@@ -30,7 +30,7 @@ fortify.phylo <- function(model, data,

     }

     if (layout %in% c("equal_angle", "daylight")) {

-        res <- layout.unrooted(x, layout.method = layout, branch.length = branch.length, ...)

+        res <- layout.unrooted(model, layout.method = layout, branch.length = branch.length, ...)

     } else {

         if (is.null(x$edge.length) || branch.length == "none") {

             xpos <- getXcoord_no_length(x)

@@ -1,11 +1,11 @@

 ##' @importFrom ape reorder.phylo

-layout.unrooted <- function(tree, branch.length="branch.length", layout.method="equal_angle", ...) {

+layout.unrooted <- function(model, branch.length="branch.length", layout.method="equal_angle", ...) {

     df <- switch(layout.method,

-                 equal_angle = layoutEqualAngle(tree, branch.length),

-                 daylight = layoutDaylight(tree, branch.length)

+                 equal_angle = layoutEqualAngle(model, branch.length),

+                 daylight = layoutDaylight(model, branch.length)

                  )

     return(df)

@@ -36,7 +36,9 @@ set_branch_length_cladogram <- function(tree) {

 ##' @param tree phylo object

 ##' @param branch.length set to 'none' for edge length of 1. Otherwise the phylogenetic tree edge length is used.

 ##' @return tree as data.frame with equal angle layout.

-layoutEqualAngle <- function(tree, branch.length ){

+layoutEqualAngle <- function(model, branch.length ){

+	tree <- as.phylo(model)

+	

     if (branch.length == "none") {

         tree <- set_branch_length_cladogram(tree)

     }

@@ -44,7 +46,7 @@ layoutEqualAngle <- function(tree, branch.length ){

     root <- getRoot(tree)

     ## Convert Phylo tree to data.frame.

     ## df <- as.data.frame.phylo_(tree)

-    df <- as_data_frame(tree) %>%

+    df <- as_data_frame(model) %>%

         mutate_(isTip = ~(! node %in% parent))

     ## NOTE: Angles (start, end, angle) are in half-rotation units (radians/pi or degrees/180)

@@ -127,15 +129,16 @@ layoutEqualAngle <- function(tree, branch.length ){

 ##' nodes = remove tip nodes.

 ##'

 ##' ```

-layoutDaylight <- function( tree, branch.length ){

-

+layoutDaylight <- function(model, branch.length ){

+	tree <- as.phylo(model)

+	

     ## How to set optimal

     MAX_COUNT <- 5

     MINIMUM_AVERAGE_ANGLE_CHANGE <- 0.05

     ## Initialize tree.

-    tree_df <- layoutEqualAngle(tree, branch.length)

+    tree_df <- layoutEqualAngle(model, branch.length)

     ## nodes = get list of nodes in tree_df

     ## Get list of node id's.