@@ -1,7 +1,7 @@

 Package: ggtree

 Type: Package

 Title: a phylogenetic tree viewer for different types of tree annotations

-Version: 0.99.16

+Version: 0.99.17

 Author: Guangchuang Yu

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

@@ -1,3 +1,7 @@

+CHANGES IN VERSION 0.99.17

+------------------------

+ o add angle and branch.y variable in cladogram layout <2015-02-10, Tue>

+ 

 CHANGES IN VERSION 0.99.16

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

  o correct typo in vignette <2015-02-10, Tue>

@@ -653,3 +653,18 @@ getYcoord_scale_category <- function(tr, df, yscale, yscale_mapping=NULL, ...) {

     }

     return(y)

 }

+

+

+add_angle_cladogram <- function(res) {

+    dy <- (res[, "y"] - res[res$parent, "y"]) / diff(range(res[, "y"]))

+    dx <- (res[, "x"] - res[res$parent, "x"]) / diff(range(res[, "x"]))

+    theta <- atan(dy/dx)

+    theta[is.na(theta)] <- 0 ## root node

+    res$angle <- theta/pi * 180

+    branch.y <- (res[res$parent, "y"] + res[, "y"])/2

+    idx <- is.na(branch.y)

+    branch.y[idx] <- res[idx, "y"]

+    res[, "branch.y"] <- branch.y

+    return(res)

+}

+

@@ -185,7 +185,7 @@ fortify.beast <- function(model, data,

     stats <- stats[,colnames(stats) != "node"]

     df <- cbind(df, stats)

-    df <- scaleY(phylo, df, yscale, ...)

+    df <- scaleY(phylo, df, yscale, layout, ...)

     return(df)

 }

@@ -231,7 +231,7 @@ fortify.codeml <- function(model, data,

     res <- merge_phylo_anno.codeml_mlc(df, dNdS, ndigits)

     df <- merge_phylo_anno.paml_rst(res, model@rst)

-    scaleY(phylo, df, yscale, ...)

+    scaleY(phylo, df, yscale, layout, ...)

 }

@@ -254,7 +254,7 @@ fortify.codeml_mlc <- function(model, data,

     dNdS <- model@dNdS

     df <- merge_phylo_anno.codeml_mlc(df, dNdS, ndigits)

-    scaleY(phylo, df, yscale, ...)

+    scaleY(phylo, df, yscale, layout, ...)

 }

 merge_phylo_anno.codeml_mlc <- function(df, dNdS, ndigits = NULL) {

@@ -308,7 +308,7 @@ fortify.paml_rst <- function(model, data, layout = "phylogram", yscale="none",

                              ladderize=TRUE, right=FALSE, ...) {

     df <- fortify.phylo(model@phylo, data, layout, ladderize, right, ...)

     df <- merge_phylo_anno.paml_rst(df, model)

-    scaleY(model@phylo, df, yscale, ...)

+    scaleY(model@phylo, df, yscale, layout, ...)

 }

 merge_phylo_anno.paml_rst <- function(df, model) {

@@ -337,13 +337,13 @@ fortify.jplace <- function(model, data,

     df <- df %add2% place

-    scaleY(model@phylo, df, yscale, ...)

+    scaleY(model@phylo, df, yscale, layout, ...)

 }

-scaleY <- function(phylo, df, yscale, ...) {

+scaleY <- function(phylo, df, yscale, layout, ...) {

     if (yscale == "none") {

         return(df)

-    }

+    } 

     if (! yscale %in% colnames(df)) {

         warning("yscale is not available...\n")

         return(df)

@@ -360,6 +360,9 @@ scaleY <- function(phylo, df, yscale, ...) {

     }

     df[, "y"] <- y

+    if (layout == "cladogram") {

+        df <- add_angle_cladogram(df)

+    }

     return(df)

 }

@@ -371,7 +374,7 @@ fortify.phylo4 <- function(model, data, layout="phylogram", yscale="none",

     phylo <- as.phylo.phylo4(model)

     df <- fortify.phylo(phylo, data,

                         layout, ladderize, right, ...)

-    scaleY(phylo, df, yscale)

+    scaleY(phylo, df, yscale, layout, ...)

 }

 as.phylo.phylo4 <- function(phylo4) {

@@ -425,6 +428,9 @@ fortify.phylo <- function(model, data, layout="phylogram",

     rownames(df) <- df$node

     cn <- colnames(df)

     colnames(df)[grep("length", cn)] <- "branch.length"

+    if(layout == "cladogram") {

+        df <- add_angle_cladogram(df)

+    }

     return(df)

 }

@@ -489,18 +495,19 @@ as.data.frame.phylo_ <- function(x, layout="phylogram",

     isTip <- rep(FALSE, N)

     isTip[1:Ntip] <- TRUE

     res$isTip <- isTip

-    res$branch <- (res$x[res$parent] + res$x)/2

+    res$branch <- (res[res$parent, "x"] + res[, "x"])/2

     if (!is.null(res$length)) {

         res$length[is.na(res$length)] <- 0

     }

     res$branch[is.na(res$branch)] <- 0

     if (layout == "fan") {

-      idx <- match(1:N, order(res$y))

-      angle <- -360/N * 1:N

-      angle <- angle[idx]

-      res$angle <- angle

-    }

+        idx <- match(1:N, order(res$y))

+        angle <- -360/N * 1:N

+        angle <- angle[idx]

+        res$angle <- angle

+    } 

+    

     return(res)

 }