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
Showing22 changed files

... ...
@@ -13,17 +13,19 @@ Description: 'ggtree' extends the 'ggplot2' plotting system which implemented
13 13
     the grammar of graphics. 'ggtree' is designed for visualization and annotation
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     of phylogenetic trees with their covariates and other associated data.
15 15
 Depends:
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-    R (>= 3.3.2),
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+    R (>= 3.4.0),
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     ggplot2 (>= 2.2.0),
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-    treeio
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+    treeio (>= 1.3.2)
19 19
 Imports:
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     ape,
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+    dplyr,
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     grDevices,
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     grid,
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     magrittr,
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     methods,
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     rvcheck,
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     scales,
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+    tibble,
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     tidyr,
28 30
     utils
29 31
 Suggests:
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@@ -43,4 +45,4 @@ BugReports: https://github.com/GuangchuangYu/ggtree/issues
43 45
 Packaged: 2014-12-03 08:16:14 UTC; root
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 biocViews: Alignment, Annotation, Clustering, DataImport,
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     MultipleSequenceAlignment, ReproducibleResearch, Software, Visualization
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-RoxygenNote: 6.0.1.9000
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+RoxygenNote: 6.0.1
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@@ -2,8 +2,7 @@
2 2
 
3 3
 S3method(as.binary,phylo)
4 4
 S3method(as.data.frame,phylo)
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-S3method(as.data.frame,treedata)
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-S3method(fortify,beast)
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+S3method(as_data_frame,treedata)
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 S3method(fortify,codeml)
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 S3method(fortify,codeml_mlc)
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 S3method(fortify,hyphy)
... ...
@@ -81,6 +80,7 @@ export(nodeid)
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 export(nodepie)
82 81
 export(open_tree)
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 export(phylopic)
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+export(range_format)
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 export(reroot)
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 export(rescale_tree)
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 export(revts)
... ...
@@ -112,6 +112,7 @@ importFrom(ape,ladderize)
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 importFrom(ape,read.tree)
113 113
 importFrom(ape,reorder.phylo)
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 importFrom(ape,write.tree)
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+importFrom(dplyr,full_join)
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 importFrom(ggplot2,Geom)
116 117
 importFrom(ggplot2,GeomCurve)
117 118
 importFrom(ggplot2,GeomLabel)
... ...
@@ -190,6 +191,8 @@ importFrom(methods,setGeneric)
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 importFrom(methods,setOldClass)
191 192
 importFrom(rvcheck,get_fun_from_pkg)
192 193
 importFrom(scales,alpha)
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+importFrom(tibble,as_data_frame)
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+importFrom(tibble,data_frame)
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 importFrom(tidyr,gather)
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 importFrom(treeio,as.phylo)
195 198
 importFrom(treeio,as.treedata)
... ...
@@ -1,5 +1,6 @@
1 1
 CHANGES IN VERSION 1.11.2
2 2
 ------------------------
3
+ o remove beast object support as read.beast output treedata object in treeio <2017-12-05, Tue>
3 4
  o deprecate subview, annotation_image and phylopic; remove theme_transparent <2017-12-04, Mon>
4 5
  o geom_tiplab now supports geom = "image" or geom = "phylopic" <2017-12-04, Mon>
5 6
  o A new layer geom_nodelab that equivalent to geom_tiplab but works for internal node <2017-12-04, Mon>
... ...
@@ -14,13 +14,14 @@ scaleX_by_time_from_mrsd <- function(df, mrsd, as.Date) {
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     date <- Date2decimal(mrsd)
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     df$x <- df$x + date - max(df$x)
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-    df$branch <- (df[df$parent, "x"] + df[, "x"])/2
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+    df$branch <- with(df, (x[match(parent, node)] + x)/2)
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+    ## df$branch <- (df[df$parent, "x"] + df[, "x"])/2
18 19
 
19 20
     if (as.Date) {
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         df$x <- decimal2Date(df$x)
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         df$branch <- decimal2Date(df$branch)
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     }
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-    
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+
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     return(df)
25 26
 }
26 27
 
... ...
@@ -28,7 +29,7 @@ scaleX_by_time_from_mrsd <- function(df, mrsd, as.Date) {
28 29
 
29 30
 ##' convert Date to decimal format, eg "2014-05-05" to "2014.34"
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 ##'
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-##' 
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+##'
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 ##' @title Date2decimal
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 ##' @param x Date
34 35
 ##' @return numeric
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@@ -38,7 +39,7 @@ Date2decimal <- function(x) {
38 39
     if (is(x, "numeric")) {
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         return(x)
40 41
     }
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-    
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+
42 43
     if (is(x, "character")) {
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         x <- as.Date(x)
44 45
     }
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@@ -49,7 +50,7 @@ Date2decimal <- function(x) {
49 50
 
50 51
 ##' convert decimal format to Date, eg "2014.34" to "2014-05-05"
51 52
 ##'
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-##' 
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+##'
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 ##' @title decimal2Date
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 ##' @param x numerical number, eg 2014.34
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 ##' @return Date
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@@ -1,31 +1,3 @@
1
-
2
-## ##' @export
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-## ape::read.tree
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-
5
-
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-## ##' generate random tree
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-## ##' @export
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-## ##' @rdname rtree
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-## ##' @param n number of tips in the tree
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-## ##' @param rooted logcial
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-## ##' @param tip.label tip label
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-## ##' @param br one of the following: (i) an R function used to generate the
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-## ##'           branch lengths ('rtree'; use 'NULL' to simulate only a
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-## ##'           topology), or the coalescence times ('rcoal'); (ii) a
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-## ##'           character to simulate a genuine coalescent tree for 'rcoal'
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-## ##'           (the default); or (iii) a numeric vector for the branch
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-## ##'           lengths or the coalescence times.
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-## ##' @param ... additional parameters to be passed to 'br'
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-## ##' @source
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-## ##' This is just the imported function
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-## ##' from the ape package. The documentation you should
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-## ##' read for the rtree function can be found here: \link[ape]{rtree}
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-## ##'
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-## ##' @seealso
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-## ##' \link[ape]{rtree}
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-## rtree <- ape::rtree
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-
28
-
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 ##' merge phylo and output of boot.phylo to 'apeBootstrap' object
30 2
 ##'
31 3
 ##'
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@@ -41,49 +13,3 @@ apeBoot <- function(phylo, boot) {
41 13
     as.treedata(phylo, boot)
42 14
 }
43 15
 
44
-## apeBoot <- function(phylo, boot) {
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-##     ## phylo is a phylo object
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-##     ## boot is output from boot.phylo
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-##     new("apeBootstrap",
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-##         phylo=phylo,
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-##         bootstrap=data.frame(node=(1:Nnode(phylo)) + Ntip(phylo), bootstrap=boot)
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-##         )
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-## }
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-
53
-
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-## ##' @rdname show-methods
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-## ##' @importFrom ape print.phylo
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-## ##' @exportMethod show
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-## setMethod("show", signature(object = "apeBootstrap"),
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-##           function(object) {
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-##               cat("'apeBoot' S4 object that stored bootstrap value generated by 'ape::boot.phylo'", ".\n\n")
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-##               cat("...@ tree: ")
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-##               print.phylo(get.tree(object))
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-##           })
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-
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-
65
-
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-
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-## ##' @rdname groupClade-methods
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-## ##' @exportMethod groupClade
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-## setMethod("groupClade", signature(object="apeBootstrap"),
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-##           function(object, node, group_name="group") {
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-##               groupClade_(object, node, group_name)
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-##           })
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-
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-## ##' @rdname scale_color-methods
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-## ##' @exportMethod scale_color
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-## setMethod("scale_color", signature(object="apeBootstrap"),
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-##           function(object, by="bootstrap", ...) {
78
-##               scale_color_(object, by, ...)
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-##           })
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-
81
-
82
-## ##' @rdname get.fields-methods
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-## ##' @exportMethod get.fields
84
-## setMethod("get.fields", signature(object="apeBootstrap"),
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-##           function(object, ...) {
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-##               get.fields.tree(object)
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-##           }
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-##           )
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-
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new file mode 100644
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@@ -0,0 +1,20 @@
1
+##' format a list of range (HPD, CI, etc that has length of 2)
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+##'
3
+##'
4
+##' @title range_format
5
+##' @param x input list
6
+##' @param trans transformation function
7
+##' @return character vector of '[lower, upper]'
8
+##' @export
9
+##' @author guangchuang yu
10
+range_format <- function(x, trans = NULL) {
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+    sapply(x, function(y) {
12
+        if(length(y) == 1 && is.na(y)) {
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+            return(NA)
14
+        } else {
15
+            if (!is.null(trans) && is(trans, 'function'))
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+                y <- trans(y)
17
+            return(sprintf("[%f, %f]", y[1], y[2]))
18
+        }
19
+    })
20
+}
... ...
@@ -3,12 +3,13 @@
3 3
 ##'
4 4
 ##' @title geom_range
5 5
 ##' @param range range, e.g. "height_0.95_HPD"
6
+##' @param branch.length corresponding branch.length
6 7
 ##' @param ... additional parameter, e.g. color, size, alpha
7 8
 ##' @return ggplot layer
8 9
 ##' @importFrom ggplot2 aes_string
9 10
 ##' @export
10 11
 ##' @author Guangchuang Yu
11
-geom_range <- function(range="height_0.95_HPD", ...) {
12
+geom_range <- function(range = "length_0.95_HPD", branch.length = "branch.length", ...) {
12 13
     position = "identity"
13 14
     show.legend = NA
14 15
     na.rm = TRUE
... ...
@@ -16,11 +17,10 @@ geom_range <- function(range="height_0.95_HPD", ...) {
16 17
 
17 18
     default_aes <- aes_(x=~x, y=~y, xend=~x, yend=~y)
18 19
 
19
-    if (grepl("^height", range)) {
20
-        mapping <- modifyList(default_aes, aes_string(branch.length="height", label=range))
21
-    } else {
22
-        mapping <- modifyList(default_aes, aes_string(branch.length="branch.length", label=range))
23
-    }
20
+    lower <- paste0('range_lower(', range, ')')
21
+    upper <- paste0('range_upper(', range, ')')
22
+
23
+    mapping <- modifyList(default_aes, aes_string(branch.length=branch.length, lower=lower, upper=upper))
24 24
 
25 25
     layer(
26 26
         stat = StatRange,
... ...
@@ -39,21 +39,28 @@ geom_range <- function(range="height_0.95_HPD", ...) {
39 39
 
40 40
 StatRange <- ggproto("StatRange", Stat,
41 41
                      compute_group = function(self, data, scales, params) {
42
-                         ## label is actually the range
43
-
44
-                         df <- data[!is.na(data[,"label"]),]
45
-                         rr <- gsub("\\[", "", df[,"label"])
46
-                         rr <- gsub("\\]", "", rr)
47
-                         rr2 <- strsplit(rr, split=',') %>% do.call('rbind', .)
48
-                         rr2 <- matrix(as.numeric(rr2), ncol=2, byrow=FALSE)
49
-                         rr2 <- rr2 + df$x - df$branch
50
-
51
-                         data.frame(x = rr2[,1],
52
-                                    xend = rr2[,2],
53
-                                    y = df$y,
54
-                                    yend = df$y)
42
+                         df <- data[!is.na(data[["lower"]]),]
43
+                         df[["lower"]] <- df[["lower"]] + df[["x"]] - df[["branch.length"]]
44
+                         df[["upper"]] <- df[["upper"]] + df[["x"]] - df[["branch.length"]]
45
+
46
+                         data.frame(x = df[["lower"]],
47
+                                    xend = df[["upper"]],
48
+                                    y = df[["y"]],
49
+                                    yend = df[["y"]])
55 50
                      },
56 51
                      required_aes = c("x", "y", "xend", "yend")
57 52
                      )
58 53
 
59 54
 
55
+range_lower <- function(range) {
56
+    sapply(range, function(x) as.numeric(x[1]))
57
+}
58
+
59
+range_upper <- function(range) {
60
+    sapply(range, function(x) {
61
+        if (length(x) == 1 && is.na(x))
62
+            return(NA)
63
+        as.numeric(x[2])
64
+    })
65
+}
66
+
... ...
@@ -106,118 +106,118 @@ rm.singleton.newick <- function(nwk, outfile = NULL) {
106 106
     invisible(tree)
107 107
 }
108 108
 
109
-##' @method fortify beast
110
-##' @export
111
-fortify.beast <- function(model, data,
112
-                          layout        = "rectangular",
113
-                          yscale        = "none",
114
-                          ladderize     = TRUE,
115
-                          right         = FALSE,
116
-                          branch.length = "branch.length",
117
-                          ndigits       = NULL,
118
-                          mrsd = NULL, ...) {
119
-
120
-    model <- set_branch_length(model, branch.length)
121
-    phylo <- model@phylo
122
-    df    <- fortify(phylo,
123
-                     layout = layout,
124
-                     branch.length = branch.length,
125
-                     ladderize = ladderize,
126
-                     right = right,
127
-                     mrsd = mrsd, ...)
128
-
129
-    stats <- model@stats
130
-
131
-    scn <- colnames(stats)
132
-    scn <- scn[scn != 'node']
133
-
134
-    for (cn in scn) {
135
-        if (cn %in% colnames(df)) {
136
-            colnames(stats)[colnames(stats) == cn] <- paste0(cn, "_")
137
-            msg <- paste("feature", cn, "was renamed to", paste0(cn, "_"), "due to name conflict...")
138
-            warning(msg)
139
-        }
140
-    }
141
-
142
-    idx <- which(colnames(stats) != "node")
143
-    for (ii in idx) {
144
-        if (is.character_beast(stats, ii)) {
145
-            len <- sapply(stats[,ii], length)
146
-            if (any(len > 1)) {
147
-                stats[,ii] %<>% sapply(., function(x) {
148
-                    y <- unlist(x) %>% as.character %>%
149
-                        gsub("\"", "", .) %>% gsub("'", "", .)
150
-                    if (length(y) == 1) {
151
-                        return(y)
152
-                    } else {
153
-                        return(paste0('{', paste0(y, collapse = ','), '}'))
154
-                    }
155
-                })
156
-            } else {
157
-                stats[,ii] %<>% unlist %>% as.character %>%
158
-                    gsub("\"", "", .) %>% gsub("'", "", .)
159
-            }
160
-            next
161
-        }
162
-
163
-        len <- sapply(stats[,ii], length)
164
-        if ( all(len == 1) ) {
165
-            stats[, ii] %<>% unlist %>% as.character %>% as.numeric
166
-            if (!is.null(ndigits)) {
167
-                stats[, ii] %<>% round(., ndigits)
168
-            }
169
-        } else if (all(len <= 2)) {
170
-            stats[, ii] %<>% sapply(., function(x) {
171
-                y <- unlist(x) %>% as.character %>% as.numeric
172
-                if (!is.null(ndigits)) {
173
-                    y %<>% round(., ndigits)
174
-                }
175
-                if (length(y) == 1) {
176
-                    return(y)
177
-                } else {
178
-                    return(paste0('[', paste0(y, collapse = ','), ']'))
179
-                }
180
-            })
181
-        } else {
182
-            stats[,ii] %<>% sapply(., function(x) {
183
-                y <- unlist(x) %>% as.character %>% as.numeric
184
-                if (!is.null(ndigits)) {
185
-                    y %<>% round(., ndigits)
186
-                }
187
-                if (length(y) == 1) {
188
-                    return(y)
189
-                } else {
190
-                    return(paste0('{', paste0(y, collapse = ','), '}'))
191
-                }
192
-            })
193
-        }
194
-    }
195
-
196
-
197
-    cn <- colnames(stats)
198
-    lo <- cn[grep("_lower", cn)]
199
-    hi <- gsub("lower$", "upper", lo)
200
-    rid <- gsub("_lower$", "", lo)
201
-
202
-    for (i in seq_along(rid)) {
203
-        stats[, rid[i]] <- paste0("[", stats[, lo[i]], ",", stats[, hi[i]], "]")
204
-        stats[is.na(stats[, lo[i]]), rid[i]] <- NA
205
-    }
206
-
207
-    idx   <- match(df$node, stats$node)
208
-    stats <- stats[idx,]
209
-    cn_stats <- colnames(stats)
210
-    stats <- stats[, cn_stats != "node"]
211
-
212
-    df <- cbind(df, stats)
213
-    if (is(stats, "data.frame") == FALSE) {
214
-        colnames(df)[colnames(df) == "stats"] <- cn_stats[cn_stats != "node"]
215
-    }
216
-
217
-    df <- scaleY(phylo, df, yscale, layout, ...)
109
+## ##' @method fortify beast
110
+## ##' @export
111
+## fortify.beast <- function(model, data,
112
+##                           layout        = "rectangular",
113
+##                           yscale        = "none",
114
+##                           ladderize     = TRUE,
115
+##                           right         = FALSE,
116
+##                           branch.length = "branch.length",
117
+##                           ndigits       = NULL,
118
+##                           mrsd = NULL, ...) {
119
+
120
+##     model <- set_branch_length(model, branch.length)
121
+##     phylo <- model@phylo
122
+##     df    <- fortify(phylo,
123
+##                      layout = layout,
124
+##                      branch.length = branch.length,
125
+##                      ladderize = ladderize,
126
+##                      right = right,
127
+##                      mrsd = mrsd, ...)
128
+
129
+##     stats <- model@stats
130
+
131
+##     scn <- colnames(stats)
132
+##     scn <- scn[scn != 'node']
133
+
134
+##     for (cn in scn) {
135
+##         if (cn %in% colnames(df)) {
136
+##             colnames(stats)[colnames(stats) == cn] <- paste0(cn, "_")
137
+##             msg <- paste("feature", cn, "was renamed to", paste0(cn, "_"), "due to name conflict...")
138
+##             warning(msg)
139
+##         }
140
+##     }
141
+
142
+##     idx <- which(colnames(stats) != "node")
143
+##     for (ii in idx) {
144
+##         if (is.character_beast(stats, ii)) {
145
+##             len <- sapply(stats[,ii], length)
146
+##             if (any(len > 1)) {
147
+##                 stats[,ii] %<>% sapply(., function(x) {
148
+##                     y <- unlist(x) %>% as.character %>%
149
+##                         gsub("\"", "", .) %>% gsub("'", "", .)
150
+##                     if (length(y) == 1) {
151
+##                         return(y)
152
+##                     } else {
153
+##                         return(paste0('{', paste0(y, collapse = ','), '}'))
154
+##                     }
155
+##                 })
156
+##             } else {
157
+##                 stats[,ii] %<>% unlist %>% as.character %>%
158
+##                     gsub("\"", "", .) %>% gsub("'", "", .)
159
+##             }
160
+##             next
161
+##         }
162
+
163
+##         len <- sapply(stats[,ii], length)
164
+##         if ( all(len == 1) ) {
165
+##             stats[, ii] %<>% unlist %>% as.character %>% as.numeric
166
+##             if (!is.null(ndigits)) {
167
+##                 stats[, ii] %<>% round(., ndigits)
168
+##             }
169
+##         } else if (all(len <= 2)) {
170
+##             stats[, ii] %<>% sapply(., function(x) {
171
+##                 y <- unlist(x) %>% as.character %>% as.numeric
172
+##                 if (!is.null(ndigits)) {
173
+##                     y %<>% round(., ndigits)
174
+##                 }
175
+##                 if (length(y) == 1) {
176
+##                     return(y)
177
+##                 } else {
178
+##                     return(paste0('[', paste0(y, collapse = ','), ']'))
179
+##                 }
180
+##             })
181
+##         } else {
182
+##             stats[,ii] %<>% sapply(., function(x) {
183
+##                 y <- unlist(x) %>% as.character %>% as.numeric
184
+##                 if (!is.null(ndigits)) {
185
+##                     y %<>% round(., ndigits)
186
+##                 }
187
+##                 if (length(y) == 1) {
188
+##                     return(y)
189
+##                 } else {
190
+##                     return(paste0('{', paste0(y, collapse = ','), '}'))
191
+##                 }
192
+##             })
193
+##         }
194
+##     }
195
+
196
+
197
+##     cn <- colnames(stats)
198
+##     lo <- cn[grep("_lower", cn)]
199
+##     hi <- gsub("lower$", "upper", lo)
200
+##     rid <- gsub("_lower$", "", lo)
201
+
202
+##     for (i in seq_along(rid)) {
203
+##         stats[, rid[i]] <- paste0("[", stats[, lo[i]], ",", stats[, hi[i]], "]")
204
+##         stats[is.na(stats[, lo[i]]), rid[i]] <- NA
205
+##     }
206
+
207
+##     idx   <- match(df$node, stats$node)
208
+##     stats <- stats[idx,]
209
+##     cn_stats <- colnames(stats)
210
+##     stats <- stats[, cn_stats != "node"]
211
+
212
+##     df <- cbind(df, stats)
213
+##     if (is(stats, "data.frame") == FALSE) {
214
+##         colnames(df)[colnames(df) == "stats"] <- cn_stats[cn_stats != "node"]
215
+##     }
216
+
217
+##     df <- scaleY(phylo, df, yscale, layout, ...)
218 218
 
219
-    append_extraInfo(df, model)
220
-}
219
+##     append_extraInfo(df, model)
220
+## }
221 221
 
222 222
 
223 223
 ##' @method fortify codeml
... ...
@@ -392,7 +392,7 @@ scaleY <- function(phylo, df, yscale, layout, ...) {
392 392
         warning("yscale is not available...\n")
393 393
         return(df)
394 394
     }
395
-    if (is.numeric(df[, yscale])) {
395
+    if (is.numeric(df[[yscale]])) {
396 396
         y <- getYcoord_scale_numeric(phylo, df, yscale, ...)
397 397
         ## if (order.y) {
398 398
         ##     y <- getYcoord_scale2(phylo, df, yscale)
... ...
@@ -68,15 +68,15 @@ setMethod("gzoom", signature(object="ggtree"),
68 68
 ##           })
69 69
 
70 70
 
71
-##' zoom selected subtree
72
-##'
73
-##'
74
-##' @rdname gzoom-methods
75
-##' @exportMethod gzoom
76
-setMethod("gzoom", signature(object="beast"),
77
-          function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
78
-              gzoom.phylo(get.tree(object), focus, subtree, widths)
79
-          })
71
+## ##' zoom selected subtree
72
+## ##'
73
+## ##'
74
+## ##' @rdname gzoom-methods
75
+## ##' @exportMethod gzoom
76
+## setMethod("gzoom", signature(object="beast"),
77
+##           function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
78
+##               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
 
88
-
88
+##' zoom selected subtree
89
+##'
90
+##'
89 91
 ##' @rdname gzoom-methods
90 92
 ##' @exportMethod gzoom
91 93
 setMethod("gzoom", signature(object="treedata"),
... ...
@@ -1,16 +1,16 @@
1 1
 
2
-##' @rdname reroot-methods
3
-##' @exportMethod reroot
4
-setMethod("reroot", signature(object="beast"),
5
-          function(object, node, ...) {
6
-              object@phylo <- reroot(object@phylo, node, ...)
2
+## ##' @rdname reroot-methods
3
+## ##' @exportMethod reroot
4
+## setMethod("reroot", signature(object="beast"),
5
+##           function(object, node, ...) {
6
+##               object@phylo <- reroot(object@phylo, node, ...)
7 7
 
8
-              node_map <- attr(object@phylo, "node_map")
9
-              idx <- match(object@stats$node, node_map[,1])
10
-              object@stats$node <- node_map[idx, 2]
8
+##               node_map <- attr(object@phylo, "node_map")
9
+##               idx <- match(object@stats$node, node_map[,1])
10
+##               object@stats$node <- node_map[idx, 2]
11 11
 
12
-              return(object)
13
-          })
12
+##               return(object)
13
+##           })
14 14
 
15 15
 ## ##' @rdname reroot-methods
16 16
 ## ##' @exportMethod reroot
... ...
@@ -1,14 +1,16 @@
1
+## ##' scale color by a numerical tree attribute
2
+## ##'
3
+## ##'
4
+## ##' @rdname scale_color-methods
5
+## ##' @exportMethod scale_color
6
+## setMethod("scale_color", signature(object="beast"),
7
+##           function(object, by, ...) {
8
+##               scale_color_(object, by, ...)
9
+##           })
10
+
1 11
 ##' scale color by a numerical tree attribute
2 12
 ##'
3 13
 ##'
4
-##' @rdname scale_color-methods
5
-##' @exportMethod scale_color
6
-setMethod("scale_color", signature(object="beast"),
7
-          function(object, by, ...) {
8
-              scale_color_(object, by, ...)
9
-          })
10
-
11
-
12 14
 ##' @rdname scale_color-methods
13 15
 ##' @exportMethod scale_color
14 16
 setMethod("scale_color", signature(object="treedata"),
... ...
@@ -18,14 +18,12 @@ fortify.treedata <- function(model, data, layout="rectangular", yscale="none",
18 18
     }
19 19
     ypos <- getYcoord(x)
20 20
     N <- Nnode(x, internal.only=FALSE)
21
-    xypos <- data.frame(node=1:N, x=xpos, y=ypos)
21
+    xypos <- data_frame(node=1:N, x=xpos, y=ypos)
22 22
 
23
-    df <- as.data.frame(model, branch.length="branch.length") # already set by set_branch_length
24
-    idx <- is.na(df$parent)
25
-    df$parent[idx] <- df$node[idx]
26
-    rownames(df) <- df$node
23
+    df <- as_data_frame(model, branch.length="branch.length") # already set by set_branch_length
24
+    ##rownames(df) <- as.character(df$node)
27 25
 
28
-    res <- merge(df, xypos, by='node', all.y=TRUE)
26
+    res <- full_join(df, xypos, by = "node")
29 27
 
30 28
     ## add branch mid position
31 29
     res <- calculate_branch_mid(res)
... ...
@@ -39,31 +37,41 @@ fortify.treedata <- function(model, data, layout="rectangular", yscale="none",
39 37
     scaleY(as.phylo(model), res, yscale, layout, ...)
40 38
 }
41 39
 
42
-##' @method as.data.frame treedata
40
+##' @method as_data_frame treedata
41
+##' @importFrom tibble as_data_frame
43 42
 ##' @export
44 43
 ## @importFrom treeio Nnode
45 44
 ## @importFrom treeio Ntip
46
-as.data.frame.treedata <- function(x, row.names, optional, branch.length = "branch.length", ...) {
45
+as_data_frame.treedata <- function(x, row.names, optional, branch.length = "branch.length", ...) {
47 46
     tree <- set_branch_length(x, branch.length)
48 47
 
49 48
     ## res <- as.data.frame(tree@phylo)
50
-    res <- as.data.frame_(tree@phylo)
51
-    tree_anno <- get_tree_data(x)
49
+    res <- as_data_frame_(tree@phylo)
50
+    tree_anno <- as_data_frame(get_tree_data(x))
52 51
     if (nrow(tree_anno) > 0) {
53
-        res <- merge(res, tree_anno, by="node", all.x=TRUE)
52
+        by <- "node"
53
+        tree_anno$node <- as.integer(tree_anno$node)
54
+        if ("parent" %in% colnames(tree_anno)) {
55
+            by <- c(by, "parent")
56
+            tree_anno$parent <- as.integer(tree_anno$parent)
57
+        }
58
+
59
+        res <- full_join(res, tree_anno, by=by)
54 60
     }
55 61
     return(res)
56 62
 }
57 63
 
58 64
 ##@method as.data.frame phylo
59 65
 ##@export
60
-as.data.frame_ <- function(x, row.names, optional, branch.length = "branch.length", ...) {
66
+##' @importFrom tibble data_frame
67
+##' @importFrom dplyr full_join
68
+as_data_frame_ <- function(x, row.names, optional, branch.length = "branch.length", ...) {
61 69
     phylo <- x
62 70
     ntip <- Ntip(phylo)
63 71
     N <- Nnode(phylo, internal.only=FALSE)
64 72
 
65 73
     tip.label <- phylo[["tip.label"]]
66
-    res <- as.data.frame(phylo[["edge"]])
74
+    res <- as_data_frame(phylo[["edge"]])
67 75
     colnames(res) <- c("parent", "node")
68 76
     if (!is.null(phylo$edge.length))
69 77
         res$branch.length <- phylo$edge.length
... ...
@@ -73,11 +81,14 @@ as.data.frame_ <- function(x, row.names, optional, branch.length = "branch.lengt
73 81
     if ( !is.null(phylo$node.label) ) {
74 82
         label[(ntip+1):N] <- phylo$node.label
75 83
     }
76
-    label.df <- data.frame(node=1:N, label=label)
77
-    res <- merge(res, label.df, by='node', all.y=TRUE)
78 84
     isTip <- rep(FALSE, N)
79 85
     isTip[1:ntip] <- TRUE
80
-    res$isTip <- isTip
86
+
87
+    label.df <- data_frame(node=1:N, label=label, isTip = isTip)
88
+    res <- full_join(res, label.df, by='node')
89
+
90
+    idx <- is.na(res$parent)
91
+    res$parent[idx] <- res$node[idx]
81 92
 
82 93
     return(res)
83 94
 }
... ...
@@ -1449,7 +1460,7 @@ getYcoord_scale_numeric <- function(tr, df, yscale, ...) {
1449 1460
 }
1450 1461
 
1451 1462
 .assign_parent_status <- function(tr, df, variable) {
1452
-    yy <- df[, variable]
1463
+    yy <- df[[variable]]
1453 1464
     na.idx <- which(is.na(yy))
1454 1465
     if (length(na.idx) > 0) {
1455 1466
         tree <- get.tree(tr)
... ...
@@ -1470,7 +1481,7 @@ getYcoord_scale_numeric <- function(tr, df, yscale, ...) {
1470 1481
 }
1471 1482
 
1472 1483
 .assign_child_status <- function(tr, df, variable, yscale_mapping=NULL) {
1473
-    yy <- df[, variable]
1484
+    yy <- df[[variable]]
1474 1485
     if (!is.null(yscale_mapping)) {
1475 1486
         yy <- yscale_mapping[yy]
1476 1487
     }
... ...
@@ -1507,7 +1518,7 @@ getYcoord_scale_category <- function(tr, df, yscale, yscale_mapping=NULL, ...) {
1507 1518
     }
1508 1519
 
1509 1520
     if (yscale == "label") {
1510
-        yy <- df[, yscale]
1521
+        yy <- df[[yscale]]
1511 1522
         ii <- which(is.na(yy))
1512 1523
         if (length(ii)) {
1513 1524
             df[ii, yscale] <- df[ii, "node"]
... ...
@@ -1518,7 +1529,7 @@ getYcoord_scale_category <- function(tr, df, yscale, yscale_mapping=NULL, ...) {
1518 1529
     df <- .assign_parent_status(tr, df, yscale)
1519 1530
     df <- .assign_child_status(tr, df, yscale, yscale_mapping)
1520 1531
 
1521
-    y <- df[, yscale]
1532
+    y <- df[[yscale]]
1522 1533
 
1523 1534
     if (anyNA(y)) {
1524 1535
         warning("NA found in y scale mapping, all were setting to 0")
... ...
@@ -1543,7 +1554,8 @@ add_angle_slanted <- function(res) {
1543 1554
 }
1544 1555
 
1545 1556
 calculate_branch_mid <- function(res) {
1546
-    res$branch <- (res[res$parent, "x"] + res[, "x"])/2
1557
+    res$branch <- with(res, (x[match(parent, node)] + x)/2)
1558
+    ## res$branch <- (res[match(res$parent, res$node), "x"] + res[, "x"])/2
1547 1559
     if (!is.null(res$length)) {
1548 1560
         res$length[is.na(res$length)] <- 0
1549 1561
     }
... ...
@@ -1566,6 +1578,9 @@ set_branch_length <- function(tree_object, branch.length) {
1566 1578
 
1567 1579
     tree_anno <- get_tree_data(tree_object)
1568 1580
 
1581
+    if (is(tree_anno, "matrix"))
1582
+        tree_anno <- as.data.frame(tree_anno)
1583
+
1569 1584
     phylo <- get.tree(tree_object)
1570 1585
 
1571 1586
     cn <- colnames(tree_anno)
... ...
@@ -1573,7 +1588,7 @@ set_branch_length <- function(tree_object, branch.length) {
1573 1588
 
1574 1589
     length <- match.arg(branch.length, cn)
1575 1590
 
1576
-    if (all(is.na(as.numeric(tree_anno[, length])))) {
1591
+    if (all(is.na(as.numeric(tree_anno[[length]])))) {
1577 1592
         stop("branch.length should be numerical attributes...")
1578 1593
     }
1579 1594
 
... ...
@@ -1584,7 +1599,7 @@ set_branch_length <- function(tree_object, branch.length) {
1584 1599
                 by  = "node",
1585 1600
                 all.x = TRUE)
1586 1601
     dd <- dd[match(edge$node, dd$node),]
1587
-    len <- unlist(dd[, length])
1602
+    len <- unlist(dd[[length]])
1588 1603
     len <- as.numeric(len)
1589 1604
     len[is.na(len)] <- 0
1590 1605
 
... ...
@@ -1,7 +1,7 @@
1 1
 ---
2 2
 output:
3 3
   md_document:
4
-    variant: gfm
4
+    variant: markdown_github
5 5
 html_preview: false
6 6
 ---
7 7
 
... ...
@@ -1,70 +1,35 @@
1 1
 <!-- README.md is generated from README.Rmd. Please edit that file -->
2
-
3
-# ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
2
+ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
3
+===========================================================================================================================
4 4
 
5 5
 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
6 6
 
7
-[![releaseVersion](https://img.shields.io/badge/release%20version-1.10.0-green.svg?style=flat)](https://bioconductor.org/packages/ggtree)
8
-[![develVersion](https://img.shields.io/badge/devel%20version-1.11.1-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree)
9
-[![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
10
-[![total](https://img.shields.io/badge/downloads-21911/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
11
-[![month](https://img.shields.io/badge/downloads-1156/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
12
-
13
-[![Project Status: Active - The project has reached a stable, usable
14
-state and is being actively
15
-developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
16
-[![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
17
-[![Last-changedate](https://img.shields.io/badge/last%20change-2017--12--04-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
18
-[![GitHub
19
-forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network)
20
-[![GitHub
21
-stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers)
22
-[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
23
-
24
-[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)
25
-[![Build
26
-Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/)
27
-[![Linux/Mac Travis Build
28
-Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree)
29
-[![AppVeyor Build
30
-Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree)
31
-[![Backers on Open
32
-Collective](https://opencollective.com/ggtree/backers/badge.svg)](#backers)
33
-[![Sponsors on Open
34
-Collective](https://opencollective.com/ggtree/sponsors/badge.svg)](#sponsors)
35
-
36
-The `ggtree` package extending the `ggplot2` package. It based on
37
-grammar of graphics and takes all the good parts of `ggplot2`. `ggtree`
38
-is designed for not only viewing phylogenetic tree but also displaying
39
-annotation data on the
40
-tree.
7
+[![releaseVersion](https://img.shields.io/badge/release%20version-1.10.0-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.11.2-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![total](https://img.shields.io/badge/downloads-21911/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1156/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
8
+
9
+[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2017--12--05-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
10
+
11
+[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree) [![Backers on Open Collective](https://opencollective.com/ggtree/backers/badge.svg)](#backers) [![Sponsors on Open Collective](https://opencollective.com/ggtree/sponsors/badge.svg)](#sponsors)
12
+
13
+The `ggtree` package extending the `ggplot2` package. It based on grammar of graphics and takes all the good parts of `ggplot2`. `ggtree` is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.
41 14
 
42 15
 [![Twitter](https://img.shields.io/twitter/url/https/github.com/GuangchuangYu/ggtree.svg?style=social)](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu)
43 16
 
44
-For details, please visit our project website,
45
-<https://guangchuangyu.github.io/ggtree>.
17
+For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>.
46 18
 
47
-  - [Documentation](https://guangchuangyu.github.io/ggtree/documentation/)
48
-  - [FAQ](https://guangchuangyu.github.io/ggtree/faq/)
49
-  - [Featured
50
-    Articles](https://guangchuangyu.github.io/ggtree/featuredArticles/)
51
-  - [Feedback](https://guangchuangyu.github.io/ggtree/#feedback)
19
+-   [Documentation](https://guangchuangyu.github.io/ggtree/documentation/)
20
+-   [FAQ](https://guangchuangyu.github.io/ggtree/faq/)
21
+-   [Featured Articles](https://guangchuangyu.github.io/ggtree/featuredArticles/)
22
+-   [Feedback](https://guangchuangyu.github.io/ggtree/#feedback)
52 23
 
24
+------------------------------------------------------------------------
53 25
 
54 26
 Please cite the following article when using `ggtree`:
55 27
 
56
-**G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R
57
-package for visualization and annotation of phylogenetic trees with
58
-their covariates and other associated data. ***Methods in Ecology and
59
-Evolution***. 2017,
60
-8(1):28-36.
28
+**G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ***Methods in Ecology and Evolution***. 2017, 8(1):28-36.
61 29
 
62
-[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628)
63
-[![Altmetric](https://img.shields.io/badge/Altmetric-333-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
64
-[![citation](https://img.shields.io/badge/cited%20by-51-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
30
+[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-333-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-52-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
65 31
 
32
+------------------------------------------------------------------------
66 33
 
67 34
 ### Citation
68 35
 
... ...
@@ -72,38 +37,25 @@ Evolution***. 2017,
72 37
 
73 38
 ### Download stats
74 39
 
75
-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
76
-[![total](https://img.shields.io/badge/downloads-21911/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
77
-[![month](https://img.shields.io/badge/downloads-1156/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
40
+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-21911/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1156/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
78 41
 
79 42
 <img src="docs/images/dlstats.png" width="890"/>
80 43
 
81
-## Contributors
44
+Contributors
45
+------------
82 46
 
83
-This project exists thanks to all the people who contribute.
84
-[\[Contribute\]](CONTRIBUTING.md).
85
-<a href="https://github.com/GuangchuangYu/ggtree/graphs/contributors"><img src="https://opencollective.com/ggtree/contributors.svg?width=890" /></a>
47
+This project exists thanks to all the people who contribute. [\[Contribute\]](CONTRIBUTING.md). <a href="https://github.com/GuangchuangYu/ggtree/graphs/contributors"><img src="https://opencollective.com/ggtree/contributors.svg?width=890" /></a>
86 48
 
87
-## Backers
49
+Backers
50
+-------
88 51
 
89
-Thank you to all our backers\! 🙏 \[[Become a
90
-backer](https://opencollective.com/ggtree#backer)\]
52
+Thank you to all our backers! 🙏 \[[Become a backer](https://opencollective.com/ggtree#backer)\]
91 53
 
92 54
 <a href="https://opencollective.com/ggtree#backers" target="_blank"><img src="https://opencollective.com/ggtree/backers.svg?width=890"></a>
93 55
 
94
-## Sponsors
95
-
96
-Support this project by becoming a sponsor. Your logo will show up here
97
-with a link to your website. \[[Become a
98
-sponsor](https://opencollective.com/ggtree#sponsor)\]
99
-
100
-<a href="https://opencollective.com/ggtree/sponsor/0/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/0/avatar.svg"></a>
101
-<a href="https://opencollective.com/ggtree/sponsor/1/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/1/avatar.svg"></a>
102
-<a href="https://opencollective.com/ggtree/sponsor/2/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/2/avatar.svg"></a>
103
-<a href="https://opencollective.com/ggtree/sponsor/3/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/3/avatar.svg"></a>
104
-<a href="https://opencollective.com/ggtree/sponsor/4/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/4/avatar.svg"></a>
105
-<a href="https://opencollective.com/ggtree/sponsor/5/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/5/avatar.svg"></a>
106
-<a href="https://opencollective.com/ggtree/sponsor/6/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/6/avatar.svg"></a>
107
-<a href="https://opencollective.com/ggtree/sponsor/7/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/7/avatar.svg"></a>
108
-<a href="https://opencollective.com/ggtree/sponsor/8/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/8/avatar.svg"></a>
109
-<a href="https://opencollective.com/ggtree/sponsor/9/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/9/avatar.svg"></a>
56
+Sponsors
57
+--------
58
+
59
+Support this project by becoming a sponsor. Your logo will show up here with a link to your website. \[[Become a sponsor](https://opencollective.com/ggtree#sponsor)\]
60
+
61
+<a href="https://opencollective.com/ggtree/sponsor/0/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/0/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/1/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/1/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/2/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/2/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/3/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/3/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/4/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/4/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/5/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/5/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/6/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/6/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/7/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/7/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/8/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/8/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/9/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/9/avatar.svg"></a>
110 62
Binary files a/docs/images/citation.png and b/docs/images/citation.png differ
... ...
@@ -4,11 +4,13 @@
4 4
 \alias{geom_range}
5 5
 \title{geom_range}
6 6
 \usage{
7
-geom_range(range = "height_0.95_HPD", ...)
7
+geom_range(range = "length_0.95_HPD", branch.length = "branch.length", ...)
8 8
 }
9 9
 \arguments{
10 10
 \item{range}{range, e.g. "height_0.95_HPD"}
11 11
 
12
+\item{branch.length}{corresponding branch.length}
13
+
12 14
 \item{...}{additional parameter, e.g. color, size, alpha}
13 15
 }
14 16
 \value{
... ...
@@ -5,7 +5,6 @@
5 5
 \alias{gzoom}
6 6
 \alias{gzoom}
7 7
 \alias{gzoom,ggtree-method}
8
-\alias{gzoom,beast-method}
9 8
 \alias{gzoom,codeml-method}
10 9
 \alias{gzoom,treedata-method}
11 10
 \alias{gzoom,paml_rst-method}
... ...
@@ -17,9 +16,6 @@ gzoom(object, focus, subtree = FALSE, widths = c(0.3, 0.7), ...)
17 16
 \S4method{gzoom}{ggtree}(object, focus, widths = c(0.3, 0.7),
18 17
   xmax_adjust = 0)
19 18
 
20
-\S4method{gzoom}{beast}(object, focus, subtree = FALSE, widths = c(0.3,
21
-  0.7))
22
-
23 19
 \S4method{gzoom}{codeml}(object, focus, subtree = FALSE, widths = c(0.3,
24 20
   0.7))
25 21
 
26 22
new file mode 100644
... ...
@@ -0,0 +1,22 @@
1
+% Generated by roxygen2: do not edit by hand
2
+% Please edit documentation in R/format.R
3
+\name{range_format}
4
+\alias{range_format}
5
+\title{range_format}
6
+\usage{
7
+range_format(x, trans = NULL)
8
+}
9
+\arguments{
10
+\item{x}{input list}
11
+
12
+\item{trans}{transformation function}
13
+}
14
+\value{
15
+character vector of '[lower, upper]'
16
+}
17
+\description{
18
+format a list of range (HPD, CI, etc that has length of 2)
19
+}
20
+\author{
21
+guangchuang yu
22
+}
... ...
@@ -3,14 +3,11 @@
3 3
 \docType{methods}
4 4
 \name{reroot}
5 5
 \alias{reroot}
6
-\alias{reroot,beast-method}
7 6
 \alias{reroot,phylo-method}
8 7
 \title{reroot method}
9 8
 \usage{
10 9
 reroot(object, node, ...)
11 10
 
12
-\S4method{reroot}{beast}(object, node, ...)
13
-
14 11
 \S4method{reroot}{phylo}(object, node, ...)
15 12
 }
16 13
 \arguments{
... ...
@@ -3,7 +3,6 @@
3 3
 \docType{methods}
4 4
 \name{scale_color}
5 5
 \alias{scale_color}
6
-\alias{scale_color,beast-method}
7 6
 \alias{scale_color,treedata-method}
8 7
 \alias{scale_color,paml_rst-method}
9 8
 \alias{scale_color,phylo-method}
... ...
@@ -11,8 +10,6 @@
11 10
 \usage{
12 11
 scale_color(object, by, ...)
13 12
 
14
-\S4method{scale_color}{beast}(object, by, ...)
15
-
16 13
 \S4method{scale_color}{treedata}(object, by, ...)
17 14
 
18 15
 \S4method{scale_color}{paml_rst}(object, by, ...)
... ...
@@ -43,7 +43,7 @@ library("ggtree")
43 43
 
44 44
 If you use `ggtree` in published research, please cite:
45 45
 
46
-__G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36. doi:[10.1111/2041-210X.12628](http://dx.doi.org/10.1111/2041-210X.12628)
46
+__G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36. doi:[10.1111/2041-210X.12628](http://dx.doi.org/10.1111/2041-210X.12628).
47 47
 
48 48
 
49 49
 # Introduction
... ...
@@ -135,7 +135,7 @@ get.fields(beast)
135 135
 Users can use `ggtree(beast)` to visualize the tree and add layer to annotate it.
136 136
 
137 137
 ```{r warning=FALSE, fig.width=10, fig.height=10}
138
-ggtree(beast, ndigits=2, branch.length = 'none') + geom_text(aes(x=branch, label=length_0.95_HPD), vjust=-.5, color='firebrick')
138
+ggtree(beast, branch.length = 'none') + geom_text(aes(x=branch, label=range_format(length_0.95_HPD)), vjust=-.5, color='firebrick')
139 139
 ```
140 140
 
141 141
 `ggtree` provides `geom_range` layer to display uncertainty of branch length.