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

-}

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

 ##' download phylopic and convert to grob object

 ##'

-##' 

+##'

 ##' @title get.phylopic

 ##' @param id phylopic id

 ##' @param size size of the phylopic

@@ -34,9 +34,9 @@ download.phylopic <- function(id, size=512, color="black", alpha=1) {

     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')

@@ -44,7 +44,7 @@ download.phylopic <- function(id, size=512, color="black", alpha=1) {

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

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

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

-    

+

     return(img)

 }

@@ -59,13 +59,13 @@ download.phylopic_internal <- function(id, size=512, outfile=NULL) {

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

     }

     ## mode = "wb" for Windows platform

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

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

 }

 ##' add phylopic layer

 ##'

-##' 

+##'

 ##' @title phylopic

 ##' @param tree_view tree view

 ##' @param phylopic_id phylopic id

@@ -84,6 +84,9 @@ download.phylopic_internal <- function(id, size=512, outfile=NULL) {

 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) ) {

@@ -104,7 +107,7 @@ phylopic <- function(tree_view, phylopic_id,

         ymin <- y - AR * width/2

         ymax <- y + AR * width/2

     }

-    

+

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

                                   xmax=xmax, ymax=ymax,

                                   rasterGrob(img))

@@ -118,7 +121,7 @@ getAR <- function(img) {

 ##' 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

@@ -149,7 +152,7 @@ annotation_image <- function(tree_view, img_info, width=0.1, align=TRUE, linetyp

         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) {

@@ -32,8 +32,9 @@ download.phylopic <- function(id, size=512, color="black", alpha=1) {

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

     download.phylopic_internal(id, size, imgfile)

-    requireNamespace("EBImage")

-    channel <- eval(parse(text=paste0("EBImage::", "channel")))

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

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

+    

     img <- readImage(imgfile)

     color <- col2rgb(color) / 255

@@ -135,6 +136,7 @@ annotation_image <- function(tree_view, img_info, width=0.1, align=TRUE, linetyp

     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)

@@ -93,8 +93,9 @@ phylopic <- function(tree_view, phylopic_id,

             if (is.null(node)) {

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

             }

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

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

+            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

@@ -32,12 +32,8 @@ download.phylopic <- function(id, size=512, color="black", alpha=1) {

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

     download.phylopic_internal(id, size, imgfile)

-    EBImage <- "EBImage"

-    require(EBImage, character.only = TRUE)

-

-    readImage <- eval(parse(text="readImage"))

-    channel <- eval(parse(text="channel"))

-    

+    requireNamespace("EBImage")

+    channel <- eval(parse(text=paste0("EBImage::", "channel")))

     img <- readImage(imgfile)

     color <- col2rgb(color) / 255

@@ -51,6 +47,8 @@ download.phylopic <- function(id, size=512, color="black", alpha=1) {

     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"))

@@ -136,10 +136,6 @@ annotation_image <- function(tree_view, img_info, width=0.1, align=TRUE, linetyp

     x <- df[idx, "x"]

     y <- df[idx, "y"]

-    EBImage <- "EBImage"

-    require(EBImage, character.only = TRUE)

-    readImage <- eval(parse(text="readImage"))

-    

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

     ARs <- sapply(images, getAR)

@@ -148,11 +144,11 @@ annotation_image <- function(tree_view, img_info, width=0.1, align=TRUE, linetyp

     if (align) {

         xmin <- max(df$x) + offset

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

-        xmax <- xmin + width

     } else {

-        xmin <- x - width/2

-        xmax <- x + width/2

+        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) {

@@ -24,14 +24,20 @@ get.phylopic <- function(id, size=512, color="black", alpha=1) {

 ##' @return matrix

 ##' @importFrom grDevices rgb

 ##' @importFrom grDevices col2rgb

-##' @importFrom EBImage readImage

-##' @importFrom EBImage channel

+## @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)

+    EBImage <- "EBImage"

+    require(EBImage, character.only = TRUE)

+

+    readImage <- eval(parse(text="readImage"))

+    channel <- eval(parse(text="channel"))

+    

     img <- readImage(imgfile)

     color <- col2rgb(color) / 255

@@ -130,6 +136,10 @@ annotation_image <- function(tree_view, img_info, width=0.1, align=TRUE, linetyp

     x <- df[idx, "x"]

     y <- df[idx, "y"]

+    EBImage <- "EBImage"

+    require(EBImage, character.only = TRUE)

+    readImage <- eval(parse(text="readImage"))

+    

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

     ARs <- sapply(images, getAR)

@@ -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

+}

@@ -72,7 +72,7 @@ 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=NULL) {

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

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

     if ( is.null(node) ) {

         xmin <- ymin <- -Inf

@@ -85,10 +85,7 @@ phylopic <- function(tree_view, phylopic_id,

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

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

         }

-        if (is.null(width)) {

-            width <- 5

-        }

-        

+          

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

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

         xmin <- x - width/2

@@ -52,3 +52,53 @@ download.phylopic <- function(id, size=512, color="black", alpha=1) {

     return(img)

 }

+##' 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=NULL) {

+    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...")

+            }

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

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

+        }

+        if (is.null(width)) {

+            width <- 5

+        }

+        

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

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

+        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))

+}

+

@@ -33,8 +33,12 @@ download.phylopic <- function(id, size=512, color="black", alpha=1) {

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

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

-    imgfile <- tempfile(fileext = ".PNG") ## .png is not recognize by WINDOWS platform

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

+    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

@@ -33,7 +33,7 @@ download.phylopic <- function(id, size=512, color="black", alpha=1) {

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

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

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

+    imgfile <- tempfile(fileext = ".PNG") ## .png is not recognize by WINDOWS platform

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

     img <- readImage(imgfile)

@@ -7,32 +7,44 @@

 ##' @param color color

 ##' @param alpha alpha

 ##' @return grob object

-##' @importFrom grDevices rgb

-##' @importFrom grDevices col2rgb

-##' @importFrom RCurl getURLContent

-##' @importFrom png readPNG

 ##' @importFrom grid rasterGrob

 ##' @export

 ##' @author Guangchuang Yu

-##' @references https://github.com/sckott/rphylopic/blob/master/R/add_phylopic.r

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

-    size %<>% as.character %>% match.arg(c("64", "128", "256", "512", "1024"))

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

-        getURLContent %>%

-            readPNG

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

+}

-    color %<>% col2rgb

-    n <- length(img[,,1])

+##' 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) {

+    size %<>% as.character %>%

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

+

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

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

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

+    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

-    matrix(ifelse(img[,,4] > 0,

-                  rgb(red   = rep(color[1,1], n),

-                      green = rep(color[2,1], n),

-                      blue  = rep(color[3,1], n),

-                      alpha = img[,,4] * 255 * alpha, maxColorValue = 255),

-                  rgb(red   = rep(1, n),

-                      green = rep(1, n),

-                      blue  = rep(1, n),

-                      alpha = img[,,4] * alpha)), 

-           nrow = nrow(img)) %>%

-               rasterGrob

+    return(img)

 }

+

new file mode 100644

@@ -0,0 +1,38 @@

+##' 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 grDevices rgb

+##' @importFrom grDevices col2rgb

+##' @importFrom RCurl getURLContent

+##' @importFrom png readPNG

+##' @importFrom grid rasterGrob

+##' @export

+##' @author Guangchuang Yu

+##' @references https://github.com/sckott/rphylopic/blob/master/R/add_phylopic.r

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

+    size %<>% as.character %>% match.arg(c("64", "128", "256", "512", "1024"))

+    img <- paste0("http://phylopic.org/assets/images/submissions/", id, ".", size, ".png") %>%

+        getURLContent %>%

+            readPNG

+

+    color %<>% col2rgb

+    n <- length(img[,,1])

+    

+    matrix(ifelse(img[,,4] > 0,

+                  rgb(red   = rep(color[1,1], n),

+                      green = rep(color[2,1], n),

+                      blue  = rep(color[3,1], n),

+                      alpha = img[,,4] * 255 * alpha, maxColorValue = 255),

+                  rgb(red   = rep(1, n),

+                      green = rep(1, n),

+                      blue  = rep(1, n),

+                      alpha = img[,,4] * alpha)), 

+           nrow = nrow(img)) %>%

+               rasterGrob

+}