@@ -16,6 +16,7 @@

 ##' @param branch.length variable for scaling branch, if 'none' draw cladogram

 ##' @param root.position position of the root node (default = 0)

 ##' @param xlim x limits, only works for 'inward_circular' layout

+##' @param layout.params list, the parameters of layout, when layout is a function.

 ##' @return tree

 ##' @importFrom ggplot2 ggplot

 ##' @importFrom ggplot2 xlab

@@ -53,12 +54,22 @@ ggtree <- function(tr,

                    branch.length  = "branch.length",

                    root.position  = 0,

                    xlim = NULL,

+                   layout.params = list(),

                    ...) {

     # Check if layout string is valid.

-    layout %<>% match.arg(c("rectangular", "slanted", "fan", "circular", 'inward_circular',

+    trash <- try(silent = TRUE,

+                 expr = {

+                   layout %<>% match.arg(c("rectangular", "slanted", "fan", "circular", 'inward_circular',

                             "radial", "unrooted", "equal_angle", "daylight", "dendrogram",

                             "ape", "ellipse", "roundrect"))

+                  }

+             )

+

+    dd <- check.graph.layout(tr, trash, layout, layout.params)

+    if (inherits(trash, "try-error") && !is.null(dd)){

+        layout <- "rectangular"

+    }

     if (layout == "unrooted") {

         layout <- "daylight"

@@ -89,6 +100,15 @@ ggtree <- function(tr,

                 root.position = root.position,

                 ...)

+    if (!is.null(dd)){

+        p$data <- dplyr::left_join(

+                    p$data %>% select(-c("x", "y")), 

+                    dd, 

+                    by = "node"

+        )

+        layout <- "equal_angle"

+    }

+

     if (is(tr, "multiPhylo")) {

         multiPhylo <- TRUE

     } else {

@@ -154,3 +174,30 @@ ggtree_references <- function() {

            "<http://yulab-smu.top/treedata-book/>\n"

            )

 }

+

+check.graph.layout <- function(tr, trash, layout, layout.params){

+    if (inherits(trash, "try-error")){

+        gp <- ape::as.igraph.phylo(as.phylo(tr), use.labels = FALSE)

+        #dd <- ggraph::create_layout(gp, layout = layout)

+        if (is.function(layout)){

+            dd <- do.call(layout, c(list(gp), layout.params))

+            if (!inherits(dd, "matrix")){

+                if ("xy" %in% names(dd)){

+                    dd <- dd$xx

+                }else if ("layout" %in% names(dd)){

+                    dd <- dd$layout

+                }else{

+                    stop(trash, call. = FALSE)

+                }

+            }

+            dd <- data.frame(dd)

+            colnames(dd) <- c("x", "y")

+            dd$node <- seq_len(nrow(dd))

+        }else{

+            stop(trash, call. = FALSE)

+        }

+    }else{

+        dd <- NULL

+    }

+    return(dd)

+}

@@ -21,6 +21,7 @@ ggtree(

   branch.length = "branch.length",

   root.position = 0,

   xlim = NULL,

+  layout.params = list(),

   ...

 )

 }

@@ -54,6 +55,8 @@ right-hand side? See \code{\link[ape:ladderize]{ape::ladderize()}} for more info

 \item{xlim}{x limits, only works for 'inward_circular' layout}

+\item{layout.params}{list, the parameters of layout, when layout is a function.}

+

 \item{...}{additional parameter

 some dot arguments: