1. ggtree
  2. R
  3. method-show.R
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-show.R
History View file @ 6be958c5
1 1 
deleted file mode 100644
... ... 
@@ -1,175 +0,0 @@
1 
-## ##' @rdname show-methods
2 
-## ##' @importFrom ape print.phylo
3 
-## ##' @exportMethod show
4 
-## setMethod("show", signature(object = "beast"),
5 
-##           function(object) {
6 
-##               cat("'beast' S4 object that stored information of\n\t",
7 
-##                   paste0("'", object@file, "'.\n\n"))
8 
-##               cat("...@ tree: ")
9 
-##               print.phylo(get.tree(object))
10 
-##               cat("\nwith the following features available:\n")
11 
-##               print_fields(object)
12 
-##           })
13 
-
14 
-## ##' @rdname show-methods
15 
-## ##' @exportMethod show
16 
-## setMethod("show", signature(object = "codeml"),
17 
-##           function(object) {
18 
-##               cat("'codeml' S4 object that stored information of\n\t",
19 
-##                   paste0("'", object@rst@rstfile, "' and \n\t'",
20 
-##                          object@mlc@mlcfile, "'."),
21 
-##                   "\n\n")
22 
-##               cat("...@ tree:")
23 
-##               print.phylo(get.tree(object))
24 
-##               cat("\nwith the following features available:\n")
25 
-##               print_fields(object, len=4)
26 
-##           })
27 
-
28 
-## ##' @rdname show-methods
29 
-## ##' @exportMethod show
30 
-## setMethod("show", signature(object = "codeml_mlc"),
31 
-##           function(object) {
32 
-##               cat("'codeml_mlc' S4 object that stored information of\n\t",
33 
-##                   paste0("'", object@mlcfile, "'."),
34 
-##                   "\n\n")
35 
-
36 
-##               cat("...@ tree:")
37 
-##               print.phylo(get.tree(object))
38 
-
39 
-##               cat("\nwith the following features available:\n")
40 
-##               cat("\t", paste0("'",
41 
-##                                  paste(get.fields(object), collapse="',\t'"),
42 
-##                                  "'."),
43 
-##                   "\n")
44 
-##           }
45 
-##           )
46 
-
47 
-## ##' show method for \code{jplace} instance
48 
-## ##'
49 
-## ##'
50 
-## ##' @name show
51 
-## ##' @docType methods
52 
-## ##' @rdname show-methods
53 
-## ##'
54 
-## ##' @title show method
55 
-## ##' @param object one of \code{jplace}, \code{beast} object
56 
-## ##' @return print info
57 
-## ##' @importFrom methods show
58 
-## ##' @exportMethod show
59 
-## ##' @usage show(object)
60 
-## ##' @author Guangchuang Yu \url{http://ygc.name}
61 
-## ##' @examples
62 
-## ##' jp <- system.file("extdata", "sample.jplace", package="ggtree")
63 
-## ##' jp <- read.jplace(jp)
64 
-## ##' show(jp)
65 
-## setMethod("show", signature(object = "jplace"),
66 
-##           function(object) {
67 
-##               cat("'jplace' S4 object that stored information of\n\t",
68 
-##                   paste0("'", object@file, "'."),
69 
-##                   "\n\n")
70 
-
71 
-##               cat("...@ tree: ")
72 
-
73 
-##               phylo <- get.tree(object)
74 
-##               phylo$node.label <- NULL
75 
-##               phylo$tip.label %<>% gsub("\\@\\d+", "", .)
76 
-
77 
-##               print.phylo(phylo)
78 
-
79 
-##               cat("\nwith the following features availables:\n")
80 
-##               cat("\t", paste0("'",
81 
-##                                paste(get.fields(object), collapse="',\t'"),
82 
-##                                "'."),
83 
-##                   "\n")
84 
-##           }
85 
-##           )
86 
-
87 
-
88 
-## ##' @rdname show-methods
89 
-## ##' @exportMethod show
90 
-## setMethod("show", signature(object = "nhx"),
91 
-##           function(object) {
92 
-##               cat("'nhx' S4 object that stored information of\n\t",
93 
-##                   paste0("'", object@file, "'.\n\n"))
94 
-##               cat("...@ tree: ")
95 
-##               print.phylo(get.tree(object))
96 
-##               cat("\nwith the following features available:\n")
97 
-##               print_fields(object)
98 
-##           })
99 
-
100 
-
101 
-## ##' @rdname show-methods
102 
-## ##' @exportMethod show
103 
-## setMethod("show", signature(object = "phylip"),
104 
-##           function(object) {
105 
-##               cat("'phylip' S4 object that stored information of\n\t",
106 
-##                   paste0("'", object@file, "'.\n\n"))
107 
-##               cat("...@ tree: ")
108 
-##               print.phylo(get.tree(object))
109 
-##               msg <- paste0("\nwith sequence alignment available (", length(object@sequence),
110 
-##                             " sequences of length ", nchar(object@sequence)[1], ")\n")
111 
-##               cat(msg)
112 
-##           })
113 
-
114 
-## ##' @rdname show-methods
115 
-## ##' @exportMethod show
116 
-## setMethod("show", signature(object = "paml_rst"),
117 
-##           function(object) {
118 
-##               cat("'paml_rst' S4 object that stored information of\n\t",
119 
-##                   paste0("'", object@rstfile, "'.\n\n"))
120 
-##               ## if (length(object@tip.fasfile) != 0) {
121 
-##               ##     cat(paste0(" and \n\t'", object@tip.fasfile, "'.\n\n"))
122 
-##               ## } else {
123 
-##               ##     cat(".\n\n")
124 
-##               ## }
125 
-##               fields <- get.fields(object)
126 
-
127 
-##               if (nrow(object@marginal_subs) == 0) {
128 
-##                   fields <- fields[fields != "marginal_subs"]
129 
-##                   fields <- fields[fields != "marginal_AA_subs"]
130 
-##               }
131 
-##               if (nrow(object@joint_subs) == 0) {
132 
-##                   fields <- fields[fields != "joint_subs"]
133 
-##                   fields <- fields[fields != "joint_AA_subs"]
134 
-##               }
135 
-
136 
-##               cat("...@ tree:")
137 
-##               print.phylo(get.tree(object))
138 
-##               cat("\nwith the following features available:\n")
139 
-##               cat("\t", paste0("'",
140 
-##                                paste(fields, collapse="',\t'"),
141 
-##                                "'."),
142 
-##                   "\n")
143 
-##           })
144 
-
145 
-
146 
-
147 
-## ##' @rdname show-methods
148 
-## ##' @importFrom ape print.phylo
149 
-## ##' @exportMethod show
150 
-## setMethod("show", signature(object = "r8s"),
151 
-##           function(object) {
152 
-##               cat("'r8s' S4 object that stored information of\n\t",
153 
-##                   paste0("'", object@file, "'.\n\n"))
154 
-##               cat("...@ tree: ")
155 
-##               print.phylo(get.tree(object))
156 
-##               ## cat("\nwith the following features available:\n")
157 
-##               ## print_fields(object)
158 
-##           })
159 
-
160 
-
161 
-## ##' @rdname show-methods
162 
-## ##' @importFrom ape print.phylo
163 
-## ##' @exportMethod show
164 
-## setMethod("show", signature(object = "phangorn"),
165 
-##           function(object) {
166 
-##               cat("'phangorn' S4 object that stored ancestral sequences inferred by 'phangorn::ancestral.pml'", ".\n\n")
167 
-##               cat("...@ tree: ")
168 
-##               print.phylo(get.tree(object))
169 
-##               fields <- get.fields(object)
170 
-##               cat("\nwith the following features available:\n")
171 
-##               cat("\t", paste0("'",
172 
-##                                paste(fields, collapse="',\t'"),
173 
-##                                "'."),
174 
-##                   "\n")
175 
-##           })
Browse code

depends treeio

GuangchuangYu authored on 20/12/2016 16:39:07
Showing 1 changed files
R/method-show.R
History View file @ 817c093d
... ... 
@@ -1,175 +1,175 @@
1 
-##' @rdname show-methods
2 
-##' @importFrom ape print.phylo
3 
-##' @exportMethod show
4 
-setMethod("show", signature(object = "beast"),
5 
-          function(object) {
6 
-              cat("'beast' S4 object that stored information of\n\t",
7 
-                  paste0("'", object@file, "'.\n\n"))
8 
-              cat("...@ tree: ")
9 
-              print.phylo(get.tree(object))
10 
-              cat("\nwith the following features available:\n")
11 
-              print_fields(object)
12 
-          })
13 
-
14 
-##' @rdname show-methods
15 
-##' @exportMethod show
16 
-setMethod("show", signature(object = "codeml"),
17 
-          function(object) {
18 
-              cat("'codeml' S4 object that stored information of\n\t",
19 
-                  paste0("'", object@rst@rstfile, "' and \n\t'",
20 
-                         object@mlc@mlcfile, "'."),
21 
-                  "\n\n")
22 
-              cat("...@ tree:")
23 
-              print.phylo(get.tree(object))
24 
-              cat("\nwith the following features available:\n")
25 
-              print_fields(object, len=4)
26 
-          })
27 
-
28 
-##' @rdname show-methods
29 
-##' @exportMethod show
30 
-setMethod("show", signature(object = "codeml_mlc"),
31 
-          function(object) {
32 
-              cat("'codeml_mlc' S4 object that stored information of\n\t",
33 
-                  paste0("'", object@mlcfile, "'."),
34 
-                  "\n\n")
35 
-
36 
-              cat("...@ tree:")
37 
-              print.phylo(get.tree(object))
38 
-
39 
-              cat("\nwith the following features available:\n")
40 
-              cat("\t", paste0("'",
41 
-                                 paste(get.fields(object), collapse="',\t'"),
42 
-                                 "'."),
43 
-                  "\n")
44 
-          }
45 
-          )
46 
-
47 
-##' show method for \code{jplace} instance
48 
-##'
49 
-##'
50 
-##' @name show
51 
-##' @docType methods
52 
-##' @rdname show-methods
53 
-##'
54 
-##' @title show method
55 
-##' @param object one of \code{jplace}, \code{beast} object
56 
-##' @return print info
57 
-##' @importFrom methods show
58 
-##' @exportMethod show
59 
-##' @usage show(object)
60 
-##' @author Guangchuang Yu \url{http://ygc.name}
61 
-##' @examples
62 
-##' jp <- system.file("extdata", "sample.jplace", package="ggtree")
63 
-##' jp <- read.jplace(jp)
64 
-##' show(jp)
65 
-setMethod("show", signature(object = "jplace"),
66 
-          function(object) {
67 
-              cat("'jplace' S4 object that stored information of\n\t",
68 
-                  paste0("'", object@file, "'."),
69 
-                  "\n\n")
70 
-
71 
-              cat("...@ tree: ")
72 
-
73 
-              phylo <- get.tree(object)
74 
-              phylo$node.label <- NULL
75 
-              phylo$tip.label %<>% gsub("\\@\\d+", "", .)
76 
-
77 
-              print.phylo(phylo)
78 
-
79 
-              cat("\nwith the following features availables:\n")
80 
-              cat("\t", paste0("'",
81 
-                               paste(get.fields(object), collapse="',\t'"),
82 
-                               "'."),
83 
-                  "\n")
84 
-          }
85 
-          )
86 
-
87 
-
88 
-##' @rdname show-methods
89 
-##' @exportMethod show
90 
-setMethod("show", signature(object = "nhx"),
91 
-          function(object) {
92 
-              cat("'nhx' S4 object that stored information of\n\t",
93 
-                  paste0("'", object@file, "'.\n\n"))
94 
-              cat("...@ tree: ")
95 
-              print.phylo(get.tree(object))
96 
-              cat("\nwith the following features available:\n")
97 
-              print_fields(object)
98 
-          })
99 
-
100 
-
101 
-##' @rdname show-methods
102 
-##' @exportMethod show
103 
-setMethod("show", signature(object = "phylip"),
104 
-          function(object) {
105 
-              cat("'phylip' S4 object that stored information of\n\t",
106 
-                  paste0("'", object@file, "'.\n\n"))
107 
-              cat("...@ tree: ")
108 
-              print.phylo(get.tree(object))
109 
-              msg <- paste0("\nwith sequence alignment available (", length(object@sequence),
110 
-                            " sequences of length ", nchar(object@sequence)[1], ")\n")
111 
-              cat(msg)
112 
-          })
113 
-
114 
-##' @rdname show-methods
115 
-##' @exportMethod show
116 
-setMethod("show", signature(object = "paml_rst"),
117 
-          function(object) {
118 
-              cat("'paml_rst' S4 object that stored information of\n\t",
119 
-                  paste0("'", object@rstfile, "'.\n\n"))
120 
-              ## if (length(object@tip.fasfile) != 0) {
121 
-              ##     cat(paste0(" and \n\t'", object@tip.fasfile, "'.\n\n"))
122 
-              ## } else {
123 
-              ##     cat(".\n\n")
124 
-              ## }
125 
-              fields <- get.fields(object)
126 
-
127 
-              if (nrow(object@marginal_subs) == 0) {
128 
-                  fields <- fields[fields != "marginal_subs"]
129 
-                  fields <- fields[fields != "marginal_AA_subs"]
130 
-              }
131 
-              if (nrow(object@joint_subs) == 0) {
132 
-                  fields <- fields[fields != "joint_subs"]
133 
-                  fields <- fields[fields != "joint_AA_subs"]
134 
-              }
135 
-
136 
-              cat("...@ tree:")
137 
-              print.phylo(get.tree(object))
138 
-              cat("\nwith the following features available:\n")
139 
-              cat("\t", paste0("'",
140 
-                               paste(fields, collapse="',\t'"),
141 
-                               "'."),
142 
-                  "\n")
143 
-          })
144 
-
145 
-
146 
-
147 
-##' @rdname show-methods
148 
-##' @importFrom ape print.phylo
149 
-##' @exportMethod show
150 
-setMethod("show", signature(object = "r8s"),
151 
-          function(object) {
152 
-              cat("'r8s' S4 object that stored information of\n\t",
153 
-                  paste0("'", object@file, "'.\n\n"))
154 
-              cat("...@ tree: ")
155 
-              print.phylo(get.tree(object))
156 
-              ## cat("\nwith the following features available:\n")
157 
-              ## print_fields(object)
158 
-          })
159 
-
160 
-
161 
-##' @rdname show-methods
162 
-##' @importFrom ape print.phylo
163 
-##' @exportMethod show
164 
-setMethod("show", signature(object = "phangorn"),
165 
-          function(object) {
166 
-              cat("'phangorn' S4 object that stored ancestral sequences inferred by 'phangorn::ancestral.pml'", ".\n\n")
167 
-              cat("...@ tree: ")
168 
-              print.phylo(get.tree(object))
169 
-              fields <- get.fields(object)
170 
-              cat("\nwith the following features available:\n")
171 
-              cat("\t", paste0("'",
172 
-                               paste(fields, collapse="',\t'"),
173 
-                               "'."),
174 
-                  "\n")
175 
-          })
1 
+## ##' @rdname show-methods
2 
+## ##' @importFrom ape print.phylo
3 
+## ##' @exportMethod show
4 
+## setMethod("show", signature(object = "beast"),
5 
+##           function(object) {
6 
+##               cat("'beast' S4 object that stored information of\n\t",
7 
+##                   paste0("'", object@file, "'.\n\n"))
8 
+##               cat("...@ tree: ")
9 
+##               print.phylo(get.tree(object))
10 
+##               cat("\nwith the following features available:\n")
11 
+##               print_fields(object)
12 
+##           })
13 
+
14 
+## ##' @rdname show-methods
15 
+## ##' @exportMethod show
16 
+## setMethod("show", signature(object = "codeml"),
17 
+##           function(object) {
18 
+##               cat("'codeml' S4 object that stored information of\n\t",
19 
+##                   paste0("'", object@rst@rstfile, "' and \n\t'",
20 
+##                          object@mlc@mlcfile, "'."),
21 
+##                   "\n\n")
22 
+##               cat("...@ tree:")
23 
+##               print.phylo(get.tree(object))
24 
+##               cat("\nwith the following features available:\n")
25 
+##               print_fields(object, len=4)
26 
+##           })
27 
+
28 
+## ##' @rdname show-methods
29 
+## ##' @exportMethod show
30 
+## setMethod("show", signature(object = "codeml_mlc"),
31 
+##           function(object) {
32 
+##               cat("'codeml_mlc' S4 object that stored information of\n\t",
33 
+##                   paste0("'", object@mlcfile, "'."),
34 
+##                   "\n\n")
35 
+
36 
+##               cat("...@ tree:")
37 
+##               print.phylo(get.tree(object))
38 
+
39 
+##               cat("\nwith the following features available:\n")
40 
+##               cat("\t", paste0("'",
41 
+##                                  paste(get.fields(object), collapse="',\t'"),
42 
+##                                  "'."),
43 
+##                   "\n")
44 
+##           }
45 
+##           )
46 
+
47 
+## ##' show method for \code{jplace} instance
48 
+## ##'
49 
+## ##'
50 
+## ##' @name show
51 
+## ##' @docType methods
52 
+## ##' @rdname show-methods
53 
+## ##'
54 
+## ##' @title show method
55 
+## ##' @param object one of \code{jplace}, \code{beast} object
56 
+## ##' @return print info
57 
+## ##' @importFrom methods show
58 
+## ##' @exportMethod show
59 
+## ##' @usage show(object)
60 
+## ##' @author Guangchuang Yu \url{http://ygc.name}
61 
+## ##' @examples
62 
+## ##' jp <- system.file("extdata", "sample.jplace", package="ggtree")
63 
+## ##' jp <- read.jplace(jp)
64 
+## ##' show(jp)
65 
+## setMethod("show", signature(object = "jplace"),
66 
+##           function(object) {
67 
+##               cat("'jplace' S4 object that stored information of\n\t",
68 
+##                   paste0("'", object@file, "'."),
69 
+##                   "\n\n")
70 
+
71 
+##               cat("...@ tree: ")
72 
+
73 
+##               phylo <- get.tree(object)
74 
+##               phylo$node.label <- NULL
75 
+##               phylo$tip.label %<>% gsub("\\@\\d+", "", .)
76 
+
77 
+##               print.phylo(phylo)
78 
+
79 
+##               cat("\nwith the following features availables:\n")
80 
+##               cat("\t", paste0("'",
81 
+##                                paste(get.fields(object), collapse="',\t'"),
82 
+##                                "'."),
83 
+##                   "\n")
84 
+##           }
85 
+##           )
86 
+
87 
+
88 
+## ##' @rdname show-methods
89 
+## ##' @exportMethod show
90 
+## setMethod("show", signature(object = "nhx"),
91 
+##           function(object) {
92 
+##               cat("'nhx' S4 object that stored information of\n\t",
93 
+##                   paste0("'", object@file, "'.\n\n"))
94 
+##               cat("...@ tree: ")
95 
+##               print.phylo(get.tree(object))
96 
+##               cat("\nwith the following features available:\n")
97 
+##               print_fields(object)
98 
+##           })
99 
+
100 
+
101 
+## ##' @rdname show-methods
102 
+## ##' @exportMethod show
103 
+## setMethod("show", signature(object = "phylip"),
104 
+##           function(object) {
105 
+##               cat("'phylip' S4 object that stored information of\n\t",
106 
+##                   paste0("'", object@file, "'.\n\n"))
107 
+##               cat("...@ tree: ")
108 
+##               print.phylo(get.tree(object))
109 
+##               msg <- paste0("\nwith sequence alignment available (", length(object@sequence),
110 
+##                             " sequences of length ", nchar(object@sequence)[1], ")\n")
111 
+##               cat(msg)
112 
+##           })
113 
+
114 
+## ##' @rdname show-methods
115 
+## ##' @exportMethod show
116 
+## setMethod("show", signature(object = "paml_rst"),
117 
+##           function(object) {
118 
+##               cat("'paml_rst' S4 object that stored information of\n\t",
119 
+##                   paste0("'", object@rstfile, "'.\n\n"))
120 
+##               ## if (length(object@tip.fasfile) != 0) {
121 
+##               ##     cat(paste0(" and \n\t'", object@tip.fasfile, "'.\n\n"))
122 
+##               ## } else {
123 
+##               ##     cat(".\n\n")
124 
+##               ## }
125 
+##               fields <- get.fields(object)
126 
+
127 
+##               if (nrow(object@marginal_subs) == 0) {
128 
+##                   fields <- fields[fields != "marginal_subs"]
129 
+##                   fields <- fields[fields != "marginal_AA_subs"]
130 
+##               }
131 
+##               if (nrow(object@joint_subs) == 0) {
132 
+##                   fields <- fields[fields != "joint_subs"]
133 
+##                   fields <- fields[fields != "joint_AA_subs"]
134 
+##               }
135 
+
136 
+##               cat("...@ tree:")
137 
+##               print.phylo(get.tree(object))
138 
+##               cat("\nwith the following features available:\n")
139 
+##               cat("\t", paste0("'",
140 
+##                                paste(fields, collapse="',\t'"),
141 
+##                                "'."),
142 
+##                   "\n")
143 
+##           })
144 
+
145 
+
146 
+
147 
+## ##' @rdname show-methods
148 
+## ##' @importFrom ape print.phylo
149 
+## ##' @exportMethod show
150 
+## setMethod("show", signature(object = "r8s"),
151 
+##           function(object) {
152 
+##               cat("'r8s' S4 object that stored information of\n\t",
153 
+##                   paste0("'", object@file, "'.\n\n"))
154 
+##               cat("...@ tree: ")
155 
+##               print.phylo(get.tree(object))
156 
+##               ## cat("\nwith the following features available:\n")
157 
+##               ## print_fields(object)
158 
+##           })
159 
+
160 
+
161 
+## ##' @rdname show-methods
162 
+## ##' @importFrom ape print.phylo
163 
+## ##' @exportMethod show
164 
+## setMethod("show", signature(object = "phangorn"),
165 
+##           function(object) {
166 
+##               cat("'phangorn' S4 object that stored ancestral sequences inferred by 'phangorn::ancestral.pml'", ".\n\n")
167 
+##               cat("...@ tree: ")
168 
+##               print.phylo(get.tree(object))
169 
+##               fields <- get.fields(object)
170 
+##               cat("\nwith the following features available:\n")
171 
+##               cat("\t", paste0("'",
172 
+##                                paste(fields, collapse="',\t'"),
173 
+##                                "'."),
174 
+##                   "\n")
175 
+##           })
Browse code

bug fixed

guangchuang yu authored on 14/12/2016 09:07:44
Showing 1 changed files
R/method-show.R
History View file @ 0710a7b7
... ... 
@@ -6,7 +6,7 @@ setMethod("show", signature(object = "beast"),
6 6 
               cat("'beast' S4 object that stored information of\n\t",
7 7 
                   paste0("'", object@file, "'.\n\n"))
8 8 
               cat("...@ tree: ")
9 
-              print.phylo(get.tree(object))
9 
+              print.phylo(get.tree(object))
10 10 
               cat("\nwith the following features available:\n")
11 11 
               print_fields(object)
12 12 
           })
... ... 
@@ -20,7 +20,7 @@ setMethod("show", signature(object = "codeml"),
20 20 
                          object@mlc@mlcfile, "'."),
21 21 
                   "\n\n")
22 22 
               cat("...@ tree:")
23 
-              print.phylo(get.tree(object))
23 
+              print.phylo(get.tree(object))
24 24 
               cat("\nwith the following features available:\n")
25 25 
               print_fields(object, len=4)
26 26 
           })
... ... 
@@ -32,10 +32,10 @@ setMethod("show", signature(object = "codeml_mlc"),
32 32 
               cat("'codeml_mlc' S4 object that stored information of\n\t",
33 33 
                   paste0("'", object@mlcfile, "'."),
34 34 
                   "\n\n")
35 
-
35 
+
36 36 
               cat("...@ tree:")
37 
-              print.phylo(get.tree(object))
38 
-
37 
+              print.phylo(get.tree(object))
38 
+
39 39 
               cat("\nwith the following features available:\n")
40 40 
               cat("\t", paste0("'",
41 41 
                                  paste(get.fields(object), collapse="',\t'"),
... ... 
@@ -46,7 +46,7 @@ setMethod("show", signature(object = "codeml_mlc"),
46 46
47 47 
 ##' show method for \code{jplace} instance
48 48 
 ##'
49 
-##'
49 
+##'
50 50 
 ##' @name show
51 51 
 ##' @docType methods
52 52 
 ##' @rdname show-methods
... ... 
@@ -72,8 +72,8 @@ setMethod("show", signature(object = "jplace"),
72 72
73 73 
               phylo <- get.tree(object)
74 74 
               phylo$node.label <- NULL
75 
-              phylo$tip.label %<>% gsub("\\@\\d+", "", .)
76 
-
75 
+              phylo$tip.label %<>% gsub("\\@\\d+", "", .)
76 
+
77 77 
               print.phylo(phylo)
78 78
79 79 
               cat("\nwith the following features availables:\n")
... ... 
@@ -92,7 +92,7 @@ setMethod("show", signature(object = "nhx"),
92 92 
               cat("'nhx' S4 object that stored information of\n\t",
93 93 
                   paste0("'", object@file, "'.\n\n"))
94 94 
               cat("...@ tree: ")
95 
-              print.phylo(get.tree(object))
95 
+              print.phylo(get.tree(object))
96 96 
               cat("\nwith the following features available:\n")
97 97 
               print_fields(object)
98 98 
           })
... ... 
@@ -105,7 +105,7 @@ setMethod("show", signature(object = "phylip"),
105 105 
               cat("'phylip' S4 object that stored information of\n\t",
106 106 
                   paste0("'", object@file, "'.\n\n"))
107 107 
               cat("...@ tree: ")
108 
-              print.phylo(get.tree(object))
108 
+              print.phylo(get.tree(object))
109 109 
               msg <- paste0("\nwith sequence alignment available (", length(object@sequence),
110 110 
                             " sequences of length ", nchar(object@sequence)[1], ")\n")
111 111 
               cat(msg)
... ... 
@@ -132,9 +132,9 @@ setMethod("show", signature(object = "paml_rst"),
132 132 
                   fields <- fields[fields != "joint_subs"]
133 133 
                   fields <- fields[fields != "joint_AA_subs"]
134 134 
               }
135 
-
135 
+
136 136 
               cat("...@ tree:")
137 
-              print.phylo(get.tree(object))
137 
+              print.phylo(get.tree(object))
138 138 
               cat("\nwith the following features available:\n")
139 139 
               cat("\t", paste0("'",
140 140 
                                paste(fields, collapse="',\t'"),
... ... 
@@ -152,7 +152,24 @@ setMethod("show", signature(object = "r8s"),
152 152 
               cat("'r8s' S4 object that stored information of\n\t",
153 153 
                   paste0("'", object@file, "'.\n\n"))
154 154 
               cat("...@ tree: ")
155 
-              print.phylo(get.tree(object))
155 
+              print.phylo(get.tree(object))
156 156 
               ## cat("\nwith the following features available:\n")
157 157 
               ## print_fields(object)
158 158 
           })
159 
+
160 
+
161 
+##' @rdname show-methods
162 
+##' @importFrom ape print.phylo
163 
+##' @exportMethod show
164 
+setMethod("show", signature(object = "phangorn"),
165 
+          function(object) {
166 
+              cat("'phangorn' S4 object that stored ancestral sequences inferred by 'phangorn::ancestral.pml'", ".\n\n")
167 
+              cat("...@ tree: ")
168 
+              print.phylo(get.tree(object))
169 
+              fields <- get.fields(object)
170 
+              cat("\nwith the following features available:\n")
171 
+              cat("\t", paste0("'",
172 
+                               paste(fields, collapse="',\t'"),
173 
+                               "'."),
174 
+                  "\n")
175 
+          })
Browse code

clean dependencies

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@119521 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 21/07/2016 13:16:38
Showing 1 changed files
R/method-show.R
History View file @ 27786944
... ... 
@@ -107,7 +107,7 @@ setMethod("show", signature(object = "phylip"),
107 107 
               cat("...@ tree: ")
108 108 
               print.phylo(get.tree(object))
109 109 
               msg <- paste0("\nwith sequence alignment available (", length(object@sequence),
110 
-                            " sequences of length ", width(object@sequence)[1], ")\n")
110 
+                            " sequences of length ", nchar(object@sequence)[1], ")\n")
111 111 
               cat(msg)
112 112 
           })
113 113
Browse code

support MCC trees

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@117329 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 12/05/2016 07:09:03
Showing 1 changed files
R/method-show.R
History View file @ 47fa1dcf
... ... 
@@ -1,5 +1,3 @@
1 
-
2 
-
3 1 
 ##' @rdname show-methods
4 2 
 ##' @importFrom ape print.phylo
5 3 
 ##' @exportMethod show
Browse code

support textConnection

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@116643 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 21/04/2016 11:51:12
Showing 1 changed files
R/method-show.R
History View file @ 0ed2ffd9
... ... 
@@ -27,6 +27,25 @@ setMethod("show", signature(object = "codeml"),
27 27 
               print_fields(object, len=4)
28 28 
           })
29 29
30 
+##' @rdname show-methods
31 
+##' @exportMethod show
32 
+setMethod("show", signature(object = "codeml_mlc"),
33 
+          function(object) {
34 
+              cat("'codeml_mlc' S4 object that stored information of\n\t",
35 
+                  paste0("'", object@mlcfile, "'."),
36 
+                  "\n\n")
37 
+
38 
+              cat("...@ tree:")
39 
+              print.phylo(get.tree(object))
40 
+
41 
+              cat("\nwith the following features available:\n")
42 
+              cat("\t", paste0("'",
43 
+                                 paste(get.fields(object), collapse="',\t'"),
44 
+                                 "'."),
45 
+                  "\n")
46 
+          }
47 
+          )
48 
+
30 49 
 ##' show method for \code{jplace} instance
31 50 
 ##'
32 51 
 ##'
... ... 
@@ -94,3 +113,48 @@ setMethod("show", signature(object = "phylip"),
94 113 
               cat(msg)
95 114 
           })
96 115
116 
+##' @rdname show-methods
117 
+##' @exportMethod show
118 
+setMethod("show", signature(object = "paml_rst"),
119 
+          function(object) {
120 
+              cat("'paml_rst' S4 object that stored information of\n\t",
121 
+                  paste0("'", object@rstfile, "'.\n\n"))
122 
+              ## if (length(object@tip.fasfile) != 0) {
123 
+              ##     cat(paste0(" and \n\t'", object@tip.fasfile, "'.\n\n"))
124 
+              ## } else {
125 
+              ##     cat(".\n\n")
126 
+              ## }
127 
+              fields <- get.fields(object)
128 
+
129 
+              if (nrow(object@marginal_subs) == 0) {
130 
+                  fields <- fields[fields != "marginal_subs"]
131 
+                  fields <- fields[fields != "marginal_AA_subs"]
132 
+              }
133 
+              if (nrow(object@joint_subs) == 0) {
134 
+                  fields <- fields[fields != "joint_subs"]
135 
+                  fields <- fields[fields != "joint_AA_subs"]
136 
+              }
137 
+
138 
+              cat("...@ tree:")
139 
+              print.phylo(get.tree(object))
140 
+              cat("\nwith the following features available:\n")
141 
+              cat("\t", paste0("'",
142 
+                               paste(fields, collapse="',\t'"),
143 
+                               "'."),
144 
+                  "\n")
145 
+          })
146 
+
147 
+
148 
+
149 
+##' @rdname show-methods
150 
+##' @importFrom ape print.phylo
151 
+##' @exportMethod show
152 
+setMethod("show", signature(object = "r8s"),
153 
+          function(object) {
154 
+              cat("'r8s' S4 object that stored information of\n\t",
155 
+                  paste0("'", object@file, "'.\n\n"))
156 
+              cat("...@ tree: ")
157 
+              print.phylo(get.tree(object))
158 
+              ## cat("\nwith the following features available:\n")
159 
+              ## print_fields(object)
160 
+          })
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/method-show.R
History View file @ 6f076280
... ... 
@@ -13,6 +13,60 @@ setMethod("show", signature(object = "beast"),
13 13 
               print_fields(object)
14 14 
           })
15 15
16 
+##' @rdname show-methods
17 
+##' @exportMethod show
18 
+setMethod("show", signature(object = "codeml"),
19 
+          function(object) {
20 
+              cat("'codeml' S4 object that stored information of\n\t",
21 
+                  paste0("'", object@rst@rstfile, "' and \n\t'",
22 
+                         object@mlc@mlcfile, "'."),
23 
+                  "\n\n")
24 
+              cat("...@ tree:")
25 
+              print.phylo(get.tree(object))
26 
+              cat("\nwith the following features available:\n")
27 
+              print_fields(object, len=4)
28 
+          })
29 
+
30 
+##' show method for \code{jplace} instance
31 
+##'
32 
+##'
33 
+##' @name show
34 
+##' @docType methods
35 
+##' @rdname show-methods
36 
+##'
37 
+##' @title show method
38 
+##' @param object one of \code{jplace}, \code{beast} object
39 
+##' @return print info
40 
+##' @importFrom methods show
41 
+##' @exportMethod show
42 
+##' @usage show(object)
43 
+##' @author Guangchuang Yu \url{http://ygc.name}
44 
+##' @examples
45 
+##' jp <- system.file("extdata", "sample.jplace", package="ggtree")
46 
+##' jp <- read.jplace(jp)
47 
+##' show(jp)
48 
+setMethod("show", signature(object = "jplace"),
49 
+          function(object) {
50 
+              cat("'jplace' S4 object that stored information of\n\t",
51 
+                  paste0("'", object@file, "'."),
52 
+                  "\n\n")
53 
+
54 
+              cat("...@ tree: ")
55 
+
56 
+              phylo <- get.tree(object)
57 
+              phylo$node.label <- NULL
58 
+              phylo$tip.label %<>% gsub("\\@\\d+", "", .)
59 
+
60 
+              print.phylo(phylo)
61 
+
62 
+              cat("\nwith the following features availables:\n")
63 
+              cat("\t", paste0("'",
64 
+                               paste(get.fields(object), collapse="',\t'"),
65 
+                               "'."),
66 
+                  "\n")
67 
+          }
68 
+          )
69 
+
16 70
17 71 
 ##' @rdname show-methods
18 72 
 ##' @exportMethod show
... ... 
@@ -25,3 +79,18 @@ setMethod("show", signature(object = "nhx"),
25 79 
               cat("\nwith the following features available:\n")
26 80 
               print_fields(object)
27 81 
           })
82 
+
83 
+
84 
+##' @rdname show-methods
85 
+##' @exportMethod show
86 
+setMethod("show", signature(object = "phylip"),
87 
+          function(object) {
88 
+              cat("'phylip' S4 object that stored information of\n\t",
89 
+                  paste0("'", object@file, "'.\n\n"))
90 
+              cat("...@ tree: ")
91 
+              print.phylo(get.tree(object))
92 
+              msg <- paste0("\nwith sequence alignment available (", length(object@sequence),
93 
+                            " sequences of length ", width(object@sequence)[1], ")\n")
94 
+              cat(msg)
95 
+          })
96 
+
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-show.R
History View file @ 3e4b5998
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,27 @@
1 
+
2 
+
3 
+##' @rdname show-methods
4 
+##' @importFrom ape print.phylo
5 
+##' @exportMethod show
6 
+setMethod("show", signature(object = "beast"),
7 
+          function(object) {
8 
+              cat("'beast' S4 object that stored information of\n\t",
9 
+                  paste0("'", object@file, "'.\n\n"))
10 
+              cat("...@ tree: ")
11 
+              print.phylo(get.tree(object))
12 
+              cat("\nwith the following features available:\n")
13 
+              print_fields(object)
14 
+          })
15 
+
16 
+
17 
+##' @rdname show-methods
18 
+##' @exportMethod show
19 
+setMethod("show", signature(object = "nhx"),
20 
+          function(object) {
21 
+              cat("'nhx' S4 object that stored information of\n\t",
22 
+                  paste0("'", object@file, "'.\n\n"))
23 
+              cat("...@ tree: ")
24 
+              print.phylo(get.tree(object))
25 
+              cat("\nwith the following features available:\n")
26 
+              print_fields(object)
27 
+          })