git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@116643 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -2,6 +2,8 @@ CHANGES IN VERSION 1.3.16 |
2 | 2 |
------------------------ |
3 | 3 |
o update fortify.phylo to work with phylo that has missing value of edge length <2016-04-21, Thu> |
4 | 4 |
+ https://github.com/GuangchuangYu/ggtree/issues/54 |
5 |
+ o support passing textConnection(text_string) as a file <2016-04-21, Thu> |
|
6 |
+ + https://github.com/GuangchuangYu/ggtree/pull/55#issuecomment-212859693 |
|
5 | 7 |
|
6 | 8 |
CHANGES IN VERSION 1.3.15 |
7 | 9 |
------------------------ |
... | ... |
@@ -20,7 +20,7 @@ read.codeml_mlc <- function(mlcfile) { |
20 | 20 |
dNdS = dNdS, |
21 | 21 |
## seq_type = get_seqtype(tip_seq), |
22 | 22 |
## tip_seq = tip_seq, |
23 |
- mlcfile = mlcfile) |
|
23 |
+ mlcfile = filename(mlcfile)) |
|
24 | 24 |
} |
25 | 25 |
|
26 | 26 |
|
... | ... |
@@ -49,24 +49,6 @@ setMethod("scale_color", signature(object="codeml_mlc"), |
49 | 49 |
scale_color_(object, by, ...) |
50 | 50 |
}) |
51 | 51 |
|
52 |
-##' @rdname show-methods |
|
53 |
-##' @exportMethod show |
|
54 |
-setMethod("show", signature(object = "codeml_mlc"), |
|
55 |
- function(object) { |
|
56 |
- cat("'codeml_mlc' S4 object that stored information of\n\t", |
|
57 |
- paste0("'", object@mlcfile, "'."), |
|
58 |
- "\n\n") |
|
59 |
- |
|
60 |
- cat("...@ tree:") |
|
61 |
- print.phylo(get.tree(object)) |
|
62 |
- |
|
63 |
- cat("\nwith the following features available:\n") |
|
64 |
- cat("\t", paste0("'", |
|
65 |
- paste(get.fields(object), collapse="',\t'"), |
|
66 |
- "'."), |
|
67 |
- "\n") |
|
68 |
- } |
|
69 |
- ) |
|
70 | 52 |
|
71 | 53 |
|
72 | 54 |
##' @rdname get.fields-methods |
... | ... |
@@ -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"), |
|
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+ 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) { |
|
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+ ## cat(paste0(" and \n\t'", object@tip.fasfile, "'.\n\n")) |
|
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+ ## } 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"] |
|
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+ fields <- fields[fields != "joint_AA_subs"] |
|
136 |
+ } |
|
137 |
+ |
|
138 |
+ cat("...@ tree:") |
|
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+ print.phylo(get.tree(object)) |
|
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+ cat("\nwith the following features available:\n") |
|
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+ cat("\t", paste0("'", |
|
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+ paste(fields, collapse="',\t'"), |
|
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+ "'."), |
|
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+ "\n") |
|
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+ }) |
|
146 |
+ |
|
147 |
+ |
|
148 |
+ |
|
149 |
+##' @rdname show-methods |
|
150 |
+##' @importFrom ape print.phylo |
|
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+##' @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: ") |
|
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+ print.phylo(get.tree(object)) |
|
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+ ## cat("\nwith the following features available:\n") |
|
159 |
+ ## print_fields(object) |
|
160 |
+ }) |
... | ... |
@@ -46,7 +46,7 @@ read.paml_rst <- function(rstfile) { |
46 | 46 |
seq_type = type, |
47 | 47 |
marginal_ancseq = ms, |
48 | 48 |
joint_ancseq = read.ancseq_paml_rst(rstfile, by = "Joint"), |
49 |
- rstfile = rstfile |
|
49 |
+ rstfile = filename(rstfile) |
|
50 | 50 |
) |
51 | 51 |
## if (!is.null(tip.fasfile)) { |
52 | 52 |
## seqs <- readBStringSet(tip.fasfile) |
... | ... |
@@ -86,36 +86,6 @@ setMethod("get.tipseq", signature(object="paml_rst"), |
86 | 86 |
} |
87 | 87 |
}) |
88 | 88 |
|
89 |
-##' @rdname show-methods |
|
90 |
-##' @exportMethod show |
|
91 |
-setMethod("show", signature(object = "paml_rst"), |
|
92 |
- function(object) { |
|
93 |
- cat("'paml_rst' S4 object that stored information of\n\t", |
|
94 |
- paste0("'", object@rstfile, "'.\n\n")) |
|
95 |
- ## if (length(object@tip.fasfile) != 0) { |
|
96 |
- ## cat(paste0(" and \n\t'", object@tip.fasfile, "'.\n\n")) |
|
97 |
- ## } else { |
|
98 |
- ## cat(".\n\n") |
|
99 |
- ## } |
|
100 |
- fields <- get.fields(object) |
|
101 |
- |
|
102 |
- if (nrow(object@marginal_subs) == 0) { |
|
103 |
- fields <- fields[fields != "marginal_subs"] |
|
104 |
- fields <- fields[fields != "marginal_AA_subs"] |
|
105 |
- } |
|
106 |
- if (nrow(object@joint_subs) == 0) { |
|
107 |
- fields <- fields[fields != "joint_subs"] |
|
108 |
- fields <- fields[fields != "joint_AA_subs"] |
|
109 |
- } |
|
110 |
- |
|
111 |
- cat("...@ tree:") |
|
112 |
- print.phylo(get.tree(object)) |
|
113 |
- cat("\nwith the following features available:\n") |
|
114 |
- cat("\t", paste0("'", |
|
115 |
- paste(fields, collapse="',\t'"), |
|
116 |
- "'."), |
|
117 |
- "\n") |
|
118 |
- }) |
|
119 | 89 |
|
120 | 90 |
##' @rdname get.fields-methods |
121 | 91 |
##' @exportMethod get.fields |
... | ... |
@@ -21,26 +21,13 @@ read.r8s <- function(file) { |
21 | 21 |
names(trees) <- label |
22 | 22 |
|
23 | 23 |
new("r8s", |
24 |
- file = file, |
|
24 |
+ file = filename(file), |
|
25 | 25 |
fields = label, |
26 | 26 |
phylo = trees) |
27 | 27 |
} |
28 | 28 |
|
29 | 29 |
|
30 | 30 |
|
31 |
-##' @rdname show-methods |
|
32 |
-##' @importFrom ape print.phylo |
|
33 |
-##' @exportMethod show |
|
34 |
-setMethod("show", signature(object = "r8s"), |
|
35 |
- function(object) { |
|
36 |
- cat("'r8s' S4 object that stored information of\n\t", |
|
37 |
- paste0("'", object@file, "'.\n\n")) |
|
38 |
- cat("...@ tree: ") |
|
39 |
- print.phylo(get.tree(object)) |
|
40 |
- ## cat("\nwith the following features available:\n") |
|
41 |
- ## print_fields(object) |
|
42 |
- }) |
|
43 |
- |
|
44 | 31 |
|
45 | 32 |
##' @rdname groupClade-methods |
46 | 33 |
##' @exportMethod groupClade |
... | ... |
@@ -1,3 +1,13 @@ |
1 |
+filename <- function(file) { |
|
2 |
+ ## textConnection(text_string) will work just like a file |
|
3 |
+ ## in this case, just set the filename as "" |
|
4 |
+ file_name <- "" |
|
5 |
+ if (is.character(file)) { |
|
6 |
+ file_name <- file |
|
7 |
+ } |
|
8 |
+ return(file_name) |
|
9 |
+} |
|
10 |
+ |
|
1 | 11 |
|
2 | 12 |
##' @importFrom ggplot2 last_plot |
3 | 13 |
get_tree_view <- function(tree_view) { |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
% Generated by roxygen2: do not edit by hand |
2 |
-% Please edit documentation in R/RAxML.R, R/ape.R, R/codeml_mlc.R, R/hyphy.R, R/method-show.R, R/paml_rst.R, R/phangorn.R, R/r8s.R |
|
2 |
+% Please edit documentation in R/RAxML.R, R/ape.R, R/hyphy.R, R/method-show.R, R/phangorn.R |
|
3 | 3 |
\docType{methods} |
4 | 4 |
\name{show,raxml-method} |
5 | 5 |
\alias{show} |
... | ... |
@@ -20,14 +20,14 @@ |
20 | 20 |
|
21 | 21 |
\S4method{show}{apeBootstrap}(object) |
22 | 22 |
|
23 |
-\S4method{show}{codeml_mlc}(object) |
|
24 |
- |
|
25 | 23 |
\S4method{show}{hyphy}(object) |
26 | 24 |
|
27 | 25 |
\S4method{show}{beast}(object) |
28 | 26 |
|
29 | 27 |
\S4method{show}{codeml}(object) |
30 | 28 |
|
29 |
+\S4method{show}{codeml_mlc}(object) |
|
30 |
+ |
|
31 | 31 |
show(object) |
32 | 32 |
|
33 | 33 |
\S4method{show}{nhx}(object) |
... | ... |
@@ -36,9 +36,9 @@ show(object) |
36 | 36 |
|
37 | 37 |
\S4method{show}{paml_rst}(object) |
38 | 38 |
|
39 |
-\S4method{show}{phangorn}(object) |
|
40 |
- |
|
41 | 39 |
\S4method{show}{r8s}(object) |
40 |
+ |
|
41 |
+\S4method{show}{phangorn}(object) |
|
42 | 42 |
} |
43 | 43 |
\arguments{ |
44 | 44 |
\item{object}{one of \code{jplace}, \code{beast} object} |