1. ggtree
  2. R
  3. method-gzoom.R
Browse code

remove gzoom function

Guangchuang Yu authored on 08/08/2019 16:26:32
Showing 1 changed files
R/method-gzoom.R
History View file @ 4f72df86
1 1 
deleted file mode 100644
... ... 
@@ -1,89 +0,0 @@
1 
-##' plots simultaneously a whole phylogenetic tree and a portion of it.
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-##'
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-##'
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-##' @title gzoom
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-##' @param phy phylo object
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-##' @param focus selected tips
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-##' @param subtree logical
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-##' @param widths widths
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-##' @return a list of ggplot object
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-##' @importFrom ggplot2 xlim
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-##' @importFrom ggplot2 scale_color_manual
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-##' @author ygc
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-##' @examples
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-##' require(ape)
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-##' data(chiroptera)
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-##' gzoom(chiroptera, grep("Plecotus", chiroptera$tip.label))
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-gzoom.phylo <- function(phy, focus, subtree=FALSE, widths=c(.3, .7)) {
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-    if (is.character(focus)) {
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-        focus <- which(phy$tip.label %in% focus)
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-    }
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-
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-    group_name <- "focus"
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-    phy <- gfocus(phy, focus, group_name)
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-
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-    foc <- attr(phy, group_name)
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-    ## foc should +1 since the group index start from 0
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-    cols <- c("black", "red")[foc+1]
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-
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-    p1 <- ggtree(phy, colour=cols)
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-
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-    subtr <- drop.tip(phy, phy$tip.label[-focus],
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-                      subtree=subtree, rooted=TRUE)
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-
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-    p2 <- ggtree(subtr, colour="red") + geom_tiplab(hjust=-0.05)
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-    p2 <- p2 + xlim(0, max(p2$data$x)*1.2)
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-    multiplot(p1, p2, ncol=2, widths=widths)
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-
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-    invisible(list(p1=p1, p2=p2))
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-}
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-
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-gzoom.ggtree <- function(tree_view, focus, widths=c(.3, .7), xmax_adjust=0) {
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-    node <- MRCA(tree_view, focus[1], focus[2])
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-    if (length(focus) > 2) {
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-        for (i in 3:length(focus)) {
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-            node <- MRCA(tree_view, focus[i], node)
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-        }
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-    }
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-
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-    cpos <- get_clade_position(tree_view, node)
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-    p2 <- with(cpos, tree_view+
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-                     xlim(xmin, xmax+xmax_adjust)+
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-                     ylim(ymin, ymax))
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-    multiplot(tree_view, p2, ncol=2, widths=widths)
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-    invisible(list(p1=tree_view, p2=p2))
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-}
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-
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-##' @name gzoom
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-##' @title gzoom method
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-##' @rdname gzoom-methods
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-##' @exportMethod gzoom
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-##' @param xmax_adjust adjust xmax (xlim[2])
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-##' @aliases gzoom,ggtree-method
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-setMethod("gzoom", signature(object="ggtree"),
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-          function(object, focus, widths=c(.3, .7), xmax_adjust=0) {
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-              gzoom.ggtree(object, focus, widths, xmax_adjust)
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-          })
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-
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-
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-##' zoom selected subtree
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-##'
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-##'
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-##' @rdname gzoom-methods
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-##' @exportMethod gzoom
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-setMethod("gzoom", signature(object="treedata"),
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-          function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
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-              gzoom.phylo(get.tree(object), focus, subtree, widths)
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-          })
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-
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-
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-##' @rdname gzoom-methods
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-##' @exportMethod gzoom
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-setMethod("gzoom", signature(object="phylo"),
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-          function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
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-              gzoom.phylo(object, focus, subtree, widths)
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-          })
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-
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-
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-gfocus <- getFromNamespace("gfocus", "treeio")
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-
Browse code

rootnode parameter

Guangchuang Yu authored on 08/08/2019 11:04:10
Showing 1 changed files
R/method-gzoom.R
History View file @ 4d023b21
... ... 
@@ -26,12 +26,12 @@ gzoom.phylo <- function(phy, focus, subtree=FALSE, widths=c(.3, .7)) {
26 26 
     ## foc should +1 since the group index start from 0
27 27 
     cols <- c("black", "red")[foc+1]
28 28
29 
-    p1 <- ggtree(phy, color=cols)
29 
+    p1 <- ggtree(phy, colour=cols)
30 30
31 31 
     subtr <- drop.tip(phy, phy$tip.label[-focus],
32 32 
                       subtree=subtree, rooted=TRUE)
33 33
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-    p2 <- ggtree(subtr, color="red") + geom_tiplab(hjust=-0.05)
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+    p2 <- ggtree(subtr, colour="red") + geom_tiplab(hjust=-0.05)
35 35 
     p2 <- p2 + xlim(0, max(p2$data$x)*1.2)
36 36 
     multiplot(p1, p2, ncol=2, widths=widths)
37 37
Browse code

new MRCA methods

Guangchuang Yu authored on 10/01/2019 13:18:05
Showing 1 changed files
R/method-gzoom.R
History View file @ b6760093
... ... 
@@ -39,7 +39,13 @@ gzoom.phylo <- function(phy, focus, subtree=FALSE, widths=c(.3, .7)) {
39 39 
 }
40 40
41 41 
 gzoom.ggtree <- function(tree_view, focus, widths=c(.3, .7), xmax_adjust=0) {
42 
-    node <- MRCA(tree_view, focus)
42 
+    node <- MRCA(tree_view, focus[1], focus[2])
43 
+    if (length(focus) > 2) {
44 
+        for (i in 3:length(focus)) {
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+            node <- MRCA(tree_view, focus[i], node)
46 
+        }
47 
+    }
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+
43 49 
     cpos <- get_clade_position(tree_view, node)
44 50 
     p2 <- with(cpos, tree_view+
45 51 
                      xlim(xmin, xmax+xmax_adjust)+
Browse code

clean up code

guangchuang yu authored on 14/12/2017 08:47:21
Showing 1 changed files
R/method-gzoom.R
History View file @ 14ff9149
... ... 
@@ -60,31 +60,6 @@ setMethod("gzoom", signature(object="ggtree"),
60 60 
           })
61 61
62 62
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-## ##' @rdname gzoom-methods
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-## ##' @exportMethod gzoom
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-## setMethod("gzoom", signature(object="apeBootstrap"),
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-##           function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
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-##               gzoom.phylo(get.tree(object), focus, subtree, widths)
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-##           })
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-
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-
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-## ##' zoom selected subtree
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-## ##'
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-## ##'
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-## ##' @rdname gzoom-methods
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-## ##' @exportMethod gzoom
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-## setMethod("gzoom", signature(object="beast"),
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-##           function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
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-##               gzoom.phylo(get.tree(object), focus, subtree, widths)
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-##           })
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-
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-## ##' @rdname gzoom-methods
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-## ##' @exportMethod gzoom
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-## setMethod("gzoom", signature(object="codeml"),
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-##           function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
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-##               gzoom.phylo(get.tree(object), focus, subtree, widths)
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-##           })
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-
88 63 
 ##' zoom selected subtree
89 64 
 ##'
90 65 
 ##'
... ... 
@@ -96,14 +71,6 @@ setMethod("gzoom", signature(object="treedata"),
96 71 
           })
97 72
98 73
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-## ##' @rdname gzoom-methods
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-## ##' @exportMethod gzoom
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-## setMethod("gzoom", signature(object="paml_rst"),
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-##           function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
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-##               gzoom.phylo(get.tree(object), focus, subtree, widths)
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-##           })
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-
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-
107 74 
 ##' @rdname gzoom-methods
108 75 
 ##' @exportMethod gzoom
109 76 
 setMethod("gzoom", signature(object="phylo"),
... ... 
@@ -112,4 +79,5 @@ setMethod("gzoom", signature(object="phylo"),
112 79 
           })
113 80
114 81
115 
-gfocus <- treeio:::gfocus
82 
+gfocus <- getFromNamespace("gfocus", "treeio")
83 
+
Browse code

remove paml_rst, codeml_mlc, codeml and jplace fortify methods according to the change of treeio (v = 1.3.3)

guangchuang yu authored on 07/12/2017 07:21:58
Showing 1 changed files
R/method-gzoom.R
History View file @ 6be958c5
... ... 
@@ -78,12 +78,12 @@ setMethod("gzoom", signature(object="ggtree"),
78 78 
 ##               gzoom.phylo(get.tree(object), focus, subtree, widths)
79 79 
 ##           })
80 80
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-##' @rdname gzoom-methods
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-##' @exportMethod gzoom
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-setMethod("gzoom", signature(object="codeml"),
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-          function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
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-              gzoom.phylo(get.tree(object), focus, subtree, widths)
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-          })
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+## ##' @rdname gzoom-methods
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+## ##' @exportMethod gzoom
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+## setMethod("gzoom", signature(object="codeml"),
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+##           function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
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+##               gzoom.phylo(get.tree(object), focus, subtree, widths)
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+##           })
87 87
88 88 
 ##' zoom selected subtree
89 89 
 ##'
... ... 
@@ -96,12 +96,12 @@ setMethod("gzoom", signature(object="treedata"),
96 96 
           })
97 97
98 98
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-##' @rdname gzoom-methods
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-##' @exportMethod gzoom
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-setMethod("gzoom", signature(object="paml_rst"),
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-          function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
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-              gzoom.phylo(get.tree(object), focus, subtree, widths)
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-          })
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+## ##' @rdname gzoom-methods
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+## ##' @exportMethod gzoom
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+## setMethod("gzoom", signature(object="paml_rst"),
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+##           function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
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+##               gzoom.phylo(get.tree(object), focus, subtree, widths)
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+##           })
105 105
106 106
107 107 
 ##' @rdname gzoom-methods
Browse code

remove beast object support as read.beast output treedata object in treeio <2017-12-05, Tue>

guangchuang yu authored on 05/12/2017 11:05:11
Showing 1 changed files
R/method-gzoom.R
History View file @ 13af7bc0
... ... 
@@ -68,15 +68,15 @@ setMethod("gzoom", signature(object="ggtree"),
68 68 
 ##           })
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70 70
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-##' zoom selected subtree
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-##'
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-##'
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-##' @rdname gzoom-methods
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-##' @exportMethod gzoom
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-setMethod("gzoom", signature(object="beast"),
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-          function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
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-              gzoom.phylo(get.tree(object), focus, subtree, widths)
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-          })
71 
+## ##' zoom selected subtree
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+## ##'
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+## ##'
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+## ##' @rdname gzoom-methods
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+## ##' @exportMethod gzoom
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+## setMethod("gzoom", signature(object="beast"),
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+##           function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
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+##               gzoom.phylo(get.tree(object), focus, subtree, widths)
79 
+##           })
80 80
81 81 
 ##' @rdname gzoom-methods
82 82 
 ##' @exportMethod gzoom
... ... 
@@ -85,7 +85,9 @@ setMethod("gzoom", signature(object="codeml"),
85 85 
               gzoom.phylo(get.tree(object), focus, subtree, widths)
86 86 
           })
87 87
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-
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+##' zoom selected subtree
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+##'
90 
+##'
89 91 
 ##' @rdname gzoom-methods
90 92 
 ##' @exportMethod gzoom
91 93 
 setMethod("gzoom", signature(object="treedata"),
Browse code

remove apeBootstrap and raxml object support as they were removed from treeio

guangchuang yu authored on 28/02/2017 07:11:57
Showing 1 changed files
R/method-gzoom.R
History View file @ 69a22a72
... ... 
@@ -60,12 +60,12 @@ setMethod("gzoom", signature(object="ggtree"),
60 60 
           })
61 61
62 62
63 
-##' @rdname gzoom-methods
64 
-##' @exportMethod gzoom
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-setMethod("gzoom", signature(object="apeBootstrap"),
66 
-          function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
67 
-              gzoom.phylo(get.tree(object), focus, subtree, widths)
68 
-          })
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+## ##' @rdname gzoom-methods
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+## ##' @exportMethod gzoom
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+## setMethod("gzoom", signature(object="apeBootstrap"),
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+##           function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
67 
+##               gzoom.phylo(get.tree(object), focus, subtree, widths)
68 
+##           })
69 69
70 70
71 71 
 ##' zoom selected subtree
Browse code

move code to treeio

guangchuang yu authored on 21/12/2016 08:57:38
Showing 1 changed files
R/method-gzoom.R
History View file @ 1d7f426b
... ... 
@@ -53,6 +53,7 @@ gzoom.ggtree <- function(tree_view, focus, widths=c(.3, .7), xmax_adjust=0) {
53 53 
 ##' @rdname gzoom-methods
54 54 
 ##' @exportMethod gzoom
55 55 
 ##' @param xmax_adjust adjust xmax (xlim[2])
56 
+##' @aliases gzoom,ggtree-method
56 57 
 setMethod("gzoom", signature(object="ggtree"),
57 58 
           function(object, focus, widths=c(.3, .7), xmax_adjust=0) {
58 59 
               gzoom.ggtree(object, focus, widths, xmax_adjust)
Browse code

depends treeio

GuangchuangYu authored on 20/12/2016 16:39:07
Showing 1 changed files
R/method-gzoom.R
History View file @ 817c093d
... ... 
@@ -48,6 +48,8 @@ gzoom.ggtree <- function(tree_view, focus, widths=c(.3, .7), xmax_adjust=0) {
48 48 
     invisible(list(p1=tree_view, p2=p2))
49 49 
 }
50 50
51 
+##' @name gzoom
52 
+##' @title gzoom method
51 53 
 ##' @rdname gzoom-methods
52 54 
 ##' @exportMethod gzoom
53 55 
 ##' @param xmax_adjust adjust xmax (xlim[2])
... ... 
@@ -85,7 +87,7 @@ setMethod("gzoom", signature(object="codeml"),
85 87
86 88 
 ##' @rdname gzoom-methods
87 89 
 ##' @exportMethod gzoom
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-setMethod("gzoom", signature(object="nhx"),
90 
+setMethod("gzoom", signature(object="treedata"),
89 91 
           function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
90 92 
               gzoom.phylo(get.tree(object), focus, subtree, widths)
91 93 
           })
... ... 
@@ -105,3 +107,6 @@ setMethod("gzoom", signature(object="phylo"),
105 107 
           function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
106 108 
               gzoom.phylo(object, focus, subtree, widths)
107 109 
           })
110 
+
111 
+
112 
+gfocus <- treeio:::gfocus
Browse code

fixed R check

guangchuang yu authored on 06/12/2016 12:05:09
Showing 1 changed files
R/method-gzoom.R
History View file @ 9bd4fbab
... ... 
@@ -38,7 +38,7 @@ gzoom.phylo <- function(phy, focus, subtree=FALSE, widths=c(.3, .7)) {
38 38 
     invisible(list(p1=p1, p2=p2))
39 39 
 }
40 40
41 
-gzoom.ggplot <- function(tree_view, focus, widths=c(.3, .7), xmax_adjust=0) {
41 
+gzoom.ggtree <- function(tree_view, focus, widths=c(.3, .7), xmax_adjust=0) {
42 42 
     node <- MRCA(tree_view, focus)
43 43 
     cpos <- get_clade_position(tree_view, node)
44 44 
     p2 <- with(cpos, tree_view+
... ... 
@@ -51,9 +51,9 @@ gzoom.ggplot <- function(tree_view, focus, widths=c(.3, .7), xmax_adjust=0) {
51 51 
 ##' @rdname gzoom-methods
52 52 
 ##' @exportMethod gzoom
53 53 
 ##' @param xmax_adjust adjust xmax (xlim[2])
54 
-setMethod("gzoom", signature(object="gg"),
54 
+setMethod("gzoom", signature(object="ggtree"),
55 55 
           function(object, focus, widths=c(.3, .7), xmax_adjust=0) {
56 
-              gzoom.ggplot(object, focus, widths, xmax_adjust)
56 
+              gzoom.ggtree(object, focus, widths, xmax_adjust)
57 57 
           })
58 58
59 59
Browse code

fixed drop.tip issues

guangchuang yu authored on 11/11/2016 05:33:47
Showing 1 changed files
R/method-gzoom.R
History View file @ 0b9c272f
... ... 
@@ -1,6 +1,6 @@
1 
-##' plots simultaneously a whole phylogenetic tree and a portion of it.
1 
+##' plots simultaneously a whole phylogenetic tree and a portion of it.
2 
+##'
2 3 
 ##'
3 
-##'
4 4 
 ##' @title gzoom
5 5 
 ##' @param phy phylo object
6 6 
 ##' @param focus selected tips
... ... 
@@ -9,7 +9,6 @@
9 9 
 ##' @return a list of ggplot object
10 10 
 ##' @importFrom ggplot2 xlim
11 11 
 ##' @importFrom ggplot2 scale_color_manual
12 
-##' @importFrom ape drop.tip
13 12 
 ##' @author ygc
14 13 
 ##' @examples
15 14 
 ##' require(ape)
... ... 
@@ -28,14 +27,14 @@ gzoom.phylo <- function(phy, focus, subtree=FALSE, widths=c(.3, .7)) {
28 27 
     cols <- c("black", "red")[foc+1]
29 28
30 29 
     p1 <- ggtree(phy, color=cols)
31 
-
30 
+
32 31 
     subtr <- drop.tip(phy, phy$tip.label[-focus],
33 32 
                       subtree=subtree, rooted=TRUE)
34 
-
33 
+
35 34 
     p2 <- ggtree(subtr, color="red") + geom_tiplab(hjust=-0.05)
36 35 
     p2 <- p2 + xlim(0, max(p2$data$x)*1.2)
37 
-    multiplot(p1, p2, ncol=2, widths=widths)
38 
-
36 
+    multiplot(p1, p2, ncol=2, widths=widths)
37 
+
39 38 
     invisible(list(p1=p1, p2=p2))
40 39 
 }
41 40
... ... 
@@ -68,7 +67,7 @@ setMethod("gzoom", signature(object="apeBootstrap"),
68 67
69 68 
 ##' zoom selected subtree
70 69 
 ##'
71 
-##'
70 
+##'
72 71 
 ##' @rdname gzoom-methods
73 72 
 ##' @exportMethod gzoom
74 73 
 setMethod("gzoom", signature(object="beast"),
Browse code

new features

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@113679 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 16/02/2016 04:04:44
Showing 1 changed files
R/method-gzoom.R
History View file @ 90df068e
... ... 
@@ -10,7 +10,6 @@
10 10 
 ##' @importFrom ggplot2 xlim
11 11 
 ##' @importFrom ggplot2 scale_color_manual
12 12 
 ##' @importFrom ape drop.tip
13 
-##' @importFrom gridExtra grid.arrange
14 13 
 ##' @author ygc
15 14 
 ##' @examples
16 15 
 ##' require(ape)
... ... 
@@ -35,7 +34,7 @@ gzoom.phylo <- function(phy, focus, subtree=FALSE, widths=c(.3, .7)) {
35 34
36 35 
     p2 <- ggtree(subtr, color="red") + geom_tiplab(hjust=-0.05)
37 36 
     p2 <- p2 + xlim(0, max(p2$data$x)*1.2)
38 
-    grid.arrange(p1, p2, ncol=2, widths=widths)
37 
+    multiplot(p1, p2, ncol=2, widths=widths)
39 38
40 39 
     invisible(list(p1=p1, p2=p2))
41 40 
 }
... ... 
@@ -46,7 +45,7 @@ gzoom.ggplot <- function(tree_view, focus, widths=c(.3, .7), xmax_adjust=0) {
46 45 
     p2 <- with(cpos, tree_view+
47 46 
                      xlim(xmin, xmax+xmax_adjust)+
48 47 
                      ylim(ymin, ymax))
49 
-    grid.arrange(tree_view, p2, ncol=2, widths=widths)
48 
+    multiplot(tree_view, p2, ncol=2, widths=widths)
50 49 
     invisible(list(p1=tree_view, p2=p2))
51 50 
 }
52 51
Browse code

inset function and update vignette

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@112112 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 04/01/2016 09:56:10
Showing 1 changed files
R/method-gzoom.R
History View file @ 245479db
... ... 
@@ -1,3 +1,72 @@
1 
+##' plots simultaneously a whole phylogenetic tree and a portion of it.
2 
+##'
3 
+##'
4 
+##' @title gzoom
5 
+##' @param phy phylo object
6 
+##' @param focus selected tips
7 
+##' @param subtree logical
8 
+##' @param widths widths
9 
+##' @return a list of ggplot object
10 
+##' @importFrom ggplot2 xlim
11 
+##' @importFrom ggplot2 scale_color_manual
12 
+##' @importFrom ape drop.tip
13 
+##' @importFrom gridExtra grid.arrange
14 
+##' @author ygc
15 
+##' @examples
16 
+##' require(ape)
17 
+##' data(chiroptera)
18 
+##' gzoom(chiroptera, grep("Plecotus", chiroptera$tip.label))
19 
+gzoom.phylo <- function(phy, focus, subtree=FALSE, widths=c(.3, .7)) {
20 
+    if (is.character(focus)) {
21 
+        focus <- which(phy$tip.label %in% focus)
22 
+    }
23 
+
24 
+    group_name <- "focus"
25 
+    phy <- gfocus(phy, focus, group_name)
26 
+
27 
+    foc <- attr(phy, group_name)
28 
+    ## foc should +1 since the group index start from 0
29 
+    cols <- c("black", "red")[foc+1]
30 
+
31 
+    p1 <- ggtree(phy, color=cols)
32 
+
33 
+    subtr <- drop.tip(phy, phy$tip.label[-focus],
34 
+                      subtree=subtree, rooted=TRUE)
35 
+
36 
+    p2 <- ggtree(subtr, color="red") + geom_tiplab(hjust=-0.05)
37 
+    p2 <- p2 + xlim(0, max(p2$data$x)*1.2)
38 
+    grid.arrange(p1, p2, ncol=2, widths=widths)
39 
+
40 
+    invisible(list(p1=p1, p2=p2))
41 
+}
42 
+
43 
+gzoom.ggplot <- function(tree_view, focus, widths=c(.3, .7), xmax_adjust=0) {
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+    node <- MRCA(tree_view, focus)
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+    cpos <- get_clade_position(tree_view, node)
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+    p2 <- with(cpos, tree_view+
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+                     xlim(xmin, xmax+xmax_adjust)+
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+                     ylim(ymin, ymax))
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+    grid.arrange(tree_view, p2, ncol=2, widths=widths)
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+    invisible(list(p1=tree_view, p2=p2))
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+}
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+
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+##' @rdname gzoom-methods
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+##' @exportMethod gzoom
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+##' @param xmax_adjust adjust xmax (xlim[2])
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+setMethod("gzoom", signature(object="gg"),
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+          function(object, focus, widths=c(.3, .7), xmax_adjust=0) {
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+              gzoom.ggplot(object, focus, widths, xmax_adjust)
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+          })
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+
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+
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+##' @rdname gzoom-methods
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+##' @exportMethod gzoom
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+setMethod("gzoom", signature(object="apeBootstrap"),
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+          function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
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+              gzoom.phylo(get.tree(object), focus, subtree, widths)
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+          })
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+
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+
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 ##' zoom selected subtree
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 ##'
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 ##'
... ... 
@@ -8,6 +77,13 @@ setMethod("gzoom", signature(object="beast"),
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               gzoom.phylo(get.tree(object), focus, subtree, widths)
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           })
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+##' @rdname gzoom-methods
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+##' @exportMethod gzoom
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+setMethod("gzoom", signature(object="codeml"),
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+          function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
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+              gzoom.phylo(get.tree(object), focus, subtree, widths)
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+          })
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+
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 ##' @rdname gzoom-methods
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 ##' @exportMethod gzoom
Browse code

lots of new layers

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@111815 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 22/12/2015 04:13:13
Showing 1 changed files
R/method-gzoom.R
History View file @ 3e4b5998
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new file mode 100644
... ... 
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+##' zoom selected subtree
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+##'
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+##'
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+##' @rdname gzoom-methods
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+##' @exportMethod gzoom
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+setMethod("gzoom", signature(object="beast"),
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+          function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
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+              gzoom.phylo(get.tree(object), focus, subtree, widths)
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+          })
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+
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+
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+##' @rdname gzoom-methods
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+##' @exportMethod gzoom
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+setMethod("gzoom", signature(object="nhx"),
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+          function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
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+              gzoom.phylo(get.tree(object), focus, subtree, widths)
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+          })
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+
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+
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+##' @rdname gzoom-methods
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+##' @exportMethod gzoom
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+setMethod("gzoom", signature(object="paml_rst"),
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+          function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
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+              gzoom.phylo(get.tree(object), focus, subtree, widths)
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+          })
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+
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+
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+##' @rdname gzoom-methods
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+##' @exportMethod gzoom
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+setMethod("gzoom", signature(object="phylo"),
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+          function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
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+              gzoom.phylo(object, focus, subtree, widths)
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+          })