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

 CHANGES IN VERSION 1.5.4

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

+ o bug fixed in scaleClade, now y positions are (hopefully) always correct. <2016-05-20, Fri>

  o bug fixed in collapse <2016-05-20, Fri>

    + if user collapse a node that is an offspring of a collapsed node, print warning msg and return the tree directly

  o use byte compiler <2016-05-18, Wed>

@@ -70,16 +70,8 @@ collapse <- function(tree_view=NULL, node) {

     df[sp, "x"] <- NA

     df[sp, "y"] <- NA

-    root <- which(df$node == df$parent)

-    pp <- df[node, "parent"]

-    while(any(pp != root)) {

-        df[pp, "y"] <- mean(df[getChild.df(df, pp), "y"])

-        pp <- df[pp, "parent"]

-    }

-    j <- getChild.df(df, pp)

-    j <- j[j!=pp]

-    df[pp, "y"] <- mean(df[j, "y"])

-

+    df <- reassign_y_from_node_to_root(df, node)

+    

     ## re-calculate branch mid position

     df <- calculate_branch_mid(df)

@@ -260,7 +252,7 @@ scaleClade <- function(tree_view=NULL, node, scale=1, vertical_only=TRUE) {

     ## new_span <- span * scale

     old.sp.df <- sp.df

     sp.df$y <- df[node, "y"] + (sp.df$y - df[node, "y"]) * scale

-    if (vertical_only == FALSE) {

+    if (! vertical_only) {

         sp.df$x <- df[node, "x"] + (sp.df$x - df[node, "x"]) * scale

     }

@@ -284,9 +276,25 @@ scaleClade <- function(tree_view=NULL, node, scale=1, vertical_only=TRUE) {

     }

     df[sp, "scale"] <- df[sp, "scale"] * scale

+    df <- reassign_y_from_node_to_root(df, node)

+    

     ## re-calculate branch mid position

     df <- calculate_branch_mid(df)

     tree_view$data <- df

     tree_view

 }

+

+

+reassign_y_from_node_to_root <- function(df, node) {

+    root <- which(df$node == df$parent)

+    pp <- df[node, "parent"]

+    while(any(pp != root)) {

+        df[pp, "y"] <- mean(df[getChild.df(df, pp), "y"])

+        pp <- df[pp, "parent"]

+    }

+    j <- getChild.df(df, pp)

+    j <- j[j!=pp]

+    df[pp, "y"] <- mean(df[j, "y"])

+    return(df)

+}