@@ -1,7 +1,7 @@

 Package: ggtree

 Type: Package

 Title: a phylogenetic tree viewer for different types of tree annotations

-Version: 1.3.7

+Version: 1.3.8

 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

@@ -19,10 +19,9 @@ Imports:

     jsonlite,

     magrittr,

     methods,

-    reshape2,

-    stats4

+    stats4,

+    tidyr

 Suggests:

-    BiocStyle,

     EBImage,

     knitr,

     phylobase,

@@ -62,13 +62,15 @@ export(get_heatmap_column_position)

 export(get_taxa_name)

 export(ggtree)

 export(gheatmap)

-export(gplot)

 export(groupClade)

 export(groupOTU)

 export(gzoom)

+export(inset)

 export(mask)

 export(merge_tree)

 export(msaplot)

+export(nodebar)

+export(nodepie)

 export(phyPML)

 export(phylopic)

 export(plot)

@@ -92,6 +94,7 @@ export(scale_color)

 export(scale_x_ggtree)

 export(stat_hilight)

 export(subview)

+export(theme_inset)

 export(theme_transparent)

 export(theme_tree)

 export(theme_tree2)

@@ -158,8 +161,8 @@ importFrom(ggplot2,draw_key_text)

 importFrom(ggplot2,element_blank)

 importFrom(ggplot2,element_line)

 importFrom(ggplot2,element_rect)

-importFrom(ggplot2,element_text)

 importFrom(ggplot2,fortify)

+importFrom(ggplot2,geom_bar)

 importFrom(ggplot2,geom_rect)

 importFrom(ggplot2,geom_segment)

 importFrom(ggplot2,geom_text)

@@ -169,7 +172,6 @@ importFrom(ggplot2,ggplotGrob)

 importFrom(ggplot2,ggproto)

 importFrom(ggplot2,guide_legend)

 importFrom(ggplot2,guides)

-importFrom(ggplot2,labs)

 importFrom(ggplot2,layer)

 importFrom(ggplot2,position_nudge)

 importFrom(ggplot2,scale_color_manual)

@@ -188,7 +190,6 @@ importFrom(ggplot2,ylab)

 importFrom(grDevices,col2rgb)

 importFrom(grDevices,rgb)

 importFrom(grid,rasterGrob)

-importFrom(grid,unit)

 importFrom(gridExtra,grid.arrange)

 importFrom(jsonlite,fromJSON)

 importFrom(magrittr,"%<>%")

@@ -196,6 +197,6 @@ importFrom(magrittr,"%>%")

 importFrom(magrittr,add)

 importFrom(magrittr,equals)

 importFrom(methods,show)

-importFrom(reshape2,melt)

 importFrom(stats4,plot)

+importFrom(tidyr,gather)

 importMethodsFrom(Biostrings,width)

@@ -1,3 +1,9 @@

+CHANGES IN VERSION 1.3.8

+------------------------

+ o 05 advance tree annotation vignette <2016-01-04, Mon>

+ o export theme_inset <2016-01-04, Mon>

+ o inset, nodebar, nodepie functions <2015-12-31, Thu>

+ 

 CHANGES IN VERSION 1.3.7

 ------------------------

  o split the long vignette to several vignettes

@@ -92,12 +92,6 @@ setMethod("scale_color", signature(object="apeBootstrap"),

           })

-##' @rdname gzoom-methods

-##' @exportMethod gzoom

-setMethod("gzoom", signature(object="apeBootstrap"),

-          function(object, focus, subtree=FALSE, widths=c(.3, .7)) {

-              gzoom.phylo(get.tree(object), focus, subtree, widths)

-          })

 ##' @rdname get.tree-methods

@@ -39,12 +39,6 @@ setMethod("scale_color", signature(object="codeml"),

           })

-##' @rdname gzoom-methods

-##' @exportMethod gzoom

-setMethod("gzoom", signature(object="codeml"),

-          function(object, focus, subtree=FALSE, widths=c(.3, .7)) {

-              gzoom.phylo(get.tree(object), focus, subtree, widths)

-          })

 ##' @rdname show-methods

 ##' @exportMethod show

@@ -114,7 +114,12 @@ get_clade_position_ <- function(data, node) {

     sp.df <- data[c(sp, node),]

     x <- sp.df$x

     y <- sp.df$y

-    data.frame(xmin=min(x)-data[node, "branch.length"]/2,

+    if ("branch.length" %in% colnames(data)) {

+        xmin <- min(x)-data[node, "branch.length"]/2

+    } else {

+        xmin <- min(sp.df$branch)

+    }

+    data.frame(xmin=xmin,

                xmax=max(x),

                ymin=min(y)-0.5,

                ymax=max(y)+0.5)

@@ -13,19 +13,21 @@

 ##' @param colnames_position one of 'bottom' or 'top'

 ##' @param font.size font size of matrix colnames

 ##' @return tree view

-##' @importFrom reshape2 melt

 ##' @importFrom ggplot2 geom_tile

 ##' @importFrom ggplot2 geom_text

 ##' @importFrom ggplot2 theme

 ##' @importFrom ggplot2 element_blank

 ##' @importFrom ggplot2 guides

 ##' @importFrom ggplot2 guide_legend

+##' @importFrom ggplot2 scale_fill_gradient

+##' @importFrom ggplot2 scale_fill_discrete

 ##' @export

 ##' @author Guangchuang Yu

 gheatmap <- function(p, data, offset=0, width=1, low="green", high="red",

                      color="white", colnames=TRUE, colnames_position="bottom", font.size=4) {

     colnames_position %<>% match.arg(c("bottom", "top"))

+    variable <- value <- lab <- y <- NULL

     ## if (is.null(width)) {

     ##     width <- (p$data$x %>% range %>% diff)/30

@@ -44,7 +46,8 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red",

     dd$y <- sort(df$y)

     dd$lab <- rownames(dd)

-    dd <- melt(dd, id=c("lab", "y"))

+    ## dd <- melt(dd, id=c("lab", "y"))

+    dd <- gather(dd, variable, value, -c(lab, y))

     if (any(dd$value == "")) {

         dd$value[dd$value == ""] <- NA

@@ -259,91 +262,91 @@ scale_x_ggtree <- function(p, breaks=NULL, labels=NULL) {

-##' view tree and associated matrix

-##'

-##' @title gplot

-##' @param p tree view

-##' @param data matrix

-##' @param low low color

-##' @param high high color

-##' @param widths widths of sub plot

-##' @param color color

-##' @param font.size font size

-##' @return list of figure

-##' @importFrom gridExtra grid.arrange

-##' @importFrom ggplot2 scale_x_continuous

-##' @importFrom ggplot2 scale_y_continuous

-##' @export

-##' @author Guangchuang Yu \url{http://ygc.name}

-##' @examples

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

-##' tree <- read.tree(nwk)

-##' p <- ggtree(tree)

-##' d <- matrix(abs(rnorm(52)), ncol=4)

-##' rownames(d) <- tree$tip.label

-##' colnames(d) <- paste0("G", 1:4)

-##' gplot(p, d, low="green", high="red")

-gplot <- function(p, data, low="green", high="red", widths=c(0.5, 0.5), color="white", font.size=14) {

-    ## p <- p + scale_x_continuous(expand = c(0, 0)) + scale_y_continuous(expand = c(0, 0.6))

-    p1 <- p + scale_y_continuous(expand = c(0, 0.6))

-    ## p1 <- p + theme(panel.margin=unit(0, "null"))

-    ## p1 <- p1 + theme(plot.margin = unit(c(1, -1, 1.5, 1), "lines"))

-    p2 <- gplot.heatmap(p, data, low, high, color, font.size)

-    grid.arrange(p1, p2, ncol=2, widths=widths)

-    invisible(list(p1=p1, p2=p2))

-}

-

-

-##' @importFrom grid unit

-##' @importFrom ggplot2 scale_fill_gradient

-##' @importFrom ggplot2 scale_fill_discrete

-##' @importFrom ggplot2 element_text

-##' @importFrom ggplot2 geom_tile

-##' @importFrom ggplot2 labs

-##' @importFrom ggplot2 guides

-##' @importFrom ggplot2 guide_legend

-##' @importFrom reshape2 melt

-gplot.heatmap <- function(p, data, low, high, color="white", font.size) {

-    isTip <- x <- Var1 <- Var2 <- value <- NULL

-    dd=melt(as.matrix(data))

-    ## p <- ggtree(tree) ## + theme_tree2()

-    ## p <- p + geom_text(aes(x = max(x)*1.1, label=label), subset=.(isTip), hjust=0)

-    ## p <- p+geom_segment(aes(x=x*1.02, xend=max(x)*1.08, yend=y), subset=.(isTip), linetype="dashed", size=0.4)

-    df=p$data

-    df=df[df$isTip,]

+## ##' view tree and associated matrix

+## ##'

+## ##' @title gplot

+## ##' @param p tree view

+## ##' @param data matrix

+## ##' @param low low color

+## ##' @param high high color

+## ##' @param widths widths of sub plot

+## ##' @param color color

+## ##' @param font.size font size

+## ##' @return list of figure

+## ##' @importFrom gridExtra grid.arrange

+## ##' @importFrom ggplot2 scale_x_continuous

+## ##' @importFrom ggplot2 scale_y_continuous

+## ##' @export

+## ##' @author Guangchuang Yu \url{http://ygc.name}

+## ##' @examples

+## ##' nwk <- system.file("extdata", "sample.nwk", package="ggtree")

+## ##' tree <- read.tree(nwk)

+## ##' p <- ggtree(tree)

+## ##' d <- matrix(abs(rnorm(52)), ncol=4)

+## ##' rownames(d) <- tree$tip.label

+## ##' colnames(d) <- paste0("G", 1:4)

+## ##' gplot(p, d, low="green", high="red")

+## gplot <- function(p, data, low="green", high="red", widths=c(0.5, 0.5), color="white", font.size=14) {

+##     ## p <- p + scale_x_continuous(expand = c(0, 0)) + scale_y_continuous(expand = c(0, 0.6))

+##     p1 <- p + scale_y_continuous(expand = c(0, 0.6))

+##     ## p1 <- p + theme(panel.margin=unit(0, "null"))

+##     ## p1 <- p1 + theme(plot.margin = unit(c(1, -1, 1.5, 1), "lines"))

+##     p2 <- gplot.heatmap(p, data, low, high, color, font.size)

+##     grid.arrange(p1, p2, ncol=2, widths=widths)

+##     invisible(list(p1=p1, p2=p2))

+## }

+

+

+## ##' @importFrom grid unit

+## ##' @importFrom ggplot2 scale_fill_gradient

+## ##' @importFrom ggplot2 scale_fill_discrete

+## ##' @importFrom ggplot2 element_text

+## ##' @importFrom ggplot2 geom_tile

+## ##' @importFrom ggplot2 labs

+## ##' @importFrom ggplot2 guides

+## ##' @importFrom ggplot2 guide_legend

+## ##' @importFrom reshape2 melt

+## gplot.heatmap <- function(p, data, low, high, color="white", font.size) {

+##     isTip <- x <- Var1 <- Var2 <- value <- NULL

+##     dd=melt(as.matrix(data))

+##     ## p <- ggtree(tree) ## + theme_tree2()

+##     ## p <- p + geom_text(aes(x = max(x)*1.1, label=label), subset=.(isTip), hjust=0)

+##     ## p <- p+geom_segment(aes(x=x*1.02, xend=max(x)*1.08, yend=y), subset=.(isTip), linetype="dashed", size=0.4)

+##     df=p$data

+##     df=df[df$isTip,]

-    dd$Var1 <- factor(dd$Var1, levels = df$label[order(df$y)])

-    if (any(dd$value == "")) {

-        dd$value[dd$value == ""] <- NA

-    }

+##     dd$Var1 <- factor(dd$Var1, levels = df$label[order(df$y)])

+##     if (any(dd$value == "")) {

+##         dd$value[dd$value == ""] <- NA

+##     }

-    p2 <- ggplot(dd, aes(Var2, Var1, fill=value))+geom_tile(color=color)

-    if (is(dd$value,"numeric")) {

-        p2 <- p2 + scale_fill_gradient(low=low, high=high, na.value="white")

-    } else {

-        p2 <- p2 + scale_fill_discrete(na.value="white")

-    }

+##     p2 <- ggplot(dd, aes(Var2, Var1, fill=value))+geom_tile(color=color)

+##     if (is(dd$value,"numeric")) {

+##         p2 <- p2 + scale_fill_gradient(low=low, high=high, na.value="white")

+##     } else {

+##         p2 <- p2 + scale_fill_discrete(na.value="white")

+##     }

-    p2 <- p2+xlab("")+ylab("")

-    p2 <- p2+theme_tree2() + theme(axis.ticks.x = element_blank(),

-                                   axis.line.x=element_blank())

-    ## p1 <- p1 + theme(axis.text.x = element_text(size = font.size))

-    p2 <- p2 + theme(axis.ticks.margin = unit(0, "lines")) 

-    p2 <- p2 + theme(axis.text.x = element_text(size = font.size))

-    ## p2 <- p2 + theme(axis.text.y = element_text(size=font.size))

+##     p2 <- p2+xlab("")+ylab("")

+##     p2 <- p2+theme_tree2() + theme(axis.ticks.x = element_blank(),

+##                                    axis.line.x=element_blank())

+##     ## p1 <- p1 + theme(axis.text.x = element_text(size = font.size))

+##     p2 <- p2 + theme(axis.ticks.margin = unit(0, "lines")) 

+##     p2 <- p2 + theme(axis.text.x = element_text(size = font.size))

+##     ## p2 <- p2 + theme(axis.text.y = element_text(size=font.size))

-    ## plot.margin   margin around entire plot (unit with the sizes of the top, right, bottom, and left margins) 

-    ## units can be given in "lines" or  something more specific like "cm"...

+##     ## plot.margin   margin around entire plot (unit with the sizes of the top, right, bottom, and left margins) 

+##     ## units can be given in "lines" or  something more specific like "cm"...

-    p2 <- p2 + theme(panel.margin=unit(0, "null"))

-    p2 <- p2 + theme(plot.margin = unit(c(1, 1, .5, -0.5), "lines"))

-    p2 <- p2 + theme(legend.position = "right")

-    p2 <- p2 + guides(fill = guide_legend(override.aes = list(colour = NULL)))

-    ## p2 <- p2 + labs(fill="")

+##     p2 <- p2 + theme(panel.margin=unit(0, "null"))

+##     p2 <- p2 + theme(plot.margin = unit(c(1, 1, .5, -0.5), "lines"))

+##     p2 <- p2 + theme(legend.position = "right")

+##     p2 <- p2 + guides(fill = guide_legend(override.aes = list(colour = NULL)))

+##     ## p2 <- p2 + labs(fill="")

-    return(p2)

-}

+##     return(p2)

+## }

 coplot <- function(tree1, tree2, hjust=0) {

new file mode 100644

@@ -0,0 +1,110 @@

+##' add insets in a tree

+##'

+##' 

+##' @title inset

+##' @param tree_view tree view

+##' @param insets a list of ggplot objects, named by node number

+##' @param width width of inset

+##' @param height height of inset

+##' @param hjust horizontal adjustment

+##' @param vjust vertical adjustment

+##' @param x x position, one of 'node' and 'branch'

+##' @return tree view with insets

+##' @export

+##' @author Guangchuang Yu

+inset <- function(tree_view, insets, width=0.05, height=0.05, hjust=0, vjust=0, x="node") {

+    df <- tree_view$data[names(insets),]

+    x <- match.arg(x, c("node", "branch", "edge"))

+

+    if (x == 'node') {

+        xx <- df$x

+    } else {

+        xx <- df$branch

+    }

+    yy <- df$y

+    

+    xx <- xx - hjust

+    yy <- yy - vjust

+

+    for (i in seq_along(insets)) {

+        tree_view %<>% subview(insets[[i]],

+                               x = xx[i],

+                               y = yy[i],

+                               width = width,

+                               height = height)

+    }

+    return(tree_view)

+}

+

+##' generate a list of bar charts for results of ancestral state reconstruction

+##'

+##' 

+##' @title nodebar

+##' @param position position of bar, one of 'stack' and 'dodge'

+##' @inheritParams nodepie

+##' @return list of ggplot objects

+##' @export

+##' @importFrom ggplot2 geom_bar

+##' @importFrom tidyr gather

+##' @author Guangchuang Yu

+nodebar <- function(data, cols, color, alpha=1, position="stack") {

+    if (! "node" %in% colnames(data)) {

+        stop("data should have a column 'node'...")

+    }

+    type <- value <- NULL

+    

+    ldf <- gather(data, type, value, cols) %>% split(., .$node)

+    bars <- lapply(ldf, function(df) ggplot(df, aes_(x=1, y=~value, fill=~type)) +

+                                     geom_bar(stat='identity', alpha=alpha, position=position) +

+                                     theme_inset()

+                   )

+

+    if (missingArg(color) || is.null(color) || is.na(color)) {

+        ## do nothing

+    } else {

+        bars <- lapply(bars, function(p) p+scale_fill_manual(values=color))

+    }

+    return(bars)

+}

+

+##' generate a list of pie charts for results of ancestral stat reconstruction

+##'

+##' 

+##' @title nodepie

+##' @param data a data.frame of stats with an additional column of node number

+##' @param cols column of stats

+##' @param color color of bar

+##' @param alpha alpha

+##' @return list of ggplot objects

+##' @export

+##' @author Guangchuang Yu

+nodepie <- function(data, cols, color, alpha=1) {

+    if (! "node" %in% colnames(data)) {

+        stop("data should have a column 'node'...")

+    }

+    type <- value <- NULL

+    if (missingArg(color)) {

+        color <- NA

+    }

+    ldf <- gather(data, type, value, cols) %>% split(., .$node)

+    lapply(ldf, function(df) ggpie(df, y=~value, fill=~type, color, alpha))

+}

+

+

+ggpie <- function(data, y, fill, color, alpha=1) {

+    p <- ggplot(data, aes_(x=1, y=y, fill=fill)) +

+        geom_bar(stat='identity', alpha=alpha) +

+        coord_polar(theta='y') + theme_inset()

+    

+    if (missingArg(color) || is.null(color) || is.na(color)) {

+        ## do nothing

+    } else {

+        p <- p+scale_fill_manual(values=color)

+    }

+    return(p)

+}

+

+

+

+

+

@@ -1,3 +1,72 @@

+##' plots simultaneously a whole phylogenetic tree and a portion of it. 

+##'

+##' 

+##' @title gzoom

+##' @param phy phylo object

+##' @param focus selected tips

+##' @param subtree logical

+##' @param widths widths

+##' @return a list of ggplot object

+##' @importFrom ggplot2 xlim

+##' @importFrom ggplot2 scale_color_manual

+##' @importFrom ape drop.tip

+##' @importFrom gridExtra grid.arrange

+##' @author ygc

+##' @examples

+##' require(ape)

+##' data(chiroptera)

+##' gzoom(chiroptera, grep("Plecotus", chiroptera$tip.label))

+gzoom.phylo <- function(phy, focus, subtree=FALSE, widths=c(.3, .7)) {

+    if (is.character(focus)) {

+        focus <- which(phy$tip.label %in% focus)

+    }

+

+    group_name <- "focus"

+    phy <- gfocus(phy, focus, group_name)

+

+    foc <- attr(phy, group_name)

+    ## foc should +1 since the group index start from 0

+    cols <- c("black", "red")[foc+1]

+

+    p1 <- ggtree(phy, color=cols)

+    

+    subtr <- drop.tip(phy, phy$tip.label[-focus],

+                      subtree=subtree, rooted=TRUE)

+    

+    p2 <- ggtree(subtr, color="red") + geom_tiplab(hjust=-0.05)

+    p2 <- p2 + xlim(0, max(p2$data$x)*1.2)

+    grid.arrange(p1, p2, ncol=2, widths=widths)

+    

+    invisible(list(p1=p1, p2=p2))

+}

+

+gzoom.ggplot <- function(tree_view, focus, widths=c(.3, .7), xmax_adjust=0) {

+    node <- MRCA(tree_view, focus)

+    cpos <- get_clade_position(tree_view, node)

+    p2 <- with(cpos, tree_view+

+                     xlim(xmin, xmax+xmax_adjust)+

+                     ylim(ymin, ymax))

+    grid.arrange(tree_view, p2, ncol=2, widths=widths)

+    invisible(list(p1=tree_view, p2=p2))

+}

+

+##' @rdname gzoom-methods

+##' @exportMethod gzoom

+##' @param xmax_adjust adjust xmax (xlim[2])

+setMethod("gzoom", signature(object="gg"),

+          function(object, focus, widths=c(.3, .7), xmax_adjust=0) {

+              gzoom.ggplot(object, focus, widths, xmax_adjust)

+          })

+

+

+##' @rdname gzoom-methods

+##' @exportMethod gzoom

+setMethod("gzoom", signature(object="apeBootstrap"),

+          function(object, focus, subtree=FALSE, widths=c(.3, .7)) {

+              gzoom.phylo(get.tree(object), focus, subtree, widths)

+          })

+

+

 ##' zoom selected subtree

 ##'

 ##' 

@@ -8,6 +77,13 @@ setMethod("gzoom", signature(object="beast"),

               gzoom.phylo(get.tree(object), focus, subtree, widths)

           })

+##' @rdname gzoom-methods

+##' @exportMethod gzoom

+setMethod("gzoom", signature(object="codeml"),

+          function(object, focus, subtree=FALSE, widths=c(.3, .7)) {

+              gzoom.phylo(get.tree(object), focus, subtree, widths)

+          })

+

 ##' @rdname gzoom-methods

 ##' @exportMethod gzoom

@@ -77,3 +77,19 @@ theme_transparent <- function(...) {

               fill = "transparent",

               colour = NA), ...)

 }

+

+##' inset theme

+##'

+##' theme for inset function

+##' @title theme_inset

+##' @param ... additional parameter

+##' @return ggplot object

+##' @export

+##' @author Guangchuang Yu

+theme_inset <- function(...) {

+    list(xlab(NULL),

+         ylab(NULL),

+         theme_tree(...),

+         theme_transparent()

+         )

+}

@@ -124,46 +124,6 @@ gfocus <- function(phy, focus, group_name) {

     phy

 }

-##' plots simultaneously a whole phylogenetic tree and a portion of it. 

-##'

-##' 

-##' @title gzoom

-##' @param phy phylo object

-##' @param focus selected tips

-##' @param subtree logical

-##' @param widths widths

-##' @return a list of ggplot object

-##' @importFrom ggplot2 xlim

-##' @importFrom ggplot2 scale_color_manual

-##' @importFrom ape drop.tip

-##' @author ygc

-##' @examples

-##' require(ape)

-##' data(chiroptera)

-##' gzoom(chiroptera, grep("Plecotus", chiroptera$tip.label))

-gzoom.phylo <- function(phy, focus, subtree=FALSE, widths=c(.3, .7)) {

-    if (is.character(focus)) {

-        focus <- which(phy$tip.label %in% focus)

-    }

-

-    group_name <- "focus"

-    phy <- gfocus(phy, focus, group_name)

-

-    foc <- attr(phy, group_name)

-    ## foc should +1 since the group index start from 0

-    cols <- c("black", "red")[foc+1]

-

-    p1 <- ggtree(phy, color=cols)

-    

-    subtr <- drop.tip(phy, phy$tip.label[-focus],

-                      subtree=subtree, rooted=TRUE)

-    

-    p2 <- ggtree(subtr, color="red") + geom_tiplab(hjust=-0.05)

-    p2 <- p2 + xlim(0, max(p2$data$x)*1.2)

-    grid.arrange(p1, p2, ncol=2, widths=widths)

-    

-    invisible(list(p1=p1, p2=p2))

-}

 ##' update tree 

deleted file mode 100644

@@ -1,43 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/gplot.R

-\name{gplot}

-\alias{gplot}

-\title{gplot}

-\usage{

-gplot(p, data, low = "green", high = "red", widths = c(0.5, 0.5),

-  color = "white", font.size = 14)

-}

-\arguments{

-\item{p}{tree view}

-

-\item{data}{matrix}

-

-\item{low}{low color}

-

-\item{high}{high color}

-

-\item{widths}{widths of sub plot}

-

-\item{color}{color}

-

-\item{font.size}{font size}

-}

-\value{

-list of figure

-}

-\description{

-view tree and associated matrix

-}

-\examples{

-nwk <- system.file("extdata", "sample.nwk", package="ggtree")

-tree <- read.tree(nwk)

-p <- ggtree(tree)

-d <- matrix(abs(rnorm(52)), ncol=4)

-rownames(d) <- tree$tip.label

-colnames(d) <- paste0("G", 1:4)

-gplot(p, d, low="green", high="red")

-}

-\author{

-Guangchuang Yu \url{http://ygc.name}

-}

-

@@ -1,5 +1,5 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/AllGenerics.R, R/RAxML.R, R/ape.R, R/codeml.R, R/codeml_mlc.R, R/hyphy.R, R/method-gzoom.R, R/phangorn.R, R/r8s.R

+% Please edit documentation in R/AllGenerics.R, R/RAxML.R, R/codeml_mlc.R, R/hyphy.R, R/method-gzoom.R, R/phangorn.R, R/r8s.R

 \docType{methods}

 \name{gzoom}

 \alias{gzoom}

@@ -7,6 +7,7 @@

 \alias{gzoom,beast-method}

 \alias{gzoom,codeml-method}

 \alias{gzoom,codeml_mlc-method}

+\alias{gzoom,gg-method}

 \alias{gzoom,hyphy-method}

 \alias{gzoom,nhx-method}

 \alias{gzoom,paml_rst-method}

@@ -21,21 +22,23 @@ gzoom(object, focus, subtree = FALSE, widths = c(0.3, 0.7), ...)

 \S4method{gzoom}{raxml}(object, focus, subtree = FALSE, widths = c(0.3,

   0.7))

-\S4method{gzoom}{apeBootstrap}(object, focus, subtree = FALSE,

-  widths = c(0.3, 0.7))

-

-\S4method{gzoom}{codeml}(object, focus, subtree = FALSE, widths = c(0.3,

-  0.7))

-

 \S4method{gzoom}{codeml_mlc}(object, focus, subtree = FALSE, widths = c(0.3,

   0.7))

 \S4method{gzoom}{hyphy}(object, focus, subtree = FALSE, widths = c(0.3,

   0.7))

+\S4method{gzoom}{gg}(object, focus, widths = c(0.3, 0.7), xmax_adjust = 0)

+

+\S4method{gzoom}{apeBootstrap}(object, focus, subtree = FALSE,

+  widths = c(0.3, 0.7))

+

 \S4method{gzoom}{beast}(object, focus, subtree = FALSE, widths = c(0.3,

   0.7))

+\S4method{gzoom}{codeml}(object, focus, subtree = FALSE, widths = c(0.3,

+  0.7))

+

 \S4method{gzoom}{nhx}(object, focus, subtree = FALSE, widths = c(0.3, 0.7))

 \S4method{gzoom}{paml_rst}(object, focus, subtree = FALSE, widths = c(0.3,

@@ -61,6 +64,8 @@ gzoom(object, focus, subtree = FALSE, widths = c(0.3, 0.7), ...)

 \item{...}{additional parameter}

+\item{xmax_adjust}{adjust xmax (xlim[2])}

+

 \item{tree}{which tree selected}

 }

 \value{

@@ -1,5 +1,5 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/tree-utilities.R

+% Please edit documentation in R/method-gzoom.R

 \name{gzoom.phylo}

 \alias{gzoom.phylo}

 \title{gzoom}

new file mode 100644

@@ -0,0 +1,34 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/inset.R

+\name{inset}

+\alias{inset}

+\title{inset}

+\usage{

+inset(tree_view, insets, width = 0.05, height = 0.05, hjust = 0,

+  vjust = 0, x = "node")

+}

+\arguments{

+\item{tree_view}{tree view}

+

+\item{insets}{a list of ggplot objects, named by node number}

+

+\item{width}{width of inset}

+

+\item{height}{height of inset}

+

+\item{hjust}{horizontal adjustment}

+

+\item{vjust}{vertical adjustment}

+

+\item{x}{x position, one of 'node' and 'branch'}

+}

+\value{

+tree view with insets

+}

+\description{

+add insets in a tree

+}

+\author{

+Guangchuang Yu

+}

+

new file mode 100644

@@ -0,0 +1,29 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/inset.R

+\name{nodebar}

+\alias{nodebar}

+\title{nodebar}

+\usage{

+nodebar(data, cols, color, alpha = 1, position = "stack")

+}

+\arguments{

+\item{data}{a data.frame of stats with an additional column of node number}

+

+\item{cols}{column of stats}

+

+\item{color}{color of bar}

+

+\item{alpha}{alpha}

+

+\item{position}{position of bar, one of 'stack' and 'dodge'}

+}

+\value{

+list of ggplot objects

+}

+\description{

+generate a list of bar charts for results of ancestral state reconstruction

+}

+\author{

+Guangchuang Yu

+}

+

new file mode 100644

@@ -0,0 +1,27 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/inset.R

+\name{nodepie}

+\alias{nodepie}

+\title{nodepie}

+\usage{

+nodepie(data, cols, color, alpha = 1)

+}

+\arguments{

+\item{data}{a data.frame of stats with an additional column of node number}

+

+\item{cols}{column of stats}

+

+\item{color}{color of bar}

+

+\item{alpha}{alpha}

+}

+\value{

+list of ggplot objects

+}

+\description{

+generate a list of pie charts for results of ancestral stat reconstruction

+}

+\author{

+Guangchuang Yu

+}

+

new file mode 100644

@@ -0,0 +1,24 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/theme.R

+\name{theme_inset}

+\alias{theme_inset}

+\title{theme_inset}

+\usage{

+theme_inset(...)

+}

+\arguments{

+\item{...}{additional parameter}

+}

+\value{

+ggplot object

+}

+\description{

+inset theme

+}

+\details{

+theme for inset function

+}

+\author{

+Guangchuang Yu

+}

+

new file mode 100644

@@ -0,0 +1,221 @@

+---

+title: "Advance Tree Annotation"

+author: "\\

+

+	Guangchuang Yu (<guangchuangyu@gmail.com>) and Tommy Tsan-Yuk Lam (<ttylam@hku.hk>)\\

+

+        School of Public Health, The University of Hong Kong"

+date: "`r Sys.Date()`"

+bibliography: ggtree.bib

+csl: nature.csl

+output: 

+  html_document:

+    toc: true

+  pdf_document:

+    toc: true

+vignette: >

+  %\VignetteIndexEntry{05 Advance Tree Annotation}

+  %\VignetteEngine{knitr::rmarkdown}

+  %\usepackage[utf8]{inputenc}

+---

+

+```{r style, echo=FALSE, results="asis", message=FALSE}

+knitr::opts_chunk$set(tidy = FALSE,

+		   message = FALSE)

+```

+

+

+```{r echo=FALSE, results="hide", message=FALSE}

+library("ape")

+library("ggplot2")

+library("gridExtra")

+library("ggtree")