1. ggtree
  2. R
  3. ape.R
Browse code

clean up code

guangchuang yu authored on 13/12/2017 14:33:32
Showing 1 changed files
R/ape.R
History View file @ eb57da3e
1 1 
deleted file mode 100644
... ... 
@@ -1,15 +0,0 @@
1 
-##' merge phylo and output of boot.phylo to 'apeBootstrap' object
2 
-##'
3 
-##'
4 
-##' @title apeBoot
5 
-##' @param phylo phylo
6 
-##' @param boot bootstrap values
7 
-##' @return an instance of 'apeBootstrap'
8 
-##' @importFrom treeio as.treedata
9 
-##' @export
10 
-##' @author Guangchuang Yu
11 
-apeBoot <- function(phylo, boot) {
12 
-    message("this function was deprecated, please use treeio::as.treedata")
13 
-    as.treedata(phylo, boot)
14 
-}
15 
-
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/ape.R
History View file @ 13af7bc0
... ... 
@@ -1,31 +1,3 @@
1 
-
2 
-## ##' @export
3 
-## ape::read.tree
4 
-
5 
-
6 
-## ##' generate random tree
7 
-## ##' @export
8 
-## ##' @rdname rtree
9 
-## ##' @param n number of tips in the tree
10 
-## ##' @param rooted logcial
11 
-## ##' @param tip.label tip label
12 
-## ##' @param br one of the following: (i) an R function used to generate the
13 
-## ##'           branch lengths ('rtree'; use 'NULL' to simulate only a
14 
-## ##'           topology), or the coalescence times ('rcoal'); (ii) a
15 
-## ##'           character to simulate a genuine coalescent tree for 'rcoal'
16 
-## ##'           (the default); or (iii) a numeric vector for the branch
17 
-## ##'           lengths or the coalescence times.
18 
-## ##' @param ... additional parameters to be passed to 'br'
19 
-## ##' @source
20 
-## ##' This is just the imported function
21 
-## ##' from the ape package. The documentation you should
22 
-## ##' read for the rtree function can be found here: \link[ape]{rtree}
23 
-## ##'
24 
-## ##' @seealso
25 
-## ##' \link[ape]{rtree}
26 
-## rtree <- ape::rtree
27 
-
28 
-
29 1 
 ##' merge phylo and output of boot.phylo to 'apeBootstrap' object
30 2 
 ##'
31 3 
 ##'
... ... 
@@ -41,49 +13,3 @@ apeBoot <- function(phylo, boot) {
41 13 
     as.treedata(phylo, boot)
42 14 
 }
43 15
44 
-## apeBoot <- function(phylo, boot) {
45 
-##     ## phylo is a phylo object
46 
-##     ## boot is output from boot.phylo
47 
-##     new("apeBootstrap",
48 
-##         phylo=phylo,
49 
-##         bootstrap=data.frame(node=(1:Nnode(phylo)) + Ntip(phylo), bootstrap=boot)
50 
-##         )
51 
-## }
52 
-
53 
-
54 
-## ##' @rdname show-methods
55 
-## ##' @importFrom ape print.phylo
56 
-## ##' @exportMethod show
57 
-## setMethod("show", signature(object = "apeBootstrap"),
58 
-##           function(object) {
59 
-##               cat("'apeBoot' S4 object that stored bootstrap value generated by 'ape::boot.phylo'", ".\n\n")
60 
-##               cat("...@ tree: ")
61 
-##               print.phylo(get.tree(object))
62 
-##           })
63 
-
64 
-
65 
-
66 
-
67 
-## ##' @rdname groupClade-methods
68 
-## ##' @exportMethod groupClade
69 
-## setMethod("groupClade", signature(object="apeBootstrap"),
70 
-##           function(object, node, group_name="group") {
71 
-##               groupClade_(object, node, group_name)
72 
-##           })
73 
-
74 
-## ##' @rdname scale_color-methods
75 
-## ##' @exportMethod scale_color
76 
-## setMethod("scale_color", signature(object="apeBootstrap"),
77 
-##           function(object, by="bootstrap", ...) {
78 
-##               scale_color_(object, by, ...)
79 
-##           })
80 
-
81 
-
82 
-## ##' @rdname get.fields-methods
83 
-## ##' @exportMethod get.fields
84 
-## setMethod("get.fields", signature(object="apeBootstrap"),
85 
-##           function(object, ...) {
86 
-##               get.fields.tree(object)
87 
-##           }
88 
-##           )
89 
-
Browse code

depends treeio

GuangchuangYu authored on 20/12/2016 16:39:07
Showing 1 changed files
R/ape.R
History View file @ 817c093d
... ... 
@@ -1,29 +1,29 @@
1 1
2 
-##' @export
3 
-ape::read.tree
2 
+## ##' @export
3 
+## ape::read.tree
4 4
5 5
6 
-##' generate random tree
7 
-##' @export
8 
-##' @rdname rtree
9 
-##' @param n number of tips in the tree
10 
-##' @param rooted logcial
11 
-##' @param tip.label tip label
12 
-##' @param br one of the following: (i) an R function used to generate the
13 
-##'           branch lengths ('rtree'; use 'NULL' to simulate only a
14 
-##'           topology), or the coalescence times ('rcoal'); (ii) a
15 
-##'           character to simulate a genuine coalescent tree for 'rcoal'
16 
-##'           (the default); or (iii) a numeric vector for the branch
17 
-##'           lengths or the coalescence times.
18 
-##' @param ... additional parameters to be passed to 'br'
19 
-##' @source
20 
-##' This is just the imported function
21 
-##' from the ape package. The documentation you should
22 
-##' read for the rtree function can be found here: \link[ape]{rtree}
23 
-##'
24 
-##' @seealso
25 
-##' \link[ape]{rtree}
26 
-rtree <- ape::rtree
6 
+## ##' generate random tree
7 
+## ##' @export
8 
+## ##' @rdname rtree
9 
+## ##' @param n number of tips in the tree
10 
+## ##' @param rooted logcial
11 
+## ##' @param tip.label tip label
12 
+## ##' @param br one of the following: (i) an R function used to generate the
13 
+## ##'           branch lengths ('rtree'; use 'NULL' to simulate only a
14 
+## ##'           topology), or the coalescence times ('rcoal'); (ii) a
15 
+## ##'           character to simulate a genuine coalescent tree for 'rcoal'
16 
+## ##'           (the default); or (iii) a numeric vector for the branch
17 
+## ##'           lengths or the coalescence times.
18 
+## ##' @param ... additional parameters to be passed to 'br'
19 
+## ##' @source
20 
+## ##' This is just the imported function
21 
+## ##' from the ape package. The documentation you should
22 
+## ##' read for the rtree function can be found here: \link[ape]{rtree}
23 
+## ##'
24 
+## ##' @seealso
25 
+## ##' \link[ape]{rtree}
26 
+## rtree <- ape::rtree
27 27
28 28
29 29 
 ##' merge phylo and output of boot.phylo to 'apeBootstrap' object
... ... 
@@ -33,51 +33,57 @@ rtree <- ape::rtree
33 33 
 ##' @param phylo phylo
34 34 
 ##' @param boot bootstrap values
35 35 
 ##' @return an instance of 'apeBootstrap'
36 
+##' @importFrom treeio as.treedata
36 37 
 ##' @export
37 38 
 ##' @author Guangchuang Yu
38 39 
 apeBoot <- function(phylo, boot) {
39 
-    ## phylo is a phylo object
40 
-    ## boot is output from boot.phylo
41 
-    new("apeBootstrap",
42 
-        phylo=phylo,
43 
-        bootstrap=data.frame(node=(1:Nnode(phylo)) + Ntip(phylo), bootstrap=boot)
44 
-        )
40 
+    message("this function was deprecated, please use treeio::as.treedata")
41 
+    as.treedata(phylo, boot)
45 42 
 }
46 43
44 
+## apeBoot <- function(phylo, boot) {
45 
+##     ## phylo is a phylo object
46 
+##     ## boot is output from boot.phylo
47 
+##     new("apeBootstrap",
48 
+##         phylo=phylo,
49 
+##         bootstrap=data.frame(node=(1:Nnode(phylo)) + Ntip(phylo), bootstrap=boot)
50 
+##         )
51 
+## }
52 
+
47 53
48 
-##' @rdname show-methods
49 
-##' @importFrom ape print.phylo
50 
-##' @exportMethod show
51 
-setMethod("show", signature(object = "apeBootstrap"),
52 
-          function(object) {
53 
-              cat("'apeBoot' S4 object that stored bootstrap value generated by 'ape::boot.phylo'", ".\n\n")
54 
-              cat("...@ tree: ")
55 
-              print.phylo(get.tree(object))
56 
-          })
54 
+## ##' @rdname show-methods
55 
+## ##' @importFrom ape print.phylo
56 
+## ##' @exportMethod show
57 
+## setMethod("show", signature(object = "apeBootstrap"),
58 
+##           function(object) {
59 
+##               cat("'apeBoot' S4 object that stored bootstrap value generated by 'ape::boot.phylo'", ".\n\n")
60 
+##               cat("...@ tree: ")
61 
+##               print.phylo(get.tree(object))
62 
+##           })
57 63
58 64
59 65
60 66
61 
-##' @rdname groupClade-methods
62 
-##' @exportMethod groupClade
63 
-setMethod("groupClade", signature(object="apeBootstrap"),
64 
-          function(object, node, group_name="group") {
65 
-              groupClade_(object, node, group_name)
66 
-          })
67 
+## ##' @rdname groupClade-methods
68 
+## ##' @exportMethod groupClade
69 
+## setMethod("groupClade", signature(object="apeBootstrap"),
70 
+##           function(object, node, group_name="group") {
71 
+##               groupClade_(object, node, group_name)
72 
+##           })
67 73
68 
-##' @rdname scale_color-methods
69 
-##' @exportMethod scale_color
70 
-setMethod("scale_color", signature(object="apeBootstrap"),
71 
-          function(object, by="bootstrap", ...) {
72 
-              scale_color_(object, by, ...)
73 
-          })
74 
+## ##' @rdname scale_color-methods
75 
+## ##' @exportMethod scale_color
76 
+## setMethod("scale_color", signature(object="apeBootstrap"),
77 
+##           function(object, by="bootstrap", ...) {
78 
+##               scale_color_(object, by, ...)
79 
+##           })
74 80
75 81
76 
-##' @rdname get.fields-methods
77 
-##' @exportMethod get.fields
78 
-setMethod("get.fields", signature(object="apeBootstrap"),
79 
-          function(object, ...) {
80 
-              get.fields.tree(object)
81 
-          }
82 
-          )
82 
+## ##' @rdname get.fields-methods
83 
+## ##' @exportMethod get.fields
84 
+## setMethod("get.fields", signature(object="apeBootstrap"),
85 
+##           function(object, ...) {
86 
+##               get.fields.tree(object)
87 
+##           }
88 
+##           )
83 89
Browse code

fixed drop.tip issues

guangchuang yu authored on 11/11/2016 05:33:47
Showing 1 changed files
R/ape.R
History View file @ 0b9c272f
... ... 
@@ -28,12 +28,11 @@ rtree <- ape::rtree
28 28
29 29 
 ##' merge phylo and output of boot.phylo to 'apeBootstrap' object
30 30 
 ##'
31 
-##'
31 
+##'
32 32 
 ##' @title apeBoot
33 33 
 ##' @param phylo phylo
34 34 
 ##' @param boot bootstrap values
35 35 
 ##' @return an instance of 'apeBootstrap'
36 
-##' @importFrom ape Nnode
37 36 
 ##' @export
38 37 
 ##' @author Guangchuang Yu
39 38 
 apeBoot <- function(phylo, boot) {
... ... 
@@ -53,7 +52,7 @@ setMethod("show", signature(object = "apeBootstrap"),
53 52 
           function(object) {
54 53 
               cat("'apeBoot' S4 object that stored bootstrap value generated by 'ape::boot.phylo'", ".\n\n")
55 54 
               cat("...@ tree: ")
56 
-              print.phylo(get.tree(object))
55 
+              print.phylo(get.tree(object))
57 56 
           })
58 57
59 58
Browse code

update citation info

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@118925 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 24/06/2016 06:22:28
Showing 1 changed files
R/ape.R
History View file @ 13e3fd30
... ... 
@@ -1,24 +1,6 @@
1 
-##' read newick tree
1 
+
2 2 
 ##' @export
3 
-##' @rdname read.tree
4 
-##' @param file file name
5 
-##' @param text alternatively, using newick text
6 
-##' @param tree.names if read several trees, specify their names
7 
-##' @param skip number of lines of the input file to skip
8 
-##' @param comment.char a single character,
9 
-##'                     the remaining of the line after this character is ignored.
10 
-##' @param keep.multi if 'TRUE' and 'tree.names = NULL'
11 
-##'                   then single trees are returned in 'multiPhylo' format
12 
-##'                   with any name that is present. Default is 'FALSE'
13 
-##' @param ... further arguments to be passed to 'scan()'.
14 
-##' @source
15 
-##' This is just the imported function
16 
-##' from the ape package. The documentation you should
17 
-##' read for the read.tree function can be found here: \link[ape]{read.tree}
18 
-##'
19 
-##' @seealso
20 
-##' \link[ape]{read.tree}
21 
-read.tree <- ape::read.tree
3 
+ape::read.tree
22 4
23 5
24 6 
 ##' generate random tree
Browse code

support phylip format

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@112578 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 15/01/2016 04:55:05
Showing 1 changed files
R/ape.R
History View file @ 6f076280
... ... 
@@ -92,17 +92,6 @@ setMethod("scale_color", signature(object="apeBootstrap"),
92 92 
           })
93 93
94 94
95 
-
96 
-
97 
-##' @rdname get.tree-methods
98 
-##' @exportMethod get.tree
99 
-setMethod("get.tree", signature(object="apeBootstrap"),
100 
-          function(object,...) {
101 
-              object@phylo
102 
-          }
103 
-          )
104 
-
105 
-
106 95 
 ##' @rdname get.fields-methods
107 96 
 ##' @exportMethod get.fields
108 97 
 setMethod("get.fields", signature(object="apeBootstrap"),
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/ape.R
History View file @ 245479db
... ... 
@@ -92,12 +92,6 @@ setMethod("scale_color", signature(object="apeBootstrap"),
92 92 
           })
93 93
94 94
95 
-##' @rdname gzoom-methods
96 
-##' @exportMethod gzoom
97 
-setMethod("gzoom", signature(object="apeBootstrap"),
98 
-          function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
99 
-              gzoom.phylo(get.tree(object), focus, subtree, widths)
100 
-          })
101 95
102 96
103 97 
 ##' @rdname get.tree-methods
Browse code

lots updates

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@111813 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 22/12/2015 04:08:02
Showing 1 changed files
R/ape.R
History View file @ f1f0d8d2
... ... 
@@ -43,3 +43,77 @@ read.tree <- ape::read.tree
43 43 
 ##' \link[ape]{rtree}
44 44 
 rtree <- ape::rtree
45 45
46 
+
47 
+##' merge phylo and output of boot.phylo to 'apeBootstrap' object
48 
+##'
49 
+##'
50 
+##' @title apeBoot
51 
+##' @param phylo phylo
52 
+##' @param boot bootstrap values
53 
+##' @return an instance of 'apeBootstrap'
54 
+##' @importFrom ape Nnode
55 
+##' @export
56 
+##' @author Guangchuang Yu
57 
+apeBoot <- function(phylo, boot) {
58 
+    ## phylo is a phylo object
59 
+    ## boot is output from boot.phylo
60 
+    new("apeBootstrap",
61 
+        phylo=phylo,
62 
+        bootstrap=data.frame(node=(1:Nnode(phylo)) + Ntip(phylo), bootstrap=boot)
63 
+        )
64 
+}
65 
+
66 
+
67 
+##' @rdname show-methods
68 
+##' @importFrom ape print.phylo
69 
+##' @exportMethod show
70 
+setMethod("show", signature(object = "apeBootstrap"),
71 
+          function(object) {
72 
+              cat("'apeBoot' S4 object that stored bootstrap value generated by 'ape::boot.phylo'", ".\n\n")
73 
+              cat("...@ tree: ")
74 
+              print.phylo(get.tree(object))
75 
+          })
76 
+
77 
+
78 
+
79 
+
80 
+##' @rdname groupClade-methods
81 
+##' @exportMethod groupClade
82 
+setMethod("groupClade", signature(object="apeBootstrap"),
83 
+          function(object, node, group_name="group") {
84 
+              groupClade_(object, node, group_name)
85 
+          })
86 
+
87 
+##' @rdname scale_color-methods
88 
+##' @exportMethod scale_color
89 
+setMethod("scale_color", signature(object="apeBootstrap"),
90 
+          function(object, by="bootstrap", ...) {
91 
+              scale_color_(object, by, ...)
92 
+          })
93 
+
94 
+
95 
+##' @rdname gzoom-methods
96 
+##' @exportMethod gzoom
97 
+setMethod("gzoom", signature(object="apeBootstrap"),
98 
+          function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
99 
+              gzoom.phylo(get.tree(object), focus, subtree, widths)
100 
+          })
101 
+
102 
+
103 
+##' @rdname get.tree-methods
104 
+##' @exportMethod get.tree
105 
+setMethod("get.tree", signature(object="apeBootstrap"),
106 
+          function(object,...) {
107 
+              object@phylo
108 
+          }
109 
+          )
110 
+
111 
+
112 
+##' @rdname get.fields-methods
113 
+##' @exportMethod get.fields
114 
+setMethod("get.fields", signature(object="apeBootstrap"),
115 
+          function(object, ...) {
116 
+              get.fields.tree(object)
117 
+          }
118 
+          )
119 
+
Browse code

upgrade to 0.99.6

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@98386 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 16/01/2015 02:39:28
Showing 1 changed files
R/ape.R
History View file @ b2b46fb5
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,45 @@
1 
+##' read newick tree
2 
+##' @export
3 
+##' @rdname read.tree
4 
+##' @param file file name
5 
+##' @param text alternatively, using newick text
6 
+##' @param tree.names if read several trees, specify their names
7 
+##' @param skip number of lines of the input file to skip
8 
+##' @param comment.char a single character,
9 
+##'                     the remaining of the line after this character is ignored.
10 
+##' @param keep.multi if 'TRUE' and 'tree.names = NULL'
11 
+##'                   then single trees are returned in 'multiPhylo' format
12 
+##'                   with any name that is present. Default is 'FALSE'
13 
+##' @param ... further arguments to be passed to 'scan()'.
14 
+##' @source
15 
+##' This is just the imported function
16 
+##' from the ape package. The documentation you should
17 
+##' read for the read.tree function can be found here: \link[ape]{read.tree}
18 
+##'
19 
+##' @seealso
20 
+##' \link[ape]{read.tree}
21 
+read.tree <- ape::read.tree
22 
+
23 
+
24 
+##' generate random tree
25 
+##' @export
26 
+##' @rdname rtree
27 
+##' @param n number of tips in the tree
28 
+##' @param rooted logcial
29 
+##' @param tip.label tip label
30 
+##' @param br one of the following: (i) an R function used to generate the
31 
+##'           branch lengths ('rtree'; use 'NULL' to simulate only a
32 
+##'           topology), or the coalescence times ('rcoal'); (ii) a
33 
+##'           character to simulate a genuine coalescent tree for 'rcoal'
34 
+##'           (the default); or (iii) a numeric vector for the branch
35 
+##'           lengths or the coalescence times.
36 
+##' @param ... additional parameters to be passed to 'br'
37 
+##' @source
38 
+##' This is just the imported function
39 
+##' from the ape package. The documentation you should
40 
+##' read for the rtree function can be found here: \link[ape]{rtree}
41 
+##'
42 
+##' @seealso
43 
+##' \link[ape]{rtree}
44 
+rtree <- ape::rtree
45 
+