
rst


## ----fig.width=10, fig.height=8, width=60, warning=FALSE-----------------
p <- plot(rst, annotation="marginal_AA_subs", annotation.color="steelblue")
print(p)


## ----fig.width=8, width=60, warning=FALSE, fig.align="center"------------
rstfile <- system.file("extdata/PAML_Codeml", "rst", package="ggtree")
rst <- read.paml_rst(rstfile)
p %<% rst


## ------------------------------------------------------------------------
mlcfile <- system.file("extdata/PAML_Codeml", "mlc", package="ggtree")
mlc <- read.codeml_mlc(mlcfile)
mlc


## ----fig.width=8, width=60, warning=FALSE, fig.align="center"------------
plot(mlc, branch.length="branch.length", annotation="dN_vs_dS", annotation.color="blue", ndigits=3)


## ------------------------------------------------------------------------
get.fields(mlc)


## ----fig.width=8, width=60, warning=FALSE, fig.align="center"------------
plot(mlc, branch.length="dN_vs_dS", annotation="dN_vs_dS", ndigits=3)


## ------------------------------------------------------------------------
ml <- read.codeml(rstfile, mlcfile)
ml


## ----fig.width=12, fig.height=8, width=60, warning=FALSE, fig.align="center"----
plot(ml, branch.length="rst.branch.length", annotation="dN_vs_dS")
plot(ml, branch.length="mlc.branch.length", annotation="marginal_AA_subs")
plot(ml, branch.length="dN", annotation="joint_AA_subs", annotation.color="darkgreen")


## ------------------------------------------------------------------------
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=12, fig.height=10, width=60, warning=FALSE, fig.align="center"----
plot(hy, annotation="AA_subs")


## ----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)
plot(raxml)


## ----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)) + facet_wrap(~.id, scales="free_x") + theme_tree2()


## ------------------------------------------------------------------------
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


## ----fig.width=20, fig.height=26, warning=FALSE--------------------------
ggtree(merged_tree, aes(color=dN), mrsd="2013-01-01", ndigits = 3) +
    geom_text(aes(label=posterior), vjust=.1, hjust=-.1, size=5) + theme_tree2() +
        scale_color_continuous(low="green", high="red") + theme(legend.position="right")


## ----fig.width=12, fig.height=10, width=60, warning=FALSE, fig.align="center"----
ggtree(ml, branch.length="dN_vs_dS") + 
    geom_text(aes(x=branch, label=dN), 
              size=3, vjust=-0.5, color="red") +
                  geom_text(aes(x=branch, label=dS),
                            size=3, vjust=1.2, color="darkgreen")


## ------------------------------------------------------------------------
nwk <- system.file("extdata", "sample.nwk", package="ggtree")
tree <- read.tree(nwk)
p <- ggtree(tree)

dd <- data.frame(taxa  = LETTERS[1:13], 
      		 place = c(rep("GZ", 5), rep("HK", 3), rep("CZ", 4), NA),
                 value = round(abs(rnorm(13, mean=70, sd=10)), digits=1))
## you don't need to order the data
## data was reshuffled just for demonstration
dd <- dd[sample(1:13, 13), ]
row.names(dd) <- NULL

## ----eval=FALSE----------------------------------------------------------
## print(dd)


## ----echo=FALSE, results='asis'------------------------------------------
knitr::kable(dd)


## ----fig.width=6, fig.height=5, warning=FALSE, fig.align="center"--------
p <- p %<+% dd + geom_text(aes(color=place, label=label), hjust=-0.5) + 
       geom_tippoint(aes(size=value, shape=place, color=place), alpha=0.25)
p+theme(legend.position="right")


## ----fig.width=6, fig.height=5, warning=FALSE, fig.align="center"--------
p <- p + geom_text(aes(color=place, label=place), hjust=1, vjust=-0.4, size=3)
print(p)


## ----fig.width=6, fig.height=5, warning=FALSE, fig.align="center"--------
p <- p + geom_text(aes(color=place, label=value), hjust=1, vjust=1.4, size=3)
print(p)


## ------------------------------------------------------------------------
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, showDistance=TRUE) + 
	   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_text(aes(label=label), hjust=-.5)


## ----fig.width=20, fig.height=16, fig.align="center"---------------------
genotype_file <- system.file("examples/Genotype.txt", package="ggtree")
genotype <- read.table(genotype_file, sep="\t", stringsAsFactor=F)
p <- ggtree(beast_tree, mrsd="2013-01-01") %>% add_legend(x=2008, y=5)
p <- p + geom_tiplab(size=3)
gheatmap(p, genotype, offset = 2, width=0.5)


## ----fig.width=20, fig.height=16, fig.align="center"---------------------
p <- ggtree(beast_tree,  mrsd="2013-01-01") + geom_tiplab(size=3, align=TRUE) + theme_tree2()
pp <- (p + scale_y_continuous(expand=c(0, 0.3))) %>%
    gheatmap(genotype, offset=4, width=0.5, colnames=FALSE) %>%
        scale_x_ggtree()
pp + theme(legend.position="right")


## ----fig.width=8, fig.height=12, fig.align='center'----------------------
fasta <- system.file("examples/FluA_H3_AA.fas", package="ggtree")
msaplot(ggtree(beast_tree), fasta) 


## ----echo=FALSE----------------------------------------------------------
sessionInfo()