@@ -2,9 +2,9 @@ Package: ggtree

 Type: Package

 Title: an R package for visualization and annotation of phylogenetic trees with

     their covariates and other associated data

-Version: 1.11.1

+Version: 1.11.2

 Authors@R: c(

-	   person("Guangchuang", "Yu",     email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph")),

+	   person("Guangchuang", "Yu",     email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-6485-8781")),

 	   person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com",   role = c("aut", "ths")),

 	   person("Justin", "Silverman",   email = "jsilve24@gmail.com",      role = "ctb")

 	   )

@@ -29,8 +29,8 @@ Imports:

 Suggests:

     Biostrings,

     colorspace,

-    EBImage,

     emojifont,

+    ggimage,

     knitr,

     prettydoc,

     rmarkdown,

@@ -38,7 +38,6 @@ export(as.binary)

 export(as.polytomy)

 export(collapse)

 export(decimal2Date)

-export(download.phylopic)

 export(expand)

 export(facet_plot)

 export(flip)

@@ -50,6 +49,7 @@ export(geom_hilight)

 export(geom_hilight_encircle)

 export(geom_label2)

 export(geom_motif)

+export(geom_nodelab)

 export(geom_nodepoint)

 export(geom_point2)

 export(geom_range)

@@ -66,7 +66,6 @@ export(geom_tree2)

 export(geom_treescale)

 export(get.offspring.tip)

 export(get.path)

-export(get.phylopic)

 export(get_balance_position)

 export(get_clade_position)

 export(get_heatmap_column_position)

@@ -167,9 +166,7 @@ importFrom(ggplot2,xlab)

 importFrom(ggplot2,xlim)

 importFrom(ggplot2,ylab)

 importFrom(ggplot2,ylim)

-importFrom(grDevices,col2rgb)

 importFrom(grDevices,colorRampPalette)

-importFrom(grDevices,rgb)

 importFrom(graphics,identify)

 importFrom(grid,convertX)

 importFrom(grid,convertY)

@@ -200,7 +197,6 @@ importFrom(treeio,as.treedata)

 importFrom(treeio,get.placements)

 importFrom(treeio,groupClade)

 importFrom(treeio,groupOTU)

-importFrom(utils,download.file)

 importFrom(utils,modifyList)

 importFrom(utils,packageDescription)

 importFrom(utils,packageVersion)

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

+CHANGES IN VERSION 1.11.2

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

+ o deprecate subview, annotation_image and phylopic <2017-12-04, Mon>

+ o geom_tiplab now supports geom = "image" or geom = "phylopic" <2017-12-04, Mon>

+ o A new layer geom_nodelab that equivalent to geom_tiplab but works for internal node <2017-12-04, Mon>

+

 CHANGES IN VERSION 1.11.1

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

  o bug fixed in geom_tiplab, now `offset` parameter works with `align=TRUE`. <2017-11-20, Mon>

new file mode 100644

@@ -0,0 +1,65 @@

+

+##' annotation taxa with images

+##'

+##'

+##' @title annotation_image

+##' @param tree_view tree view

+##' @param img_info data.frame with first column of taxa name and second column of image names

+##' @param width width of the image to be plotted in image

+##' @param align logical

+##' @param linetype line type if align = TRUE

+##' @param linesize line size if align = TRUE

+##' @param offset offset of image from the tree view

+##' @return tree view

+##' @export

+##' @author Guangchuang Yu

+annotation_image <- function(tree_view, img_info, width=0.1, align=TRUE, linetype="dotted", linesize =1, offset=0) {

+    stop('the `annotation_image` function was deprecated...\nplease use `geom_tiplab(geom="image")`')

+}

+

+

+##' add phylopic layer

+##'

+##'

+##' @title phylopic

+##' @param tree_view tree view

+##' @param phylopic_id phylopic id

+##' @param size size of phylopic to download

+##' @param color color

+##' @param alpha alpha

+##' @param node selected node

+##' @param x x position

+##' @param y y position

+##' @param width width of phylopic

+##' @return phylopic layer

+##' @export

+##' @importFrom ggplot2 annotation_custom

+##' @importFrom grid rasterGrob

+##' @author Guangchuang Yu

+phylopic <- function(tree_view, phylopic_id,

+                     size=512, color="black", alpha=0.5,

+                     node=NULL, x=NULL, y=NULL, width=.1) {

+

+    stop('the `phylopic` function was deprecated...\nplease use `geom_tiplab(geom="phylopic")` or `geom_nodelab(geom="phylopic")`')

+}

+

+

+##' add subview to mainview for ggplot2 objects

+##'

+##'

+##' @title subview

+##' @param mainview main view

+##' @param subview a ggplot or grob object

+##' @param x x position

+##' @param y y position

+##' @param width width of subview, [0,1]

+##' @param height height of subview, [0,1]

+##' @return ggplot object

+##' @importFrom ggplot2 annotation_custom

+##' @importFrom ggplot2 ggplotGrob

+##' @importFrom ggplot2 ggplot_build

+##' @export

+##' @author Guangchuang Yu

+subview <- function(mainview, subview, x, y, width=.1, height=.1) {

+    stop("The subview function was deprecated, please use ggimage::geom_subview() instead.")

+}

new file mode 100644

@@ -0,0 +1,23 @@

+##' add node label layer

+##'

+##'

+##' @title geom_nodelab

+##' @param mapping aes mapping

+##' @param nudge_x horizontal adjustment to nudge label

+##' @param nudge_y vertical adjustment to nudge label

+##' @param geom one of 'text', 'label', 'image' and 'phylopic'

+##' @param hjust horizontal alignment, one of 0, 0.5 or 1

+##' @param ... additional parameters

+##' @return geom layer

+##' @export

+##' @author guangchuang yu

+geom_nodelab <- function(mapping = NULL, nudge_x = 0, nudge_y = 0, geom = "text", hjust = 0.5, ...) {

+    self_mapping <- aes_(subset = ~!isTip)

+    if (is.null(mapping)) {

+        mapping <- self_mapping

+    } else {

+        mapping <- modifyList(self_mapping, mapping)

+    }

+

+    geom_tiplab(mapping, offset = nudge_x, nudge_y = nudge_y, geom = geom, hjust = hjust, ...)

+}

@@ -8,10 +8,11 @@

 ##' @param align align tip lab or not, logical

 ##' @param linetype linetype for adding line if align = TRUE

 ##' @param linesize line size of line if align = TRUE

-##' @param geom one of 'text' and 'label'

+##' @param geom one of 'text', 'label', 'image' and 'phylopic'

 ##' @param ... additional parameter

 ##' @return tip label layer

 ##' @importFrom ggplot2 geom_text

+##' @importFrom utils modifyList

 ##' @export

 ##' @author Yu Guangchuang

 ##' @examples

@@ -19,12 +20,18 @@

 ##' tr <- rtree(10)

 ##' ggtree(tr) + geom_tiplab()

 geom_tiplab <- function(mapping=NULL, hjust = 0,  align = FALSE, linetype = "dotted", linesize=0.5, geom="text",  offset=0, ...) {

-    geom <- match.arg(geom, c("text", "label"))

+    geom <- match.arg(geom, c("text", "label", "image", "phylopic"))

     if (geom == "text") {

-        text_geom <- geom_text2

-    } else {

-        text_geom <- geom_label2

+        label_geom <- geom_text2

+    } else if (geom == "label") {

+        label_geom <- geom_label2

+    } else if (geom == "image") {

+        label_geom <- get_fun_from_pkg("ggimage", "geom_image")

+    } else if (geom == "phylopic") {

+        label_geom <- get_fun_from_pkg("ggimage", "geom_phylopic")

     }

+

+

     x <- y <- label <- isTip <- node <- NULL

     if (align == TRUE) {

         self_mapping <- aes(x = max(x, na.rm=TRUE) + diff(range(x, na.rm=TRUE))/200, y = y, label = label, node = node, subset = isTip)

@@ -54,13 +61,14 @@ geom_tiplab <- function(mapping=NULL, hjust = 0,  align = FALSE, linetype = "dot

     }

     list(

-        text_geom(mapping=text_mapping,

-                  hjust = hjust, nudge_x = offset, stat = StatTreeData, ...)

-        ,

         if (show_segment)

             geom_segment2(mapping = segment_mapping,

                           linetype = linetype, nudge_x = offset,

                           size = linesize, stat = StatTreeData, ...)

+       ,

+        label_geom(mapping=text_mapping,

+                   hjust = hjust, nudge_x = offset, stat = StatTreeData, ...)

+

     )

 }

@@ -36,14 +36,13 @@ inset <- function(tree_view, insets, width=0.1, height=0.1, hjust=0, vjust=0,

     if (reverse_y)

         yy <- -yy

-    for (i in seq_along(insets)) {

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

-                               x = xx[i],

-                               y = yy[i],

-                               width = width,

-                               height = height)

-    }

-    return(tree_view)

+    geom_subview <- get_fun_from_pkg("ggimage", "geom_subview")

+

+    tree_view + geom_subview(subview = insets,

+                            width = width,

+                            height = height,

+                            x = xx,

+                            y = yy)

 }

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

deleted file mode 100644

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

-## ##' parsing phylip tree format

-## ##'

-## ##' 

-## ##' @title read.phylip

-## ##' @param file phylip file

-## ##' @return an instance of 'phylip'

-## ##' @export

-## ## @importFrom Biostrings BStringSet

-## ##' @author Guangchuang Yu

-## read.phylip <- function(file) {

-##     phylip <- readLines(file)

-##     i <- grep("^\\d+$", phylip)

-##     if (length(i) != 1) {

-##         stop("input file is not phylip tree format...")

-##     }

-##     n <- length(phylip)

-##     ntree <- as.numeric(phylip[i])

-##     trees <- read.tree(text=phylip[(i+1):n])

-

-##     phylipInfo <- strsplit(phylip[1], split="\\s") %>% unlist

-##     nseq <- phylipInfo[1]

-##     seqLen <- phylipInfo[2]

-##     if (nseq != i-2) {

-##         stop("only sequential format is supported...\n-> see http://evolution.genetics.washington.edu/phylip/doc/sequence.html")

-##     }

-##     seqlines <- phylip[2:(i-1)]

-##     seq_with_name <- lapply(seqlines, function(x) unlist(strsplit(x, "\\s+")))

-##     seqs <- sapply(seq_with_name, function(x) x[2])

-##     names(seqs) <- sapply(seq_with_name, function(x) x[1])

-

-##     if (any(nchar(seqs) != seqLen)) {

-##         stop(paste("sequence length not consistent...\n->", paste0(nchar(seqs), collapse=" ")))

-##     }

-    

-##     new("phylip",

-##         file = filename(file),

-##         phylo = trees,

-##         ntree = ntree,

-##         sequence = seqs

-##         )

-## }

-

-

deleted file mode 100644

@@ -1,173 +0,0 @@

-##' download phylopic and convert to grob object

-##'

-##'

-##' @title get.phylopic

-##' @param id phylopic id

-##' @param size size of the phylopic

-##' @param color color

-##' @param alpha alpha

-##' @return grob object

-##' @importFrom grid rasterGrob

-##' @export

-##' @author Guangchuang Yu

-get.phylopic <- function(id, size=512, color="black", alpha=1) {

-    download.phylopic(id, size, color, alpha) %>% rasterGrob

-}

-

-##' download phylopic

-##'

-##' @title download.phylopic

-##' @param id phyopic id

-##' @param size size of phylopic

-##' @param color color

-##' @param alpha alpha

-##' @return matrix

-##' @importFrom grDevices rgb

-##' @importFrom grDevices col2rgb

-## @importFrom EBImage readImage

-## @importFrom EBImage channel

-##' @export

-##' @author Guangchuang Yu

-download.phylopic <- function(id, size=512, color="black", alpha=1) {

-    imgfile <- tempfile(fileext = ".png")

-    download.phylopic_internal(id, size, imgfile)

-

-    channel <- get_fun_from_pkg("EBImage", "channel")

-    readImage <- get_fun_from_pkg("EBImage", "readImage")

-

-    img <- readImage(imgfile)

-

-    color <- col2rgb(color) / 255

-

-    img <- channel(img, 'rgb')

-    img[,,1] <- color[1]

-    img[,,2] <- color[2]

-    img[,,3] <- color[3]

-    img[,,4] <- img[,,4]*alpha

-

-    return(img)

-}

-

-##' @importFrom utils download.file

-##' @importFrom utils modifyList

-download.phylopic_internal <- function(id, size=512, outfile=NULL) {

-    size %<>% as.character %>%

-        match.arg(c("64", "128", "256", "512", "1024"))

-

-    imgurl <- paste0("http://phylopic.org/assets/images/submissions/", id, ".", size, ".png")

-    if (is.null(outfile)) {

-        outfile <- sub(".*/", "", imgurl)

-    }

-    ## mode = "wb" for Windows platform

-    download.file(imgurl, outfile, mode="wb", quiet = TRUE)

-}

-

-

-##' add phylopic layer

-##'

-##'

-##' @title phylopic

-##' @param tree_view tree view

-##' @param phylopic_id phylopic id

-##' @param size size of phylopic to download

-##' @param color color

-##' @param alpha alpha

-##' @param node selected node

-##' @param x x position

-##' @param y y position

-##' @param width width of phylopic

-##' @return phylopic layer

-##' @export

-##' @importFrom ggplot2 annotation_custom

-##' @importFrom grid rasterGrob

-##' @author Guangchuang Yu

-phylopic <- function(tree_view, phylopic_id,

-                     size=512, color="black", alpha=0.5,

-                     node=NULL, x=NULL, y=NULL, width=.1) {

-

-    message("The phylopic function will be defunct in next release, please use ggimage::geom_phylopic() instead.")

-

-    width <- diff(range(tree_view$data$x)) * width

-    img <- download.phylopic(phylopic_id, size, color, alpha)

-    if ( is.null(node) ) {

-        xmin <- ymin <- -Inf

-        xmax <- ymax <- Inf

-    } else {

-        if (is.null(x) || is.null(y)) {

-            if (is.null(node)) {

-                stop("node or x and y should not be NULL...")

-            }

-            df <- tree_view$data

-            x <- df[match(node, df$node), "x"]

-            y <- df[match(node, df$node), "y"]

-        }

-        AR <- getAR(img)

-        xmin <- x - width/2

-        xmax <- x + width/2

-        ymin <- y - AR * width/2

-        ymax <- y + AR * width/2

-    }

-

-    tree_view + annotation_custom(xmin=xmin, ymin=ymin,

-                                  xmax=xmax, ymax=ymax,

-                                  rasterGrob(img))

-}

-

-getAR <- function(img) {

-    dims <- dim(img)[1:2]

-    dims[1]/dims[2]

-}

-

-

-##' annotation taxa with images

-##'

-##'

-##' @title annotation_image

-##' @param tree_view tree view

-##' @param img_info data.frame with first column of taxa name and second column of image names

-##' @param width width of the image to be plotted in image

-##' @param align logical

-##' @param linetype line type if align = TRUE

-##' @param linesize line size if align = TRUE

-##' @param offset offset of image from the tree view

-##' @return tree view

-##' @export

-##' @author Guangchuang Yu

-annotation_image <- function(tree_view, img_info, width=0.1, align=TRUE, linetype="dotted", linesize =1, offset=0) {

-    df <- tree_view$data

-    idx <- match(img_info[,1], df$label)

-    x <- df[idx, "x"]

-    y <- df[idx, "y"]

-

-    readImage <- get_fun_from_pkg("EBImage", "readImage")

-    images <- lapply(img_info[,2], readImage)

-

-    ARs <- sapply(images, getAR)

-

-    width <- width * diff(range(df$x))

-    if (align) {

-        xmin <- max(df$x) + offset

-        xmin <- rep(xmin, length(x))

-    } else {

-        xmin <- x - width/2 + offset

-    }

-    xmax <- xmin + width

-

-    ymin <- y - ARs * width/2

-    ymax <- y + ARs * width/2

-    image_layers <- lapply(1:length(xmin), function(i) {

-        annotation_custom(xmin=xmin[i], ymin=ymin[i],

-                          xmax=xmax[i], ymax=ymax[i],

-                          rasterGrob(images[[i]]))

-    })

-

-    tree_view <- tree_view + image_layers

-

-    if (align && (!is.null(linetype) && !is.na(linetype))) {

-        tree_view <- tree_view + geom_segment(data=df[idx,],

-                                              x=xmin, xend = x*1.01,

-                                              y = y, yend = y,

-                                              linetype=linetype, size=linesize)

-    }

-    tree_view

-}

deleted file mode 100644

@@ -1,97 +0,0 @@

-##' add subview to mainview for ggplot2 objects

-##'

-##'

-##' @title subview

-##' @param mainview main view

-##' @param subview a ggplot or grob object

-##' @param x x position

-##' @param y y position

-##' @param width width of subview, [0,1]

-##' @param height height of subview, [0,1]

-##' @return ggplot object

-##' @importFrom ggplot2 annotation_custom

-##' @importFrom ggplot2 ggplotGrob

-##' @importFrom ggplot2 ggplot_build

-##' @export

-##' @author Guangchuang Yu

-subview <- function(mainview, subview, x, y, width=.1, height=.1) {

-    message("The subview function will be defunct in next release, please use ggimage::geom_subview() instead.")

-

-    mapping <- mainview$mapping %>% as.character

-    aes_x <- mapping["x"]

-    aes_y <- mapping["y"]

-

-    if (is.na(aes_x) || is.na(aes_y)) {

-        obj <- ggplot_build(mainview)

-        xrng <- obj$layout$panel_ranges[[1]]$x.range

-        yrng <- obj$layout$panel_ranges[[1]]$y.range

-    } else {

-        xrng <- mainview$data[, aes_x] %>% range

-        yrng <- mainview$data[, aes_y] %>% range

-    }

-

-    for (i in seq_along(mainview$layers)) {

-        layer <- mainview$layers[[i]]

-        dd <- layer$data

-        if (is(dd, "data.frame")) {

-            mapping <- as.character(layer$mapping)

-            mn <- names(mapping)

-            if ('x' %in% mn) {

-                aes_x <- mapping["x"]

-                xrng <- c(xrng, layer$data[, aes_x])

-            }

-            if ('xmin' %in% mn) {

-                aes_x <- mapping["xmin"]

-                xrng <- c(xrng, layer$data[, aes_x])

-            }

-            if ('xmax' %in% mn) {

-                aes_x <- mapping["xmax"]

-                xrng <- c(xrng, layer$data[, aes_x])

-            }

-            if ('y' %in% mn) {

-                aes_y <- mapping["y"]

-                yrng <- c(yrng, layer$data[, aes_y])

-            }

-            if ('ymin' %in% mn) {

-                aes_y <- mapping["ymin"]

-                yrng <- c(yrng, layer$data[, aes_y])

-            }

-            if ('ymax' %in% mn) {

-                aes_y <- mapping["ymax"]

-                yrng <- c(yrng, layer$data[, aes_y])

-            }

-            xrng <- range(xrng)

-            yrng <- range(yrng)

-        }

-    }

-

-    xrng <- diff(xrng)

-    yrng <- diff(yrng)

-

-    if (!any(class(subview) %in% c("ggplot", "trellis", "grob", "character"))) {

-        stop("subview should be a ggplot or grob object, or an image file...")

-    }

-

-    if (is(subview, "ggplot")) {

-        sv <- ggplotGrob(subview)

-    } else if (is(subview, "trellis")) {

-        sv <- grid::grid.grabExpr(print(subview))

-    } else if (is(subview, "grob")) {

-        sv <- subview

-    } else if (file.exists(subview)) {

-        readImage <- get_fun_from_pkg("EBImage", "readImage")

-        sv <- rasterGrob(readImage(subview))

-    } else {

-        stop("subview should be a ggplot or grob object, or an image file...")

-    }

-

-    width <- width/2

-    height <- height/2

-

-    mainview + annotation_custom(

-        sv,

-        xmin = x - width*xrng,

-        xmax = x + width*xrng,

-        ymin = y - height*yrng,

-        ymax = y + height*yrng)

-}

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

 ---

 output:

   md_document:

-    variant: markdown_github

+    variant: gfm

 html_preview: false

 ---

@@ -1,6 +1,6 @@

 <!-- README.md is generated from README.Rmd. Please edit that file -->

-ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

-===========================================================================================================================

+

+# ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />

@@ -36,33 +36,35 @@ Collective](https://opencollective.com/ggtree/sponsors/badge.svg)](#sponsors)

 The `ggtree` package extending the `ggplot2` package. It based on

 grammar of graphics and takes all the good parts of `ggplot2`. `ggtree`

 is designed for not only viewing phylogenetic tree but also displaying

-annotation data on the tree.

+annotation data on the

+tree.

 [![Twitter](https://img.shields.io/twitter/url/https/github.com/GuangchuangYu/ggtree.svg?style=social)](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu)

 For details, please visit our project website,

 <https://guangchuangyu.github.io/ggtree>.

--   [Documentation](https://guangchuangyu.github.io/ggtree/documentation/)

--   [FAQ](https://guangchuangyu.github.io/ggtree/faq/)

--   [Featured

+  - [Documentation](https://guangchuangyu.github.io/ggtree/documentation/)

+  - [FAQ](https://guangchuangyu.github.io/ggtree/faq/)

+  - [Featured

     Articles](https://guangchuangyu.github.io/ggtree/featuredArticles/)

--   [Feedback](https://guangchuangyu.github.io/ggtree/#feedback)

+  - [Feedback](https://guangchuangyu.github.io/ggtree/#feedback)

+-----

 Please cite the following article when using `ggtree`:

 **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R

 package for visualization and annotation of phylogenetic trees with

 their covariates and other associated data. ***Methods in Ecology and

-Evolution***. 2017, 8(1):28-36.

+Evolution***. 2017,

+8(1):28-36.

 [![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628)

 [![Altmetric](https://img.shields.io/badge/Altmetric-333-green.svg?style=flat)](https://www.altmetric.com/details/10533079)

 [![citation](https://img.shields.io/badge/cited%20by-51-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)

+-----

 ### Citation

@@ -76,23 +78,20 @@ Evolution***. 2017, 8(1):28-36.

 <img src="docs/images/dlstats.png" width="890"/>

-Contributors

+## Contributors

 This project exists thanks to all the people who contribute.

 [\[Contribute\]](CONTRIBUTING.md).

 <a href="https://github.com/GuangchuangYu/ggtree/graphs/contributors"><img src="https://opencollective.com/ggtree/contributors.svg?width=890" /></a>

-Backers

+## Backers

-Thank you to all our backers! 🙏 \[[Become a

+Thank you to all our backers\! 🙏 \[[Become a

 backer](https://opencollective.com/ggtree#backer)\]

 <a href="https://opencollective.com/ggtree#backers" target="_blank"><img src="https://opencollective.com/ggtree/backers.svg?width=890"></a>

-Sponsors

+## Sponsors

 Support this project by becoming a sponsor. Your logo will show up here

 with a link to your website. \[[Become a

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

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/phylopic.R

+% Please edit documentation in R/defunct.R

 \name{annotation_image}

 \alias{annotation_image}

 \title{annotation_image}

deleted file mode 100644

@@ -1,26 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/phylopic.R

-\name{download.phylopic}

-\alias{download.phylopic}

-\title{download.phylopic}

-\usage{

-download.phylopic(id, size = 512, color = "black", alpha = 1)

-}

-\arguments{

-\item{id}{phyopic id}

-

-\item{size}{size of phylopic}

-

-\item{color}{color}

-

-\item{alpha}{alpha}

-}

-\value{

-matrix

-}

-\description{

-download phylopic

-}

-\author{

-Guangchuang Yu

-}

new file mode 100644

@@ -0,0 +1,31 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/geom_nodelab.R

+\name{geom_nodelab}

+\alias{geom_nodelab}

+\title{geom_nodelab}

+\usage{

+geom_nodelab(mapping = NULL, nudge_x = 0, nudge_y = 0, geom = "text",

+  hjust = 0.5, ...)

+}

+\arguments{

+\item{mapping}{aes mapping}

+

+\item{nudge_x}{horizontal adjustment to nudge label}

+

+\item{nudge_y}{vertical adjustment to nudge label}

+

+\item{geom}{one of 'text', 'label', 'image' and 'phylopic'}

+

+\item{hjust}{horizontal alignment, one of 0, 0.5 or 1}

+

+\item{...}{additional parameters}

+}

+\value{

+geom layer

+}

+\description{

+add node label layer

+}

+\author{

+guangchuang yu

+}

@@ -18,7 +18,7 @@ geom_tiplab(mapping = NULL, hjust = 0, align = FALSE,

 \item{linesize}{line size of line if align = TRUE}

-\item{geom}{one of 'text' and 'label'}

+\item{geom}{one of 'text', 'label', 'image' and 'phylopic'}

 \item{offset}{tiplab offset}

deleted file mode 100644

@@ -1,26 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/phylopic.R

-\name{get.phylopic}

-\alias{get.phylopic}

-\title{get.phylopic}

-\usage{

-get.phylopic(id, size = 512, color = "black", alpha = 1)

-}

-\arguments{

-\item{id}{phylopic id}

-

-\item{size}{size of the phylopic}

-

-\item{color}{color}

-

-\item{alpha}{alpha}

-}

-\value{

-grob object

-}

-\description{

-download phylopic and convert to grob object

-}

-\author{

-Guangchuang Yu

-}

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

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/phylopic.R

+% Please edit documentation in R/defunct.R

 \name{phylopic}

 \alias{phylopic}

 \title{phylopic}

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

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/subview.R

+% Please edit documentation in R/defunct.R

 \name{subview}

 \alias{subview}

 \title{subview}

@@ -175,18 +175,6 @@ bx2 <- lapply(bx, function(g) g+coord_flip())

 inset(p2, bx2, width=.4, height=.06, vjust=.04, hjust=p2$data$x[1:15]-4) + xlim(NA, 4.5)

 ```

-## Annotate with image files

-

-```{r eval=FALSE}

-imgfile <- tempfile(, fileext=".png")

-download.file("https://avatars1.githubusercontent.com/u/626539?v=3&u=e731426406dd3f45a73d96dd604bc45ae2e7c36f&s=140", destfile=imgfile, mode='wb')

-img <- list(imgfile, imgfile)

-names(img) <- c("18", "22")

-inset(p, img)

-```

-

-![](figures/inset_img.png)

-

 # Plot tree with associated data

 For associating phylogenetic tree with different type of plot produced by user's data, `ggtree` provides `facet_plot` function which accepts an input `data.frame` and a `geom` function to draw the input data. The data will be displayed in an additional panel of the plot.

@@ -203,22 +191,6 @@ d2 <- data.frame(id=tr$tip.label, value = abs(rnorm(30, mean=100, sd=50)))

 facet_plot(p2, panel='bar', data=d2, geom=geom_segment, aes(x=0, xend=value, y=y, yend=y), size=3, color='steelblue') + theme_tree2()

 ```

-# Tree annotation with Phylopic

-

-

-[PhyloPic](http://phylopic.org/) is a database that stores reusable silhouette images of organisms. `ggtree` supports downloading images from [PhyloPic](http://phylopic.org/) and annotating phylogenetic tree with the downloaded images.

-

-```{r 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)

-```

-![](figures/phylopic1.png)

-

-```{r 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)

-```

-![](figures/phylopic2.png)

deleted file mode 100644

Binary files a/vignettes/figures/inset_img.png and /dev/null differ

deleted file mode 100644

Binary files a/vignettes/figures/phylopic1.png and /dev/null differ

deleted file mode 100644

Binary files a/vignettes/figures/phylopic2.png and /dev/null differ

deleted file mode 100644

Binary files a/vignettes/figures/subview_animation.gif and /dev/null differ

@@ -53,15 +53,16 @@ ggtree(beast) + geom_point2(aes(subset=!is.na(posterior) & posterior > 0.75), co

 To support viewing multiple plots, ggtree provides `multiplot` function that similar to `gridExtra::grid.arrange` with extra feature of labeling the plots.

-```{r fig.width=8, fig.height=4, warning=FALSE}

+``` {r fig.width=8, fig.height=4, warning=FALSE}

 multiplot(ggtree(rtree(30)), ggtree(rtree(40)), ncol=2, labels=c('A', 'B'))

 ```

+<!--

 # subplots in ggplot object

 `ggtree` implemented a function, `subview`, that can add subplots on a ggplot2 object.

-```{r fig.width=8, fig.height=8, warning=F}

+#``` {r fig.width=8, fig.height=8, warning=F}

 set.seed(2016-01-04)

 tr <- rtree(30)

 tr <- groupClade(tr, node=45)

@@ -69,13 +70,13 @@ p <- ggtree(tr, aes(color=group)) + geom_tippoint()

 p1 <- p + geom_hilight(node=45)

 p2 <- viewClade(p, node=45) + geom_tiplab()

 subview(p2, p1+theme_transparent(), x=2.3, y=28.5)

-```

+#```

 This is the backend of the [inset](advanceTreeAnnotation.html) function.

 This `subview` function works with any `ggplot` objects and it had successful applied to [plot pie graphs on map](http://stackoverflow.com/questions/10368180/plotting-pie-graphs-on-map-in-ggplot/32380396#32380396).

-```{r eval=FALSE}

+#``` {r eval=FALSE}

 library(ggtree)

 dd <- data.frame(x=LETTERS[1:3], y=1:3)

 pie <- ggplot(dd, aes(x=1, y, fill=x)) + geom_bar(stat="identity", width=1) + coord_polar(theta="y") + theme_inset()

@@ -88,7 +89,8 @@ for (i in seq_along(x)) {

     p <- subview(p, pie, x[i], y[i], width[i], height[i])

     print(p)

 }

-```