Browse code

version 1.5.15

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@122021 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 07/10/2016 05:18:29
Showing25 changed files

... ...
@@ -1,7 +1,7 @@
1 1
 Package: ggtree
2 2
 Type: Package
3 3
 Title: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
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-Version: 1.5.14
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+Version: 1.5.15
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 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam
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 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
7 7
 Description: 'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics.
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@@ -165,7 +165,6 @@ importFrom(ape,read.tree)
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 importFrom(ape,reorder.phylo)
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 importFrom(ape,which.edge)
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 importFrom(ape,write.tree)
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-importFrom(ggplot2,"%+replace%")
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 importFrom(ggplot2,GeomCurve)
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 importFrom(ggplot2,GeomLabel)
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 importFrom(ggplot2,GeomPoint)
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@@ -214,6 +213,7 @@ importFrom(ggplot2,theme_bw)
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 importFrom(ggplot2,xlab)
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 importFrom(ggplot2,xlim)
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 importFrom(ggplot2,ylab)
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+importFrom(ggplot2,ylim)
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 importFrom(grDevices,col2rgb)
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 importFrom(grDevices,colorRampPalette)
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 importFrom(grDevices,rgb)
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@@ -1,3 +1,9 @@
1
+CHANGES IN VERSION 1.5.15
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+------------------------
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+ o check.aes for layers defined in ggtree <2016-10-07, Fri>
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+ o recalculate 'angle' when collapse, expand and rotate clade <2016-10-06, Thu>
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+   + https://github.com/GuangchuangYu/ggtree/issues/78
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+
1 7
 CHANGES IN VERSION 1.5.14
2 8
 ------------------------
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  o subset tip in geom_tiplab2 <2016-10-05, Wed>
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@@ -75,6 +75,9 @@ collapse <- function(tree_view=NULL, node) {
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     ## re-calculate branch mid position
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     df <- calculate_branch_mid(df)
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+    ii <- which(!is.na(df$x))
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+    df$angle[ii] <- calculate_angle(df[ii,])$angle
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+    
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     tree_view$data <- df
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     clade <- paste0("clade_", node)
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     attr(tree_view, clade) <- sp.df
... ...
@@ -121,7 +124,7 @@ expand <- function(tree_view=NULL, node) {
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     ## re-calculate branch mid position
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     df <- calculate_branch_mid(df)
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-    tree_view$data <- df
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+    tree_view$data <- calculate_angle(df)
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     attr(tree_view, clade) <- NULL
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     tree_view
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 }
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@@ -156,7 +159,8 @@ rotate <- function(tree_view=NULL, node) {
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     if (pnode != node && !is.na(pnode)) {
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         df[df$node == pnode, "y"] <- mean(df[df$parent == pnode, "y"])
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     }
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-    tree_view$data <- df
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+
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+    tree_view$data <- calculate_angle(df)
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     tree_view
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 }
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... ...
@@ -218,6 +222,7 @@ flip <- function(tree_view=NULL, node1, node2) {
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     currentNode <- currentNode[!currentNode %in% anc]
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     tree_view$data <- re_assign_ycoord_df(df, currentNode)
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+    tree_view$data <- calculate_angle(tree_view$data)
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     tree_view
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 }
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... ...
@@ -281,7 +286,7 @@ scaleClade <- function(tree_view=NULL, node, scale=1, vertical_only=TRUE) {
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     ## re-calculate branch mid position
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     df <- calculate_branch_mid(df)
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-    tree_view$data <- df
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+    tree_view$data <- calculate_angle(df)
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     tree_view
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 }
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... ...
@@ -44,7 +44,8 @@ geom_balance <- function(node, fill="steelblue", color='white', alpha=.5, extend
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                   extend=extend,
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                   extendto=extendto,
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                   direction=1, 
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-                  na.rm = na.rm)
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+                  na.rm = na.rm),
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+    check.aes = FALSE
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   )
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   l2 <- layer(
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     stat=StatBalance,
... ...
@@ -61,7 +62,8 @@ geom_balance <- function(node, fill="steelblue", color='white', alpha=.5, extend
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                   extend=extend,
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                   extendto=extendto,
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                   direction=2,
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-                  na.rm = na.rm)
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+                  na.rm = na.rm),
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+    check.aes = FALSE
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   )
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   return(c(l1,l2))
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 }
... ...
@@ -113,7 +115,8 @@ stat_balance <- function(mapping=NULL, data=NULL, geom="rect",
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                   extend=extend,
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                   extendto=extendto,
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                   direction=1,
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-                  ...)
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+                  ...),
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+    check.aes = FALSE
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   )
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   l2 <- layer(
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     stat=StatBalance,
... ...
@@ -130,7 +133,8 @@ stat_balance <- function(mapping=NULL, data=NULL, geom="rect",
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                   extend=extend,
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                   extendto=extendto,
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                   direction=2,
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-                  ...)
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+                  ...),
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+    check.aes = FALSE
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   )
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   return(c(l1,l2))
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 }
... ...
@@ -205,4 +209,4 @@ get_balance_position_ <- function(data, node, direction) {
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              xmax = max(x),
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              ymin=min(y)-0.5,
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              ymax=max(y)+0.5)
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-}
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\ No newline at end of file
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+}
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@@ -128,7 +128,8 @@ stat_cladeText <- function(mapping=NULL, data=NULL,
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                       align  = align,
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                       na.rm  = na.rm,
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                       parse  = parse,
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-                      ...)
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+                      ...),
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+          check.aes = FALSE
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           )
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134 135
 }
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@@ -155,9 +156,9 @@ stat_cladeBar <- function(mapping=NULL, data=NULL,
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                       offset=offset,
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                       align=align,
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                       na.rm=na.rm,
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-                      ...)
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+                      ...),
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+          check.aes = FALSE
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           )
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-
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 }
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163 164
 StatCladeText <- ggproto("StatCladeText", Stat,
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@@ -39,7 +39,8 @@ geom_hilight <- function(node, fill="steelblue", alpha=.5, extend=0, extendto=NU
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                       alpha=alpha,
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                       extend=extend,
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                       extendto=extendto,
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-                      na.rm = na.rm)
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+                      na.rm = na.rm),
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+        check.aes = FALSE
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     )
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 }
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... ...
@@ -66,7 +66,8 @@ geom_label2 <- function(mapping = NULL, data = NULL,
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             label.size = label.size,
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             na.rm = na.rm,
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             ...
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-        )
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+        ),
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+        check.aes = FALSE
70 71
     )
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 }
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... ...
@@ -125,7 +125,8 @@ geom_point2 <- function(mapping = NULL, data = NULL,
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         params = list(
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             na.rm = na.rm,
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             ...
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-        )
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+        ),
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+        check.aes = FALSE
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     )
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 }
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... ...
@@ -67,7 +67,8 @@ geom_segment2 <- function(mapping = NULL, data = NULL,
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             lineend = lineend,
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             na.rm = na.rm,
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             ...
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-        )
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+        ),
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+        check.aes = FALSE
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     )
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 }
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... ...
@@ -97,7 +97,8 @@ stat_stripText <- function(mapping=NULL, data=NULL,
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                       barextend=barextend,
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                       na.rm=na.rm,
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                       parse=parse,
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-                      ...)
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+                      ...),
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+          check.aes = FALSE
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           )
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103 104
 }
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@@ -132,7 +133,8 @@ stat_stripBar <- function(mapping=NULL, data=NULL,
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                       align=align,
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                       barextend=barextend,
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                       na.rm=na.rm,
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-                      ...)
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+                      ...),
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+          check.aes = FALSE
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           )
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138 140
 }
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@@ -30,7 +30,8 @@ geom_taxalink <- function(taxa1, taxa2, curvature=0.5, ...) {
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                         taxa2 = taxa2,
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                         curvature = curvature,
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                         na.rm = na.rm,
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-                        ...)
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+                        ...),
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+          check.aes = FALSE
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           )
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 }
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... ...
@@ -22,7 +22,8 @@
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 ##' \link[ggplot2]{geom_text}
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 ##' @author Guangchuang Yu
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 geom_text2 <- function(mapping = NULL, data = NULL,
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-                       position = "identity", parse = FALSE, na.rm=TRUE, show.legend = NA, inherit.aes = TRUE,
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+                       position = "identity", parse = FALSE, na.rm=TRUE, show.legend = NA,
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+                       inherit.aes = TRUE,
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                        ..., nudge_x = 0, nudge_y = 0, check_overlap = FALSE) {
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28 29
     if (!missing(nudge_x) || !missing(nudge_y)) {
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@@ -53,7 +54,8 @@ geom_text2 <- function(mapping = NULL, data = NULL,
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           check_overlap = check_overlap,
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           na.rm = na.rm,
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           ...
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-        )
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+        ),
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+        check.aes = FALSE
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     )
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 }
59 61
 
... ...
@@ -91,7 +91,8 @@ geom_tiplab2 <- function(mapping=NULL, hjust=0, ...) {
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 geom_tipsegment <- function(mapping=NULL, data=NULL,
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                             geom=GeomSegmentGGtree, position = "identity",
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                             offset,  ...,
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-                            show.legend=NA, inherit.aes=FALSE, na.rm=TRUE) {
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+                            show.legend=NA, inherit.aes=FALSE,
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+                            na.rm=TRUE) {
95 96
 
96 97
     default_aes <- aes_(x=~x, y=~y)
97 98
     if (is.null(mapping)) {
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@@ -109,7 +110,8 @@ geom_tipsegment <- function(mapping=NULL, data=NULL,
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           inherit.aes = inherit.aes,
110 111
           params = list(offset = offset,
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                         na.rm = na.rm,
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-                        ...)
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+                        ...),
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+          check.aes = FALSE
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           )
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 }
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@@ -46,7 +46,8 @@ stat_tree <- function(mapping=NULL, data=NULL, geom="segment", position="identit
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                    params=list(layout = layout,
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                                lineend = lineend,
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                                na.rm = na.rm,
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-                          ...)
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+                               ...),
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+                   check.aes = FALSE
50 51
                    ),
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              layer(data=data,
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                    mapping=mapping,
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@@ -58,7 +59,8 @@ stat_tree <- function(mapping=NULL, data=NULL, geom="segment", position="identit
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                    params=list(layout = layout,
59 60
                                lineend = lineend,
60 61
                                na.rm = na.rm,
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-                               ...)
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+                               ...),
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+                   check.aes = FALSE
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                    )
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              )
64 66
     } else if (layout %in% c("slanted", "radial", "unrooted")) {
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@@ -72,7 +74,8 @@ stat_tree <- function(mapping=NULL, data=NULL, geom="segment", position="identit
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               params=list(layout = layout,
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                           lineend = lineend,
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                           na.rm = na.rm,
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-                          ...)
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+                          ...),
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+              check.aes = FALSE
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               )
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     }
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 }
... ...
@@ -21,7 +21,7 @@
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 ##' @importFrom ggplot2 ylab
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 ##' @importFrom ggplot2 annotate
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 ##' @importFrom ggplot2 scale_x_reverse
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-##' @importFrom ggplot2 scale_y_continuous
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+##' @importFrom ggplot2 ylim
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 ##' @importFrom ggplot2 coord_flip
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 ##' @importFrom ggplot2 coord_polar
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 ##' @export
... ...
@@ -86,7 +86,7 @@ ggtree <- function(tr,
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         p <- layout_circular(p)
87 87
         ## refer to: https://github.com/GuangchuangYu/ggtree/issues/6
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         ## and also have some space for tree scale (legend)
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-        p <- p + scale_y_continuous(limits=c(0, max(p$data$y)+1))
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+        p <- p + ylim(0, NA) 
90 90
     } else if (layout == "fan") {
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         p <- layout_fan(p, open.angle)
92 92
     }
... ...
@@ -74,9 +74,9 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color=
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     dd$width <- width
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76 76
     if (is.null(color)) {
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-        p2 <- p + geom_tile(data=dd, aes(x, y, fill=value, width=width), inherit.aes=FALSE)
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+        p2 <- p + geom_tile(data=dd, aes(x, y, fill=value), width=width, inherit.aes=FALSE)
78 78
     } else {
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-        p2 <- p + geom_tile(data=dd, aes(x, y, fill=value, width=width), color=color, inherit.aes=FALSE)
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+        p2 <- p + geom_tile(data=dd, aes(x, y, fill=value), width=width, color=color, inherit.aes=FALSE)
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     }
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     if (is(dd$value,"numeric")) {
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         p2 <- p2 + scale_fill_gradient(low=low, high=high, na.value="white")
... ...
@@ -12,7 +12,7 @@
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 ##' @return tree view with insets
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 ##' @export
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 ##' @author Guangchuang Yu
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-inset <- function(tree_view, insets, width=0.05, height=0.05, hjust=0, vjust=0, x="node") {
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+inset <- function(tree_view, insets, width=0.1, height=0.1, hjust=0, vjust=0, x="node") {
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     df <- tree_view$data[as.numeric(names(insets)),]
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     x <- match.arg(x, c("node", "branch", "edge"))
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... ...
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 ##' @param treeview tree view
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 ##' @param angle angle
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 ##' @return updated tree view
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+##' @importFrom ggplot2 scale_y_continuous
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 ##' @export
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 ##' @author Guangchuang Yu
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 open_tree <- function(treeview, angle) {
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@@ -36,7 +37,7 @@ open_tree <- function(treeview, angle) {
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     N <- nrow(p$data)
37 38
     idx <- match(1:N, order(p$data$y))
38 39
     NN <- N *(1+angle/(360-angle))
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-    angle <- 360/(3+NN) * (1:N+1)
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+    angle <- 360/(2+NN) * (1:N+1)
40 41
     angle <- angle[idx]
41 42
     p$data$angle <- angle
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     return(p)
... ...
@@ -558,15 +558,7 @@ as.data.frame.phylo_ <- function(x, layout="rectangular",
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     res <- calculate_branch_mid(res)
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560 560
     ## ## angle for all layout, if 'rectangular', user use coord_polar, can still use angle
561
-    ## ## if (layout == "circular") {
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-    ## idx <- match(1:N, order(res$y))
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-    ## ## angle <- -360/(3+N) * (1:N+1)
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-    ## angle <- 360/(3+N) * (1:N+1)
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-    ## angle <- angle[idx]
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-    ## ## res$angle <- angle + 90
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-    ## res$angle <- angle
568
-    ## } 
569
-    res$angle <- 360/(diff(range(res$y)) + 1) * res$y
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+    res <- calculate_angle(res)
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     return(res)
571 563
 }
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... ...
@@ -692,3 +684,9 @@ fortify.phyloseq <- function(model, data, layout="rectangular",
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 ##     ggplot(df) + geom_tree()
693 685
 
694 686
 ## }
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+
688
+
689
+calculate_angle <- function(data) {
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+    data$angle <- 360/(diff(range(data$y)) + 1) * data$y
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+    return(data)
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+}
... ...
@@ -8,7 +8,6 @@
8 8
 ##' @importFrom ggplot2 theme_bw
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 ##' @importFrom ggplot2 theme
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 ##' @importFrom ggplot2 element_blank
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-##' @importFrom ggplot2 %+replace%
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 ##' @importFrom ggplot2 xlab
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 ##' @importFrom ggplot2 ylab
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 ##' @export
... ...
@@ -21,12 +20,12 @@
21 20
 theme_tree <- function(bgcolor="white", fgcolor="black", ...) {
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     list(xlab(NULL),
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          ylab(NULL),
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-	 theme_tree2_internal() %+replace%
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-            theme(panel.background=element_rect(fill=bgcolor, colour=bgcolor),
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-            axis.line.x = element_blank(),
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-            axis.text.x = element_blank(),
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-            axis.ticks.x = element_blank(),
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-            ...)
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+	 theme_tree2_internal() + 
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+         theme(panel.background=element_rect(fill=bgcolor, colour=bgcolor),
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+               axis.line.x = element_blank(),
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+               axis.text.x = element_blank(),
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+               axis.ticks.x = element_blank(),
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+               ...)
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 	 )
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 }
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@@ -41,7 +40,6 @@ theme_tree <- function(bgcolor="white", fgcolor="black", ...) {
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 ##' @importFrom ggplot2 theme
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 ##' @importFrom ggplot2 element_blank
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 ##' @importFrom ggplot2 element_line
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-##' @importFrom ggplot2 %+replace%
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 ##' @importFrom ggplot2 element_rect
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 ##' @export
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 ##' @return updated ggplot object with new theme
... ...
@@ -65,18 +63,18 @@ theme_tree2_internal <- function(bgcolor="white", fgcolor="black",
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                                  axis.line.y=element_blank(),
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                                  axis.ticks.y=element_blank(),
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                                  axis.text.y=element_blank(),...) {
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-    theme_bw() %+replace%
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-    theme(legend.position=legend.position,
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-          panel.grid.minor=panel.grid.minor,
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-          panel.grid.major=panel.grid.major,
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-          panel.background=element_rect(fill=bgcolor, colour=bgcolor),
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-          panel.border=panel.border,
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-          ## axis.line=element_line(color=fgcolor),
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-          axis.line.x=element_line(color=fgcolor),
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-          axis.line.y=axis.line.y,
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-          axis.ticks.y=axis.ticks.y,
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-          axis.text.y=axis.text.y,
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-          ...)
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+    theme_bw() + 
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+        theme(legend.position=legend.position,
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+              panel.grid.minor=panel.grid.minor,
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+              panel.grid.major=panel.grid.major,
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+              panel.background=element_rect(fill=bgcolor, colour=bgcolor),
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+              panel.border=panel.border,
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+              ## axis.line=element_line(color=fgcolor),
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+              axis.line.x=element_line(color=fgcolor),
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+              axis.line.y=axis.line.y,
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+              axis.ticks.y=axis.ticks.y,
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+              axis.text.y=axis.text.y,
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+              ...)
80 78
 }
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82 80
 ##' transparent background theme
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@@ -1,9 +1,9 @@
1 1
 ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
2 2
 ===========================================================================================================================
3 3
 
4
-[![releaseVersion](https://img.shields.io/badge/release%20version-1.4.20-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.5.14-green.svg?style=flat)](https://github.com/GuangchuangYu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![total](https://img.shields.io/badge/downloads-14686/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
4
+[![releaseVersion](https://img.shields.io/badge/release%20version-1.4.20-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.5.15-green.svg?style=flat)](https://github.com/GuangchuangYu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![total](https://img.shields.io/badge/downloads-14686/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
5 5
 
6
-[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2016--10--05-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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+[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2016--10--07-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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8 8
 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-green.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html)
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... ...
@@ -4,7 +4,7 @@
4 4
 \alias{inset}
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 \title{inset}
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 \usage{
7
-inset(tree_view, insets, width = 0.05, height = 0.05, hjust = 0,
7
+inset(tree_view, insets, width = 0.1, height = 0.1, hjust = 0,
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   vjust = 0, x = "node")
9 9
 }
10 10
 \arguments{
... ...
@@ -112,7 +112,7 @@ inset(p, bars)
112 112
 The sizes of the insets can be ajusted by the paramter *width* and *height*.
113 113
 
114 114
 ```{r}
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-inset(p, bars, width=.03, height=.06)
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+inset(p, bars, width=.06, height=.1)
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 ```
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 Users can set the color via the parameter *color*. The *x* position can be one of 'node' or 'branch' and can be adjusted by the parameter *hjust* and *vjust* for horizontal and vertical adjustment respecitvely.
... ...
@@ -121,7 +121,7 @@ Users can set the color via the parameter *color*. The *x* position can be one o
121 121
 ```{r}
122 122
 bars2 <- nodebar(dat, cols=1:4, position='dodge',
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                  color=c(a='blue', b='red', c='green', d='cyan'))
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-p2 <- inset(p, bars2, x='branch', width=.03, vjust=-.3)
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+p2 <- inset(p, bars2, x='branch', width=.06, vjust=-.3)
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 print(p2)
126 126
 ```
127 127
 
... ...
@@ -157,7 +157,7 @@ bx <- lapply(d, function(y) {
157 157
     ggplot(dd, aes(x=1, y=y))+geom_boxplot() + ylim(ylim) + theme_inset()
158 158
 })
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 names(bx) <- 1:15
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-inset(p, bx, width=.03, height=.1, hjust=-.05)
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+inset(p, bx, width=.06, height=.2, hjust=-.05)
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 ```
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163 163
 
... ...
@@ -167,7 +167,7 @@ After annotating with insets, users can further annotate the tree with another l
167 167
 p2 <- inset(p, bars2, x='branch', width=.03, vjust=-.4)
168 168
 p2 <- inset(p2, pies, x='branch', vjust=.4)
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 bx2 <- lapply(bx, function(g) g+coord_flip())
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-inset(p2, bx2, width=.2, height=.03, vjust=.04, hjust=p2$data$x[1:15]-4) + xlim(NA, 4.5)
170
+inset(p2, bx2, width=.4, height=.06, vjust=.04, hjust=p2$data$x[1:15]-4) + xlim(NA, 4.5)
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 ```
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173 173
 ## Annotate with image files
... ...
@@ -141,7 +141,7 @@ ggtree(chiroptera, aes(color=group), layout='circular') + geom_tiplab(size=1, ae
141 141
 
142 142
 In this example, we first build a tree based on the iris data, then grouping the tree based on different spacies.
143 143
 
144
-```{r fig.width=20, fig.height=20, fig.align="center", warning=FALSE}
144
+#```{r fig.width=20, fig.height=20, fig.align="center", warning=FALSE}
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 data(iris)
146 146
 rn <- paste0(iris[,5], "_", 1:150)
147 147
 rownames(iris) <- rn
... ...
@@ -157,7 +157,7 @@ ggtree(tree_iris, aes(color=group)) +
157 157
     scale_color_manual(values=cols, breaks=1:3,
158 158
                        labels=c("Setosa", "Versicolor", "Virginica")) +
159 159
     theme(legend.position="right")
160
-```		
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+#```		
161 161
 -->
162 162
 	
163 163