@@ -12,3 +12,4 @@ __init__.pyc

 *.ignore

 .web_cache

 ggtree.Rproj

+.Rproj.user

\ No newline at end of file

@@ -194,7 +194,7 @@ layoutEqualAngle <- function(tree, branch.length ){

     df$y <- NA

     df$start <- NA # Start angle of segment of subtree.

     df$end   <- NA # End angle of segment of subtree

-    df$angle <- NA # Orthogonal angle to beta ... for labels??

+    df$angle <- NA # Orthogonal angle to beta for tip labels.

     ## Initialize root node position and angles.

     df[root, "x"] <- 0

     df[root, "y"] <- 0

@@ -246,7 +246,7 @@ layoutEqualAngle <- function(tree, branch.length ){

             ## Calculate (x,y) position of the i-th child node from current node.

             df[child, "x"] <- df[curNode, "x"] + cospi(beta) * length.child

             df[child, "y"] <- df[curNode, "y"] + sinpi(beta) * length.child

-            ## Calculate orthogonal angle to beta.

+            ## Calculate orthogonal angle to beta for tip label.

             df[child, "angle"] <- -90 - 180 * beta * sign(beta - 1)

             ## Update the start and end angles of the childs segment.

             df[child, "start"] <- start

@@ -641,6 +641,10 @@ rotateTreePoints.df <- function(df, pivot_node, nodes, angle){

     df[node, 'x'] <- cospitheta * delta_x - sinpitheta * delta_y + df[pivot_node, 'x']

     df[node, 'y'] <- sinpitheta * delta_x + cospitheta * delta_y + df[pivot_node, 'y']

+  }

+  

+  # Now update labels of rotated tree.

+  for(node in nodes){

     # Update label angle if not root node.

     # get parent

     parent_id <- getParent.df(df, node)

@@ -648,12 +652,14 @@ rotateTreePoints.df <- function(df, pivot_node, nodes, angle){

     if( parent_id != 0){

       theta_parent_child <- getNodeAngle.df(df, parent_id, node)

       if(!is.na(theta_parent_child)){

-        # Update label angle

-        df[node, 'angle'] <- -90 - 180 * theta_parent_child * sign(theta_parent_child - 1)

+        # Update tip label angle, that is parallel to edge.

+        #df[node, 'angle'] <- -90 - 180 * theta_parent_child * sign(theta_parent_child - 1)

+        df[node, 'angle'] <- 180 * theta_parent_child

       }

     }

-

   }

+  

+  

   return(df)

 }