@@ -19,6 +19,7 @@ export(add_legend)

 export(aes)

 export(annotation_clade)

 export(annotation_clade2)

+export(annotation_image)

 export(as.binary)

 export(collapse)

 export(download.phylopic)

@@ -1,5 +1,6 @@

 CHANGES IN VERSION 1.1.13

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

+ o implement annotation_image <2015-08-01, Sat>

  o better implementation of geom_tiplab for accepting aes mapping and auto add align dotted line <2015-08-01, Sat>

  o open group_name parameter of groupOTU/groupClade to user <2015-08-01, Sat>

@@ -160,7 +160,7 @@ geom_hilight <- function(tree_object, node, ...) {

 ##' @param hjust horizontal adjustment

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

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

-##' @param line.size line size of line if align = TRUE

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

 ##' @param ... additional parameter

 ##' @return tip label layer

 ##' @importFrom ggplot2 geom_text

@@ -170,7 +170,7 @@ geom_hilight <- function(tree_object, node, ...) {

 ##' require(ape)

 ##' tr <- rtree(10)

 ##' ggtree(tr) + geom_tiplab()

-geom_tiplab <- function(mapping=NULL, hjust = 0, align = FALSE, linetype = "dotted", line.size=1, ...) {

+geom_tiplab <- function(mapping=NULL, hjust = 0, align = FALSE, linetype = "dotted", linesize=1, ...) {

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

     if (align == TRUE) {

         self_mapping <- aes(x = max(x) + diff(range(x))/200, label = label)

@@ -186,7 +186,7 @@ geom_tiplab <- function(mapping=NULL, hjust = 0, align = FALSE, linetype = "dott

     }

     dot_mapping <- NULL

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

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

         dot_mapping <- aes(xend=x+diff(range(x))/200, x=max(x), yend=y)

         if (!is.null(mapping)) {

             dot_mapping <- modifyList(dot_mapping, mapping)

@@ -201,7 +201,7 @@ geom_tiplab <- function(mapping=NULL, hjust = 0, align = FALSE, linetype = "dott

             geom_segment(mapping=dot_mapping,

                          subset=.(isTip),

                          linetype = linetype,

-                         size = line.size, ...)

+                         size = linesize, ...)

         )

 }

@@ -29,16 +29,9 @@ get.phylopic <- function(id, size=512, color="black", alpha=1) {

 ##' @export

 ##' @author Guangchuang Yu

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

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

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

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

+    download.phylopic_internal(id, size, imgfile)

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

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

-    if (Sys.info()["sysname"] == "Windows") {

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

-    } else {

-        download.file(imgurl, imgfile, quiet = TRUE)

-    }

     img <- readImage(imgfile)

     color <- col2rgb(color) / 255

@@ -52,6 +45,19 @@ download.phylopic <- function(id, size=512, color="black", alpha=1) {

     return(img)

 }

+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

 ##'

 ##' 

@@ -72,7 +78,8 @@ download.phylopic <- function(id, size=512, color="black", alpha=1) {

 ##' @author Guangchuang Yu

 phylopic <- function(tree_view, phylopic_id,

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

-                     node=NULL, x=NULL, y=NULL, width=5) {

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

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

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

     if ( is.null(node) ) {

         xmin <- ymin <- -Inf

@@ -85,9 +92,7 @@ phylopic <- function(tree_view, phylopic_id,

             x <- tree_view$data[node, "x"]

             y <- tree_view$data[node, "y"]

         }

-          

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

-        AR <- dims[1]/dims[2]

+        AR <- getAR(img)

         xmin <- x - width/2

         xmax <- x + width/2

         ymin <- y - AR * width/2

@@ -99,3 +104,60 @@ phylopic <- function(tree_view, phylopic_id,

                                   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"]

+

+    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))

+        xmax <- xmin + width

+    } else {

+        xmin <- x - width/2

+        xmax <- x + width/2

+    }

+    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

+}

new file mode 100644

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

+% Generated by roxygen2 (4.1.1): do not edit by hand

+% Please edit documentation in R/phylopic.R

+\name{annotation_image}

+\alias{annotation_image}

+\title{annotation_image}

+\usage{

+annotation_image(tree_view, img_info, width = 0.1, align = TRUE,

+  linetype = "dotted", linesize = 1, offset = 0)

+}

+\arguments{

+\item{tree_view}{tree view}

+

+\item{img_info}{data.frame with first column of taxa name and second column of image names}

+

+\item{width}{width of the image to be plotted in image}

+

+\item{align}{logical}

+

+\item{linetype}{line type if align = TRUE}

+

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

+

+\item{offset}{offset of image from the tree view}

+}

+\value{

+tree view

+}

+\description{

+annotation taxa with images

+}

+\author{

+Guangchuang Yu

+}

+

@@ -5,7 +5,7 @@

 \title{geom_tiplab}

 \usage{

 geom_tiplab(mapping = NULL, hjust = 0, align = FALSE,

-  linetype = "dotted", line.size = 1, ...)

+  linetype = "dotted", linesize = 1, ...)

 }

 \arguments{

 \item{mapping}{aes mapping}

@@ -16,7 +16,7 @@ geom_tiplab(mapping = NULL, hjust = 0, align = FALSE,

 \item{linetype}{linetype for adding line if align = TRUE}

-\item{line.size}{line size of line if align = TRUE}

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

 \item{...}{additional parameter}

 }

@@ -5,7 +5,7 @@

 \title{phylopic}

 \usage{

 phylopic(tree_view, phylopic_id, size = 512, color = "black", alpha = 0.5,

-  node = NULL, x = NULL, y = NULL, width = 5)

+  node = NULL, x = NULL, y = NULL, width = 0.1)

 }

 \arguments{

 \item{tree_view}{tree view}

@@ -426,8 +426,8 @@ pp

 ```

 ```{r fig.width=5, fig.height=5, fig.align="center", warning=FALSE}

-pp %>% phylopic("67382184-5135-4faa-8e98-eadff02c3e8a", color="#86B875", alpha=.8, node=4, width=4) %>%

-    phylopic("d3563b54-780f-4711-a49a-7ea051e9dacc", color="darkcyan", alpha=.8, node=17, width=8)

+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)

 ```