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

update plot method for hclust-like class

xiangpin authored on 19/07/2022 16:02:24
Showing 1 changed files
R/ggtree.R
History View file @ bf7a47fd
... ... 
@@ -17,6 +17,9 @@
17 17 
 ##' @param root.position position of the root node (default = 0)
18 18 
 ##' @param xlim x limits, only works for 'inward_circular' layout
19 19 
 ##' @param layout.params list, the parameters of layout, when layout is a function.
20 
+##' @param hang numeric The fraction of the tree plot height by which labels should hang
21 
+##' below the rest of the plot. A negative value will cause the labels to hang down from 0. This
22 
+##' parameter only work with the 'dendrogram' layout for 'hclust' like class, default is 0.1.
20 23 
 ##' @return tree
21 24 
 ##' @importFrom ggplot2 ggplot
22 25 
 ##' @importFrom ggplot2 xlab
... ... 
@@ -59,6 +62,7 @@ ggtree <- function(tr,
59 62 
                    root.position  = 0,
60 63 
                    xlim = NULL,
61 64 
                    layout.params = list(),
65 
+                   hang = .1,
62 66 
                    ...) {
63 67
64 68 
     # Check if layout string is valid.
... ... 
@@ -102,6 +106,7 @@ ggtree <- function(tr,
102 106 
                 right         = right,
103 107 
                 branch.length = branch.length,
104 108 
                 root.position = root.position,
109 
+                hang          = hang,
105 110 
                 ...)
106 111
107 112 
     if (!is.null(dd)){
Browse code

Document update

Document update

William Lee authored on 22/03/2022 14:46:29
Showing 1 changed files
R/ggtree.R
History View file @ 3c7f66c8
... ... 
@@ -37,6 +37,10 @@
37 37 
 ##' visualization and annotation of phylogenetic trees with their covariates and
38 38 
 ##' other associated data. Methods in Ecology and Evolution, 8(1):28-36.
39 39 
 ##' <https://doi.org/10.1111/2041-210X.12628>
40 
+##'
41 
+##' For more information, please refer to
42 
+##' *Data Integration, Manipulation and Visualization of Phylogenetic Trees*
43 
+##' <http://yulab-smu.top/treedata-book/index.html> by Guangchuang Yu.
40 44 
 ##' @examples
41 45 
 ##' require(ape)
42 46 
 ##' tr <- rtree(10)
Browse code

add message of graph layout

xiangpin authored on 10/12/2021 05:41:02
Showing 1 changed files
R/ggtree.R
History View file @ a055e962
... ... 
@@ -101,6 +101,8 @@ ggtree <- function(tr,
101 101 
                 ...)
102 102
103 103 
     if (!is.null(dd)){
104 
+        message_wrap("The tree object will be displayed with graph layout since
105 
+                      layout argument was specified the graph layout function.")
104 106 
         p$data <- dplyr::left_join(
105 107 
                     p$data %>% select(-c("x", "y")),
106 108 
                     dd,
Browse code

add graph layout

xiangpin authored on 09/12/2021 13:33:49
Showing 1 changed files
R/ggtree.R
History View file @ a28c2cef
... ... 
@@ -16,6 +16,7 @@
16 16 
 ##' @param branch.length variable for scaling branch, if 'none' draw cladogram
17 17 
 ##' @param root.position position of the root node (default = 0)
18 18 
 ##' @param xlim x limits, only works for 'inward_circular' layout
19 
+##' @param layout.params list, the parameters of layout, when layout is a function.
19 20 
 ##' @return tree
20 21 
 ##' @importFrom ggplot2 ggplot
21 22 
 ##' @importFrom ggplot2 xlab
... ... 
@@ -53,12 +54,22 @@ ggtree <- function(tr,
53 54 
                    branch.length  = "branch.length",
54 55 
                    root.position  = 0,
55 56 
                    xlim = NULL,
57 
+                   layout.params = list(),
56 58 
                    ...) {
57 59
58 60 
     # Check if layout string is valid.
59 
-    layout %<>% match.arg(c("rectangular", "slanted", "fan", "circular", 'inward_circular',
61 
+    trash <- try(silent = TRUE,
62 
+                 expr = {
63 
+                   layout %<>% match.arg(c("rectangular", "slanted", "fan", "circular", 'inward_circular',
60 64 
                             "radial", "unrooted", "equal_angle", "daylight", "dendrogram",
61 65 
                             "ape", "ellipse", "roundrect"))
66 
+                  }
67 
+             )
68 
+
69 
+    dd <- check.graph.layout(tr, trash, layout, layout.params)
70 
+    if (inherits(trash, "try-error") && !is.null(dd)){
71 
+        layout <- "rectangular"
72 
+    }
62 73
63 74 
     if (layout == "unrooted") {
64 75 
         layout <- "daylight"
... ... 
@@ -89,6 +100,15 @@ ggtree <- function(tr,
89 100 
                 root.position = root.position,
90 101 
                 ...)
91 102
103 
+    if (!is.null(dd)){
104 
+        p$data <- dplyr::left_join(
105 
+                    p$data %>% select(-c("x", "y")),
106 
+                    dd,
107 
+                    by = "node"
108 
+        )
109 
+        layout <- "equal_angle"
110 
+    }
111 
+
92 112 
     if (is(tr, "multiPhylo")) {
93 113 
         multiPhylo <- TRUE
94 114 
     } else {
... ... 
@@ -154,3 +174,30 @@ ggtree_references <- function() {
154 174 
            "<http://yulab-smu.top/treedata-book/>\n"
155 175 
            )
156 176 
 }
177 
+
178 
+check.graph.layout <- function(tr, trash, layout, layout.params){
179 
+    if (inherits(trash, "try-error")){
180 
+        gp <- ape::as.igraph.phylo(as.phylo(tr), use.labels = FALSE)
181 
+        #dd <- ggraph::create_layout(gp, layout = layout)
182 
+        if (is.function(layout)){
183 
+            dd <- do.call(layout, c(list(gp), layout.params))
184 
+            if (!inherits(dd, "matrix")){
185 
+                if ("xy" %in% names(dd)){
186 
+                    dd <- dd$xx
187 
+                }else if ("layout" %in% names(dd)){
188 
+                    dd <- dd$layout
189 
+                }else{
190 
+                    stop(trash, call. = FALSE)
191 
+                }
192 
+            }
193 
+            dd <- data.frame(dd)
194 
+            colnames(dd) <- c("x", "y")
195 
+            dd$node <- seq_len(nrow(dd))
196 
+        }else{
197 
+            stop(trash, call. = FALSE)
198 
+        }
199 
+    }else{
200 
+        dd <- NULL
201 
+    }
202 
+    return(dd)
203 
+}
Browse code

update citatino

Guangchuang Yu authored on 13/10/2021 03:35:13
Showing 1 changed files
R/ggtree.R
History View file @ 15c3faed
... ... 
@@ -131,18 +131,18 @@ ggtree_citations <- function() {
131 131 
     paste0('1. ',
132 132 
            "Guangchuang Yu. ",
133 133 
            "Using ggtree to visualize data on tree-like structures. ",
134 
-           "Current Protocols in Bioinformatics, 2020, 69:e96. doi:10.1002/cpbi.96\n",
134 
+           "Current Protocols in Bioinformatics. 2020, 69:e96. doi:10.1002/cpbi.96\n",
135 135
136 136 
            '2. ',
137 137 
            "Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. ",
138 138 
            "Two methods for mapping and visualizing associated data on phylogeny using ggtree. ",
139 
-           "Molecular Biology and Evolution 2018, 35(12):3041-3043. doi:10.1093/molbev/msy194\n",
139 
+           "Molecular Biology and Evolution. 2018, 35(12):3041-3043. doi:10.1093/molbev/msy194\n",
140 140
141 141 
            # '\033[36m', '-', '\033[39m ',
142 142 
            "3. ",
143 143 
            "Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ",
144 144 
            "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ",
145 
-           "Methods in Ecology and Evolution 2017, 8(1):28-36. doi:10.1111/2041-210X.12628\n"
145 
+           "Methods in Ecology and Evolution. 2017, 8(1):28-36. doi:10.1111/2041-210X.12628\n"
146 146 
            )
147 147 
 }
148 148
Browse code

remove extra code and export continuous arg

xiangpin authored on 07/04/2021 08:16:32
Showing 1 changed files
R/ggtree.R
History View file @ 04c989dc
... ... 
@@ -27,7 +27,7 @@
27 27 
 ##' @importFrom ggplot2 coord_polar
28 28 
 ##' @export
29 29 
 ##' @author Yu Guangchuang
30 
-##' @seealso [ape::ladderize()]
30 
+##' @seealso [geom_tree()]
31 31 
 ##' @references 1. G Yu, TTY Lam, H Zhu, Y Guan (2018). Two methods for mapping and visualizing associated data
32 32 
 ##' on phylogeny using ggtree. Molecular Biology and Evolution, 35(2):3041-3043.
33 33 
 ##' <https://doi.org/10.1093/molbev/msy194>
Browse code

update

Guangchuang Yu authored on 08/01/2021 07:30:55
Showing 1 changed files
R/ggtree.R
History View file @ 7353eb90
... ... 
@@ -125,3 +125,32 @@ ggtree <- function(tr,
125 125
126 126 
     return(p)
127 127 
 }
128 
+
129 
+
130 
+ggtree_citations <- function() {
131 
+    paste0('1. ',
132 
+           "Guangchuang Yu. ",
133 
+           "Using ggtree to visualize data on tree-like structures. ",
134 
+           "Current Protocols in Bioinformatics, 2020, 69:e96. doi:10.1002/cpbi.96\n",
135 
+
136 
+           '2. ',
137 
+           "Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. ",
138 
+           "Two methods for mapping and visualizing associated data on phylogeny using ggtree. ",
139 
+           "Molecular Biology and Evolution 2018, 35(12):3041-3043. doi:10.1093/molbev/msy194\n",
140 
+
141 
+           # '\033[36m', '-', '\033[39m ',
142 
+           "3. ",
143 
+           "Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ",
144 
+           "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ",
145 
+           "Methods in Ecology and Evolution 2017, 8(1):28-36. doi:10.1111/2041-210X.12628\n"
146 
+           )
147 
+}
148 
+
149 
+
150 
+ggtree_references <- function() {
151 
+    paste0(ggtree_citations(), "\n",
152 
+           "For more information, please refer to the online book:",
153 
+           "Data Integration, Manipulation and Visualization of Phylogenetic Trees.",
154 
+           "<http://yulab-smu.top/treedata-book/>\n"
155 
+           )
156 
+}
Browse code

add another new layout roundrect

xiangpin authored on 28/09/2020 09:02:12
Showing 1 changed files
R/ggtree.R
History View file @ dfd00863
... ... 
@@ -58,7 +58,7 @@ ggtree <- function(tr,
58 58 
     # Check if layout string is valid.
59 59 
     layout %<>% match.arg(c("rectangular", "slanted", "fan", "circular", 'inward_circular',
60 60 
                             "radial", "unrooted", "equal_angle", "daylight", "dendrogram",
61 
-                            "ape", "ellipse"))
61 
+                            "ape", "ellipse", "roundrect"))
62 62
63 63 
     if (layout == "unrooted") {
64 64 
         layout <- "daylight"
Browse code

add ellipse layout

xiangpin authored on 28/09/2020 08:05:23
Showing 1 changed files
R/ggtree.R
History View file @ 68fddb0d
... ... 
@@ -58,7 +58,7 @@ ggtree <- function(tr,
58 58 
     # Check if layout string is valid.
59 59 
     layout %<>% match.arg(c("rectangular", "slanted", "fan", "circular", 'inward_circular',
60 60 
                             "radial", "unrooted", "equal_angle", "daylight", "dendrogram",
61 
-                            "ape"))
61 
+                            "ape", "ellipse"))
62 62
63 63 
     if (layout == "unrooted") {
64 64 
         layout <- "daylight"
Browse code

as_ylab in geom_tiplab()

Guangchuang Yu authored on 28/07/2020 06:36:51
Showing 1 changed files
R/ggtree.R
History View file @ 59c29a00
... ... 
@@ -57,7 +57,7 @@ ggtree <- function(tr,
57 57
58 58 
     # Check if layout string is valid.
59 59 
     layout %<>% match.arg(c("rectangular", "slanted", "fan", "circular", 'inward_circular',
60 
-                            "radial", "unrooted", "equal_angle", "daylight",
60 
+                            "radial", "unrooted", "equal_angle", "daylight", "dendrogram",
61 61 
                             "ape"))
62 62
63 63 
     if (layout == "unrooted") {
... ... 
@@ -106,6 +106,8 @@ ggtree <- function(tr,
106 106 
         p <- p + layout_inward_circular(xlim = xlim)
107 107 
     } else if (layout == "fan") {
108 108 
         p <- p + layout_fan(open.angle)
109 
+    } else if (layout == "dendrogram") {
110 
+        p <- p + layout_dendrogram()
109 111 
     } else if (layout %in% c("daylight", "equal_angle", "ape")) {
110 112 
         p <- p + ggplot2::coord_fixed()
111 113 
         d <- p$data
Browse code

layout-inward-circular

Guangchuang Yu authored on 16/07/2020 10:49:58
Showing 1 changed files
R/ggtree.R
History View file @ 76e422ba
... ... 
@@ -15,6 +15,7 @@
15 15 
 ##' right-hand side? See [ape::ladderize()] for more information.
16 16 
 ##' @param branch.length variable for scaling branch, if 'none' draw cladogram
17 17 
 ##' @param root.position position of the root node (default = 0)
18 
+##' @param xlim x limits, only works for 'inward_circular' layout
18 19 
 ##' @return tree
19 20 
 ##' @importFrom ggplot2 ggplot
20 21 
 ##' @importFrom ggplot2 xlab
... ... 
@@ -51,10 +52,11 @@ ggtree <- function(tr,
51 52 
                    right          = FALSE,
52 53 
                    branch.length  = "branch.length",
53 54 
                    root.position  = 0,
55 
+                   xlim = NULL,
54 56 
                    ...) {
55 57
56 58 
     # Check if layout string is valid.
57 
-    layout %<>% match.arg(c("rectangular", "slanted", "fan", "circular",
59 
+    layout %<>% match.arg(c("rectangular", "slanted", "fan", "circular", 'inward_circular',
58 60 
                             "radial", "unrooted", "equal_angle", "daylight",
59 61 
                             "ape"))
60 62
... ... 
@@ -100,6 +102,8 @@ ggtree <- function(tr,
100 102
101 103 
     if (layout == "circular" || layout == "radial") {
102 104 
         p <- p + layout_circular()
105 
+    } else if (layout == 'inward_circular') {
106 
+        p <- p + layout_inward_circular(xlim = xlim)
103 107 
     } else if (layout == "fan") {
104 108 
         p <- p + layout_fan(open.angle)
105 109 
     } else if (layout %in% c("daylight", "equal_angle", "ape")) {
Browse code

geom_tiplab() works with unrooted layout, #292

Guangchuang Yu authored on 23/04/2020 03:13:24
Showing 1 changed files
R/ggtree.R
History View file @ f6dd1c41
... ... 
@@ -104,6 +104,12 @@ ggtree <- function(tr,
104 104 
         p <- p + layout_fan(open.angle)
105 105 
     } else if (layout %in% c("daylight", "equal_angle", "ape")) {
106 106 
         p <- p + ggplot2::coord_fixed()
107 
+        d <- p$data
108 
+        pn <- d[d$parent, ]
109 
+        dy <- pn$y - d$y
110 
+        dx <- pn$x - d$x
111 
+        angle <- atan2(dy, dx) * 180 / pi + 180
112 
+        p$data$angle <- angle
107 113 
     } else if (yscale == "none") {
108 114 
         p <- p +
109 115 
             scale_y_continuous(expand = expansion(0, 0.6))
Browse code

import expansion

Guangchuang Yu authored on 12/03/2020 09:27:40
Showing 1 changed files
R/ggtree.R
History View file @ 210d5a66
... ... 
@@ -106,7 +106,7 @@ ggtree <- function(tr,
106 106 
         p <- p + ggplot2::coord_fixed()
107 107 
     } else if (yscale == "none") {
108 108 
         p <- p +
109 
-            scale_y_continuous(expand = expand_scale(0, 0.6))
109 
+            scale_y_continuous(expand = expansion(0, 0.6))
110 110 
     }
111 111
112 112 
     class(p) <- c("ggtree", class(p))
Browse code

if yscale is set do not scale y

Brad Jones authored on 18/02/2020 23:55:06 • GitHub committed on 18/02/2020 23:55:06
Showing 1 changed files
R/ggtree.R
History View file @ b6872f2e
... ... 
@@ -104,7 +104,7 @@ ggtree <- function(tr,
104 104 
         p <- p + layout_fan(open.angle)
105 105 
     } else if (layout %in% c("daylight", "equal_angle", "ape")) {
106 106 
         p <- p + ggplot2::coord_fixed()
107 
-    } else {
107 
+    } else if (yscale == "none") {
108 108 
         p <- p +
109 109 
             scale_y_continuous(expand = expand_scale(0, 0.6))
110 110 
     }
Browse code

added new layout 'ape' which is a copy of the 'unrooted' type in ape::plot.phylo

brj1 authored on 24/01/2020 03:03:49
Showing 1 changed files
R/ggtree.R
History View file @ b8275604
... ... 
@@ -55,7 +55,8 @@ ggtree <- function(tr,
55 55
56 56 
     # Check if layout string is valid.
57 57 
     layout %<>% match.arg(c("rectangular", "slanted", "fan", "circular",
58 
-                            "radial", "unrooted", "equal_angle", "daylight"))
58 
+                            "radial", "unrooted", "equal_angle", "daylight",
59 
+                            "ape"))
59 60
60 61 
     if (layout == "unrooted") {
61 62 
         layout <- "daylight"
... ... 
@@ -101,7 +102,7 @@ ggtree <- function(tr,
101 102 
         p <- p + layout_circular()
102 103 
     } else if (layout == "fan") {
103 104 
         p <- p + layout_fan(open.angle)
104 
-    } else if (layout %in% c("daylight", "equal_angle")) {
105 
+    } else if (layout %in% c("daylight", "equal_angle", "ape")) {
105 106 
         p <- p + ggplot2::coord_fixed()
106 107 
     } else {
107 108 
         p <- p +
Browse code

unrooted layouts (daylight and equal_angle) now use 1:1 aspect ratio

brj1 authored on 24/01/2020 03:00:12
Showing 1 changed files
R/ggtree.R
History View file @ 101a0ad5
... ... 
@@ -101,6 +101,8 @@ ggtree <- function(tr,
101 101 
         p <- p + layout_circular()
102 102 
     } else if (layout == "fan") {
103 103 
         p <- p + layout_fan(open.angle)
104 
+    } else if (layout %in% c("daylight", "equal_angle")) {
105 
+        p <- p + ggplot2::coord_fixed()
104 106 
     } else {
105 107 
         p <- p +
106 108 
             scale_y_continuous(expand = expand_scale(0, 0.6))
Browse code

add reference

Guangchuang Yu authored on 20/11/2019 03:58:34
Showing 1 changed files
R/ggtree.R
History View file @ 860448f4
... ... 
@@ -27,8 +27,16 @@
27 27 
 ##' @export
28 28 
 ##' @author Yu Guangchuang
29 29 
 ##' @seealso [ape::ladderize()]
30 
+##' @references 1. G Yu, TTY Lam, H Zhu, Y Guan (2018). Two methods for mapping and visualizing associated data
31 
+##' on phylogeny using ggtree. Molecular Biology and Evolution, 35(2):3041-3043.
32 
+##' <https://doi.org/10.1093/molbev/msy194>
33 
+##'
34 
+##' 2. G Yu, DK Smith, H Zhu, Y Guan, TTY Lam (2017). ggtree: an R package for
35 
+##' visualization and annotation of phylogenetic trees with their covariates and
36 
+##' other associated data. Methods in Ecology and Evolution, 8(1):28-36.
37 
+##' <https://doi.org/10.1111/2041-210X.12628>
30 38 
 ##' @examples
31 
-##' require(ape)
39 
+##' require(ape)
32 40 
 ##' tr <- rtree(10)
33 41 
 ##' ggtree(tr)
34 42 
 ggtree <- function(tr,
... ... 
@@ -87,13 +95,15 @@ ggtree <- function(tr,
87 95 
     p <- p + geom_tree(layout=layout, multiPhylo=multiPhylo, ...)
88 96
89 97
90 
-    p <- p + theme_tree() +
91 
-        scale_y_continuous(expand = expand_scale(0, 0.6))
98 
+    p <- p + theme_tree()
92 99
93 100 
     if (layout == "circular" || layout == "radial") {
94 101 
         p <- p + layout_circular()
95 102 
     } else if (layout == "fan") {
96 103 
         p <- p + layout_fan(open.angle)
104 
+    } else {
105 
+        p <- p +
106 
+            scale_y_continuous(expand = expand_scale(0, 0.6))
97 107 
     }
98 108
99 109 
     class(p) <- c("ggtree", class(p))
Browse code

roxygen2md

Guangchuang Yu authored on 01/11/2019 04:24:00
Showing 1 changed files
R/ggtree.R
History View file @ 1540db03
... ... 
@@ -9,10 +9,10 @@
9 9 
 ##' @param as.Date logical whether using Date class in time tree
10 10 
 ##' @param yscale y scale
11 11 
 ##' @param yscale_mapping yscale mapping for category variable
12 
-##' @param ladderize logical (default \code{TRUE}). Should the tree be re-organized to have a 'ladder'
12 
+##' @param ladderize logical (default `TRUE`). Should the tree be re-organized to have a 'ladder'
13 13 
 ##' aspect?
14 
-##' @param right logical. If \code{ladderize = TRUE}, should the ladder have the smallest clade on the
15 
-##' right-hand side? See \code{\link[ape]{ladderize}} for more information.
14 
+##' @param right logical. If `ladderize = TRUE`, should the ladder have the smallest clade on the
15 
+##' right-hand side? See [ape::ladderize()] for more information.
16 16 
 ##' @param branch.length variable for scaling branch, if 'none' draw cladogram
17 17 
 ##' @param root.position position of the root node (default = 0)
18 18 
 ##' @return tree
... ... 
@@ -26,7 +26,7 @@
26 26 
 ##' @importFrom ggplot2 coord_polar
27 27 
 ##' @export
28 28 
 ##' @author Yu Guangchuang
29 
-##' @seealso \code{\link[ape]{ladderize}}
29 
+##' @seealso [ape::ladderize()]
30 30 
 ##' @examples
31 31 
 ##' require(ape)
32 32 
 ##' tr <- rtree(10)
Browse code

ylim_ggtree

Guangchuang Yu authored on 31/10/2019 07:16:49
Showing 1 changed files
R/ggtree.R
History View file @ 6e77743a
... ... 
@@ -87,13 +87,11 @@ ggtree <- function(tr,
87 87 
     p <- p + geom_tree(layout=layout, multiPhylo=multiPhylo, ...)
88 88
89 89
90 
-    p <- p + theme_tree()
90 
+    p <- p + theme_tree() +
91 
+        scale_y_continuous(expand = expand_scale(0, 0.6))
91 92
92 93 
     if (layout == "circular" || layout == "radial") {
93 94 
         p <- p + layout_circular()
94 
-        ## refer to: https://github.com/GuangchuangYu/ggtree/issues/6
95 
-        ## and also have some space for tree scale (legend)
96 
-        p <- p + ylim(0, NA)
97 95 
     } else if (layout == "fan") {
98 96 
         p <- p + layout_fan(open.angle)
99 97 
     }
Browse code

reexport arrow and unit

Guangchuang Yu authored on 28/09/2019 10:22:18
Showing 1 changed files
R/ggtree.R
History View file @ b22e59a5
... ... 
@@ -46,7 +46,9 @@ ggtree <- function(tr,
46 46 
                    ...) {
47 47
48 48 
     # Check if layout string is valid.
49 
-    layout %<>% match.arg(c("rectangular", "slanted", "fan", "circular", "radial", "unrooted", "equal_angle", "daylight"))
49 
+    layout %<>% match.arg(c("rectangular", "slanted", "fan", "circular",
50 
+                            "radial", "unrooted", "equal_angle", "daylight"))
51 
+
50 52 
     if (layout == "unrooted") {
51 53 
         layout <- "daylight"
52 54 
         message('"daylight" method was used as default layout for unrooted tree.')
Browse code

tree layout

Guangchuang Yu authored on 24/07/2019 07:38:11
Showing 1 changed files
R/ggtree.R
History View file @ d3057fa1
... ... 
@@ -88,12 +88,12 @@ ggtree <- function(tr,
88 88 
     p <- p + theme_tree()
89 89
90 90 
     if (layout == "circular" || layout == "radial") {
91 
-        p <- layout_circular(p)
91 
+        p <- p + layout_circular()
92 92 
         ## refer to: https://github.com/GuangchuangYu/ggtree/issues/6
93 93 
         ## and also have some space for tree scale (legend)
94 94 
         p <- p + ylim(0, NA)
95 95 
     } else if (layout == "fan") {
96 
-        p <- layout_fan(p, open.angle)
96 
+        p <- p + layout_fan(open.angle)
97 97 
     }
98 98
99 99 
     class(p) <- c("ggtree", class(p))
Browse code

root.position parameter

Guangchuang Yu authored on 27/05/2019 12:52:40
Showing 1 changed files
R/ggtree.R
History View file @ 98a43cd2
... ... 
@@ -14,6 +14,7 @@
14 14 
 ##' @param right logical. If \code{ladderize = TRUE}, should the ladder have the smallest clade on the
15 15 
 ##' right-hand side? See \code{\link[ape]{ladderize}} for more information.
16 16 
 ##' @param branch.length variable for scaling branch, if 'none' draw cladogram
17 
+##' @param root.position position of the root node (default = 0)
17 18 
 ##' @return tree
18 19 
 ##' @importFrom ggplot2 ggplot
19 20 
 ##' @importFrom ggplot2 xlab
... ... 
@@ -41,6 +42,7 @@ ggtree <- function(tr,
41 42 
                    ladderize      = TRUE,
42 43 
                    right          = FALSE,
43 44 
                    branch.length  = "branch.length",
45 
+                   root.position  = 0,
44 46 
                    ...) {
45 47
46 48 
     # Check if layout string is valid.
... ... 
@@ -71,6 +73,7 @@ ggtree <- function(tr,
71 73 
                 ladderize     = ladderize,
72 74 
                 right         = right,
73 75 
                 branch.length = branch.length,
76 
+                root.position = root.position,
74 77 
                 ...)
75 78
76 79 
     if (is(tr, "multiPhylo")) {
Browse code

update docs

Guangchuang Yu authored on 01/11/2018 12:03:05
Showing 1 changed files
R/ggtree.R
History View file @ f46cfbcf
... ... 
@@ -4,6 +4,7 @@
4 4 
 ##' @title ggtree
5 5 
 ##' @inheritParams geom_tree
6 6 
 ##' @param tr phylo object
7 
+##' @param open.angle open angle, only for 'fan' layout
7 8 
 ##' @param mrsd most recent sampling date
8 9 
 ##' @param as.Date logical whether using Date class in time tree
9 10 
 ##' @param yscale y scale
Browse code

Make ggtree inherit params docs from geom_tree This reduces the need to edit the documentation at several places when the code is updated and reduces the risk that one place goes out of date

Hugo Gruson authored on 01/11/2018 07:34:55
Showing 1 changed files
R/ggtree.R
History View file @ dc219015
... ... 
@@ -2,10 +2,8 @@
2 2 
 ##'
3 3 
 ##'
4 4 
 ##' @title ggtree
5 
+##' @inheritParams geom_tree
5 6 
 ##' @param tr phylo object
6 
-##' @param mapping aes mapping
7 
-##' @param layout one of 'rectangular', 'slanted', 'fan', 'circular', 'radial', 'equal_angle' or 'daylight'
8 
-##' @param open.angle open angle, only for 'fan' layout
9 7 
 ##' @param mrsd most recent sampling date
10 8 
 ##' @param as.Date logical whether using Date class in time tree
11 9 
 ##' @param yscale y scale
... ... 
@@ -15,7 +13,6 @@
15 13 
 ##' @param right logical. If \code{ladderize = TRUE}, should the ladder have the smallest clade on the
16 14 
 ##' right-hand side? See \code{\link[ape]{ladderize}} for more information.
17 15 
 ##' @param branch.length variable for scaling branch, if 'none' draw cladogram
18 
-##' @param ... additional parameter
19 16 
 ##' @return tree
20 17 
 ##' @importFrom ggplot2 ggplot
21 18 
 ##' @importFrom ggplot2 xlab
Browse code

Update doc to explain the function of some arguments

Hugo Gruson authored on 03/10/2018 18:03:01
Showing 1 changed files
R/ggtree.R
History View file @ 908f3028
... ... 
@@ -10,8 +10,10 @@
10 10 
 ##' @param as.Date logical whether using Date class in time tree
11 11 
 ##' @param yscale y scale
12 12 
 ##' @param yscale_mapping yscale mapping for category variable
13 
-##' @param ladderize logical
14 
-##' @param right logical
13 
+##' @param ladderize logical (default \code{TRUE}). Should the tree be re-organized to have a 'ladder'
14 
+##' aspect?
15 
+##' @param right logical. If \code{ladderize = TRUE}, should the ladder have the smallest clade on the
16 
+##' right-hand side? See \code{\link[ape]{ladderize}} for more information.
15 17 
 ##' @param branch.length variable for scaling branch, if 'none' draw cladogram
16 18 
 ##' @param ... additional parameter
17 19 
 ##' @return tree
... ... 
@@ -25,6 +27,7 @@
25 27 
 ##' @importFrom ggplot2 coord_polar
26 28 
 ##' @export
27 29 
 ##' @author Yu Guangchuang
30 
+##' @seealso \code{\link[ape]{ladderize}}
28 31 
 ##' @examples
29 32 
 ##' require(ape)
30 33 
 ##' tr <- rtree(10)
Browse code

unrooted layout

guangchuang yu authored on 21/12/2017 12:07:05
Showing 1 changed files
R/ggtree.R
History View file @ b681f0b4
... ... 
@@ -49,10 +49,6 @@ ggtree <- function(tr,
49 49 
         message('"daylight" method was used as default layout for unrooted tree.')
50 50 
     }
51 51
52 
-    if (is(tr, "r8s") && branch.length == "branch.length") {
53 
-        branch.length = "TREE"
54 
-    }
55 
-
56 52 
     if(yscale != "none") {
57 53 
         ## for 2d tree
58 54 
         layout <- "slanted"
Browse code

clean up code

guangchuang yu authored on 14/12/2017 08:47:21
Showing 1 changed files
R/ggtree.R
History View file @ 14ff9149
... ... 
@@ -13,7 +13,6 @@
13 13 
 ##' @param ladderize logical
14 14 
 ##' @param right logical
15 15 
 ##' @param branch.length variable for scaling branch, if 'none' draw cladogram
16 
-##' @param ndigits number of digits to round numerical annotation variable
17 16 
 ##' @param ... additional parameter
18 17 
 ##' @return tree
19 18 
 ##' @importFrom ggplot2 ggplot
... ... 
@@ -41,7 +40,6 @@ ggtree <- function(tr,
41 40 
                    ladderize      = TRUE,
42 41 
                    right          = FALSE,
43 42 
                    branch.length  = "branch.length",
44 
-                   ndigits        = NULL,
45 43 
                    ...) {
46 44
47 45 
     # Check if layout string is valid.
... ... 
@@ -76,7 +74,7 @@ ggtree <- function(tr,
76 74 
                 ladderize     = ladderize,
77 75 
                 right         = right,
78 76 
                 branch.length = branch.length,
79 
-                ndigits       = ndigits, ...)
77 
+                ...)
80 78
81 79 
     if (is(tr, "multiPhylo")) {
82 80 
         multiPhylo <- TRUE
Browse code

remove layout.method

guangchuang yu authored on 20/04/2017 02:28:57
Showing 1 changed files
R/ggtree.R
History View file @ e9896b76
... ... 
@@ -4,8 +4,7 @@
4 4 
 ##' @title ggtree
5 5 
 ##' @param tr phylo object
6 6 
 ##' @param mapping aes mapping
7 
-##' @param layout one of 'rectangular', 'slanted', 'fan', 'circular', 'radial' or 'unrooted'
8 
-##' @param layout.method of 'equal_angle', 'daylight'.
7 
+##' @param layout one of 'rectangular', 'slanted', 'fan', 'circular', 'radial', 'equal_angle' or 'daylight'
9 8 
 ##' @param open.angle open angle, only for 'fan' layout
10 9 
 ##' @param mrsd most recent sampling date
11 10 
 ##' @param as.Date logical whether using Date class in time tree
... ... 
@@ -34,7 +33,6 @@
34 33 
 ggtree <- function(tr,
35 34 
                    mapping        = NULL,
36 35 
                    layout         = "rectangular",
37 
-                   layout.method  = "equal_angle",
38 36 
                    open.angle     = 0,
39 37 
                    mrsd           = NULL,
40 38 
                    as.Date        = FALSE,
... ... 
@@ -47,9 +45,12 @@ ggtree <- function(tr,
47 45 
                    ...) {
48 46
49 47 
     # Check if layout string is valid.
50 
-    layout %<>% match.arg(c("rectangular", "slanted", "fan", "circular", "radial", "unrooted"))
51 
-    layout.method %<>% match.arg(c("equal_angle", "daylight"))
52 
-
48 
+    layout %<>% match.arg(c("rectangular", "slanted", "fan", "circular", "radial", "unrooted", "equal_angle", "daylight"))
49 
+    if (layout == "unrooted") {
50 
+        layout <- "daylight"
51 
+        message('"daylight" method was used as default layout for unrooted tree.')
52 
+    }
53 
+
53 54 
     if (is(tr, "r8s") && branch.length == "branch.length") {
54 55 
         branch.length = "TREE"
55 56 
     }
... ... 
@@ -64,11 +65,10 @@ ggtree <- function(tr,
64 65 
     } else {
65 66 
         mapping <- modifyList(aes_(~x, ~y), mapping)
66 67 
     }
67 
-
68 
-    p <- ggplot(tr,
68 
+
69 
+    p <- ggplot(tr,
69 70 
                 mapping       = mapping,
70 71 
                 layout        = layout,
71 
-                layout.method = layout.method,
72 72 
                 mrsd          = mrsd,
73 73 
                 as.Date       = as.Date,
74 74 
                 yscale        = yscale,
Browse code

Added layout.method parameter to ggtree.R to modify behaviour of layout method (unrooted). Modified method-fortify.R to accommodate layout.method parameter. Refactored and added various functions to tidytree.R for the "daylight" layout algorithm for unrooted trees.

JustGitting authored on 06/04/2017 04:42:40
Showing 1 changed files
R/ggtree.R
History View file @ 40f0f078
... ... 
@@ -5,6 +5,7 @@
5 5 
 ##' @param tr phylo object
6 6 
 ##' @param mapping aes mapping
7 7 
 ##' @param layout one of 'rectangular', 'slanted', 'fan', 'circular', 'radial' or 'unrooted'
8 
+##' @param layout.method of 'equal_angle', 'daylight'.
8 9 
 ##' @param open.angle open angle, only for 'fan' layout
9 10 
 ##' @param mrsd most recent sampling date
10 11 
 ##' @param as.Date logical whether using Date class in time tree
... ... 
@@ -33,6 +34,7 @@
33 34 
 ggtree <- function(tr,
34 35 
                    mapping        = NULL,
35 36 
                    layout         = "rectangular",
37 
+                   layout.method  = "equal_angle",
36 38 
                    open.angle     = 0,
37 39 
                    mrsd           = NULL,
38 40 
                    as.Date        = FALSE,
... ... 
@@ -44,8 +46,10 @@ ggtree <- function(tr,
44 46 
                    ndigits        = NULL,
45 47 
                    ...) {
46 48
49 
+    # Check if layout string is valid.
47 50 
     layout %<>% match.arg(c("rectangular", "slanted", "fan", "circular", "radial", "unrooted"))
48 
-
51 
+    layout.method %<>% match.arg(c("equal_angle", "daylight"))
52 
+
49 53 
     if (is(tr, "r8s") && branch.length == "branch.length") {
50 54 
         branch.length = "TREE"
51 55 
     }
... ... 
@@ -60,8 +64,11 @@ ggtree <- function(tr,
60 64 
     } else {
61 65 
         mapping <- modifyList(aes_(~x, ~y), mapping)
62 66 
     }
63 
-    p <- ggplot(tr, mapping=mapping,
67 
+
68 
+    p <- ggplot(tr,
69 
+                mapping       = mapping,
64 70 
                 layout        = layout,
71 
+                layout.method = layout.method,
65 72 
                 mrsd          = mrsd,
66 73 
                 as.Date       = as.Date,
67 74 
                 yscale        = yscale,
Browse code

nhx move to treeio

guangchuang yu authored on 06/12/2016 11:09:15
Showing 1 changed files
R/ggtree.R
History View file @ a76f35c1
... ... 
@@ -95,14 +95,3 @@ ggtree <- function(tr,
95 95
96 96 
     return(p)
97 97 
 }
98 
-
99 
-##' test whether input object is produced by ggtree function
100 
-##'
101 
-##'
102 
-##' @title is.ggtree
103 
-##' @param x object
104 
-##' @return TRUE or FALSE
105 
-##' @export
106 
-##' @author guangchuang yu
107 
-is.ggtree <- function(x) inherits(x, 'ggtree')
108 
-
Browse code

is.ggtree

guangchuang yu authored on 06/12/2016 07:53:23
Showing 1 changed files
R/ggtree.R
History View file @ 02a6bdec
... ... 
@@ -1,6 +1,6 @@
1 1 
 ##' drawing phylogenetic tree from phylo object
2 2 
 ##'
3 
-##'
3 
+##'
4 4 
 ##' @title ggtree
5 5 
 ##' @param tr phylo object
6 6 
 ##' @param mapping aes mapping
... ... 
@@ -43,13 +43,13 @@ ggtree <- function(tr,
43 43 
                    branch.length  = "branch.length",
44 44 
                    ndigits        = NULL,
45 45 
                    ...) {
46 
-
46 
+
47 47 
     layout %<>% match.arg(c("rectangular", "slanted", "fan", "circular", "radial", "unrooted"))
48 48
49 49 
     if (is(tr, "r8s") && branch.length == "branch.length") {
50 50 
         branch.length = "TREE"
51 51 
     }
52 
-
52 
+
53 53 
     if(yscale != "none") {
54 54 
         ## for 2d tree
55 55 
         layout <- "slanted"
... ... 
@@ -76,20 +76,33 @@ ggtree <- function(tr,
76 76 
     } else {
77 77 
         multiPhylo <- FALSE
78 78 
     }
79 
-
79 
+
80 80 
     p <- p + geom_tree(layout=layout, multiPhylo=multiPhylo, ...)
81 81
82 82
83 83 
     p <- p + theme_tree()
84 
-
84 
+
85 85 
     if (layout == "circular" || layout == "radial") {
86 86 
         p <- layout_circular(p)
87 87 
         ## refer to: https://github.com/GuangchuangYu/ggtree/issues/6
88 88 
         ## and also have some space for tree scale (legend)
89 
-        p <- p + ylim(0, NA)
89 
+        p <- p + ylim(0, NA)
90 90 
     } else if (layout == "fan") {
91 91 
         p <- layout_fan(p, open.angle)
92 92 
     }
93 93
94 
+    class(p) <- c("ggtree", class(p))
95 
+
94 96 
     return(p)
95 97 
 }
98 
+
99 
+##' test whether input object is produced by ggtree function
100 
+##'
101 
+##'
102 
+##' @title is.ggtree
103 
+##' @param x object
104 
+##' @return TRUE or FALSE
105 
+##' @export
106 
+##' @author guangchuang yu
107 
+is.ggtree <- function(x) inherits(x, 'ggtree')
108 
+
Browse code

version 1.5.15

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@122021 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 07/10/2016 05:18:29
Showing 1 changed files
R/ggtree.R
History View file @ a92aaed1
... ... 
@@ -21,7 +21,7 @@
21 21 
 ##' @importFrom ggplot2 ylab
22 22 
 ##' @importFrom ggplot2 annotate
23 23 
 ##' @importFrom ggplot2 scale_x_reverse
24 
-##' @importFrom ggplot2 scale_y_continuous
24 
+##' @importFrom ggplot2 ylim
25 25 
 ##' @importFrom ggplot2 coord_flip
26 26 
 ##' @importFrom ggplot2 coord_polar
27 27 
 ##' @export
... ... 
@@ -86,7 +86,7 @@ ggtree <- function(tr,
86 86 
         p <- layout_circular(p)
87 87 
         ## refer to: https://github.com/GuangchuangYu/ggtree/issues/6
88 88 
         ## and also have some space for tree scale (legend)
89 
-        p <- p + scale_y_continuous(limits=c(0, max(p$data$y)+1))
89 
+        p <- p + ylim(0, NA)
90 90 
     } else if (layout == "fan") {
91 91 
         p <- layout_fan(p, open.angle)
92 92 
     }
Browse code

identify method for ggtree

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@118985 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 28/06/2016 06:26:04
Showing 1 changed files
R/ggtree.R
History View file @ 9e9bcff3
... ... 
@@ -43,7 +43,7 @@ ggtree <- function(tr,
43 43 
                    branch.length  = "branch.length",
44 44 
                    ndigits        = NULL,
45 45 
                    ...) {
46 
-
46 
+
47 47 
     layout %<>% match.arg(c("rectangular", "slanted", "fan", "circular", "radial", "unrooted"))
48 48
49 49 
     if (is(tr, "r8s") && branch.length == "branch.length") {
... ... 
@@ -90,6 +90,6 @@ ggtree <- function(tr,
90 90 
     } else if (layout == "fan") {
91 91 
         p <- layout_fan(p, open.angle)
92 92 
     }
93 
-
93 
+
94 94 
     return(p)
95 95 
 }
Browse code

open_tree & rotate_tree

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@117331 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 12/05/2016 10:16:07
Showing 1 changed files
R/ggtree.R
History View file @ fded823a
... ... 
@@ -4,7 +4,8 @@
4 4 
 ##' @title ggtree
5 5 
 ##' @param tr phylo object
6 6 
 ##' @param mapping aes mapping
7 
-##' @param layout one of 'rectangular', 'slanted', 'fan'/'circular', 'radial' or 'unrooted'
7 
+##' @param layout one of 'rectangular', 'slanted', 'fan', 'circular', 'radial' or 'unrooted'
8 
+##' @param open.angle open angle, only for 'fan' layout
8 9 
 ##' @param mrsd most recent sampling date
9 10 
 ##' @param as.Date logical whether using Date class in time tree
10 11 
 ##' @param yscale y scale
... ... 
@@ -32,6 +33,7 @@
32 33 
 ggtree <- function(tr,
33 34 
                    mapping        = NULL,
34 35 
                    layout         = "rectangular",
36 
+                   open.angle     = 0,
35 37 
                    mrsd           = NULL,
36 38 
                    as.Date        = FALSE,
37 39 
                    yscale         = "none",
... ... 
@@ -52,15 +54,7 @@ ggtree <- function(tr,
52 54 
         ## for 2d tree
53 55 
         layout <- "slanted"
54 56 
     }
55 
-    if (layout == "fan" || layout == "circular") {
56 
-        layout <- "circular"
57 
-        type <- "circular"
58 
-    } else if (layout == "radial") {
59 
-        layout <- "slanted"
60 
-        type <- "radial"
61 
-    } else {
62 
-        type <- "none"
63 
-    }
57 
+
64 58 
     if (is.null(mapping)) {
65 59 
         mapping <- aes_(~x, ~y)
66 60 
     } else {
... ... 
@@ -88,12 +82,14 @@ ggtree <- function(tr,
88 82
89 83 
     p <- p + theme_tree()
90 84
91 
-    if (type == "circular" || type == "radial") {
92 
-        p <- p + coord_polar(theta = "y")
85 
+    if (layout == "circular" || layout == "radial") {
86 
+        p <- layout_circular(p)
93 87 
         ## refer to: https://github.com/GuangchuangYu/ggtree/issues/6
94 88 
         ## and also have some space for tree scale (legend)
95 89 
         p <- p + scale_y_continuous(limits=c(0, max(p$data$y)+1))
96 
-    }
97 
-
90 
+    } else if (layout == "fan") {
91 
+        p <- layout_fan(p, open.angle)
92 
+    }
93 
+
98 94 
     return(p)
99 95 
 }
Browse code

more accurate ylim & angle for circular layout <2016-05-10, Tue>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@117270 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 10/05/2016 09:40:21
Showing 1 changed files
R/ggtree.R
History View file @ 5c79784c
... ... 
@@ -92,7 +92,7 @@ ggtree <- function(tr,
92 92 
         p <- p + coord_polar(theta = "y")
93 93 
         ## refer to: https://github.com/GuangchuangYu/ggtree/issues/6
94 94 
         ## and also have some space for tree scale (legend)
95 
-        p <- p + scale_y_continuous(limits=c(0, max(p$data$y)))
95 
+        p <- p + scale_y_continuous(limits=c(0, max(p$data$y)+1))
96 96 
     }
97 97
98 98 
     return(p)
Browse code

use plot

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@115874 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 06/04/2016 08:34:24
Showing 1 changed files
R/ggtree.R
History View file @ f15cdabd
... ... 
@@ -94,16 +94,6 @@ ggtree <- function(tr,
94 94 
         ## and also have some space for tree scale (legend)
95 95 
         p <- p + scale_y_continuous(limits=c(0, max(p$data$y)))
96 96 
     }
97 
-
98 
-    attr(p, "mrsd") <- mrsd
99 
-    attr(p, "param") <- list(layout        = layout,
100 
-                             yscale        = yscale,
101 
-                             ladderize     = ladderize,
102 
-                             right         = right,
103 
-                             branch.length = branch.length,
104 
-                             ndigits       = ndigits)
97 
+
105 98 
     return(p)
106 99 
 }
107 
-
108 
-
109 
-
Browse code

new features

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

g.yu authored on 16/02/2016 04:04:44
Showing 1 changed files
R/ggtree.R
History View file @ 90df068e
... ... 
@@ -76,8 +76,17 @@ ggtree <- function(tr,
76 76 
                 right         = right,
77 77 
                 branch.length = branch.length,
78 78 
                 ndigits       = ndigits, ...)
79 
+
80 
+    if (is(tr, "multiPhylo")) {
81 
+        multiPhylo <- TRUE
82 
+    } else {
83 
+        multiPhylo <- FALSE
84 
+    }
79 85
80 
-    p <- p + geom_tree(layout, ...)  + theme_tree()
86 
+    p <- p + geom_tree(layout=layout, multiPhylo=multiPhylo, ...)
87 
+
88 
+
89 
+    p <- p + theme_tree()
81 90
82 91 
     if (type == "circular" || type == "radial") {
83 92 
         p <- p + coord_polar(theta = "y")
... ... 
@@ -96,123 +105,5 @@ ggtree <- function(tr,
96 105 
     return(p)
97 106 
 }
98 107
99 
-##' add tree layer
100 
-##'
101 
-##'
102 
-##' @title geom_tree
103 
-##' @param layout one of 'rectangular', 'slanted', 'circular', 'radial' or 'unrooted'
104 
-##' @param ... additional parameter
105 
-##' @return tree layer
106 
-##' @importFrom ggplot2 geom_segment
107 
-##' @importFrom ggplot2 aes
108 
-##' @export
109 
-##' @author Yu Guangchuang
110 
-##' @examples
111 
-##' require(ape)
112 
-##' tr <- rtree(10)
113 
-##' require(ggplot2)
114 
-##' ggplot(tr) + geom_tree()
115 
-geom_tree <- function(layout="rectangular", ...) {
116 
-    x <- y <- parent <- NULL
117 
-    lineend  = "round"
118 
-    if (layout == "rectangular" || layout == "fan" || layout == "circular") {
119 
-        list(
120 
-            geom_segment(aes(x    = x[parent],
121 
-                             xend = x,
122 
-                             y    = y,
123 
-                             yend = y),
124 
-                         lineend  = lineend, ...),
125 
-
126 
-            geom_segment(aes(x    = x[parent],
127 
-                             xend = x[parent],
128 
-                             y    = y[parent],
129 
-                             yend = y),
130 
-                         lineend  = lineend, ...)
131 
-            )
132 
-    } else if (layout == "slanted" || layout == "radial" || layout == "unrooted") {
133 
-        geom_segment(aes(x    = x[parent],
134 
-                         xend = x,
135 
-                         y    = y[parent],
136 
-                         yend = y),
137 
-                     lineend  = lineend, ...)
138 
-    }
139 
-}
140 
-
141 
-
142 
-
143 
-