@@ -1,6 +1,11 @@

+## reference: http://docs.travis-ci.com/user/languages/r/

+

 language: r

 bioc_required: true

+apt_packages:

+  - libfftw3-dev

+

 r_packages:

   - ape

   - phylobase

@@ -18,7 +23,7 @@ bioc_packages:

   - Biostrings

   - EBImage

   - BiocStyle

-

+  

 after_failure:

   - ./travis-tool.sh dump_logs

@@ -1,5 +1,7 @@

 CHANGES IN VERSION 1.1.6

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

+ o add vertical_only parameter to scaleClade and set to TRUE by default.

+   only vertical will be scaled by default. <2015-05-22, Fri>

  o update add_colorbar & add_legend <2015-05-21, Thu>

  o add example of add_legend and gheatmap in vignette <2015-05-18, Mon> 

  o gheatmap implementation of gplot <2015-05-18, Mon>

@@ -302,10 +302,13 @@ hilight <- function(tree_view, node, fill="steelblue", alpha=0.5, ...) {

 ##' @param tree_view tree view

 ##' @param node clade node

 ##' @param scale scale

+##' @param vertical_only logical. If TRUE, only vertical will be scaled.

+##' If FALSE, the clade will be scaled vertical and horizontally.

+##' TRUE by default.

 ##' @return tree view

 ##' @export

 ##' @author Guangchuang Yu

-scaleClade <- function(tree_view, node, scale=1) {

+scaleClade <- function(tree_view, node, scale=1, vertical_only=TRUE) {

     if (scale == 1) {

         return(tree_view)

     }

@@ -320,8 +323,10 @@ scaleClade <- function(tree_view, node, scale=1) {

     ## new_span <- span * scale

     old.sp.df <- sp.df

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

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

-

+    if (vertical_only == FALSE) {

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

+    }

+    

     scale_diff.up <- max(sp.df$y) - max(old.sp.df$y)

     scale_diff.lw <- min(sp.df$y) - min(old.sp.df$y)

@@ -18,10 +18,6 @@ scale_color_ <- function(phylo, by, low=NULL, high=NULL, na.color=NULL, default.

         cols <- rainbow_hcl(n)

     }

-    ## if (by == "dN_vs_dS") {

-    ##     interval <- seq(0, 1.5, length.out = 100)

-    ## } 

-

     idx <- getIdx(vals, MIN=MIN, MAX=MAX, interval=interval)

     interval <- attr(idx, "interval")

new file mode 100644

@@ -0,0 +1,12 @@

++ attach user specific data to existing tree object

++ attach user specific data by node number

++ mask function that accepts tree object, feature name and a function that specific how to mask.

+  with this function, user can mask some of the features that are not needed to display on a tree.

++ defined a function, compare_sequence, that accept a function that defined sequence feature,

+  and compare the feature from parent to children and add store the info in tree object.

+  So with ancestral sequences inferred by HYPHY or PAML, we can support any type of sequence feature comparison,

+  not only substitution supported internally.

++ support more features that can be plotted at the right hand side of the tree,

+  not only matrix but also for example sequence alignment or specific window of alignment.

+  

+

@@ -4,7 +4,7 @@

 \alias{scaleClade}

 \title{scaleClade}

 \usage{

-scaleClade(tree_view, node, scale = 1)

+scaleClade(tree_view, node, scale = 1, vertical_only = TRUE)

 }

 \arguments{

 \item{tree_view}{tree view}

@@ -12,6 +12,10 @@ scaleClade(tree_view, node, scale = 1)

 \item{node}{clade node}

 \item{scale}{scale}

+

+\item{vertical_only}{logical. If TRUE, only vertical will be scaled.

+If FALSE, the clade will be scaled vertical and horizontally.

+TRUE by default.}

 }

 \value{

 tree view