1. ggtree
  2. man
  3. geom_tiplab.Rd
Browse code

rename size aesthetic according to ggplot2 (3.4.0)

xiangpin authored on 07/07/2022 12:57:13
Showing 1 changed files
man/geom_tiplab.Rd
History View file @ 69f2dbbf
... ... 
@@ -27,7 +27,7 @@ with a line connecting each tip and its corresponding label, defaults to "FALSE"
27 27
28 28 
 \item{linetype}{set linetype of the line if align = TRUE, defaults to "dotted"}
29 29
30 
-\item{linesize}{set line size of the line if align = TRUE, defaults to 0.5}
30 
+\item{linesize}{set line width if align = TRUE, defaults to 0.5}
31 31
32 32 
 \item{geom}{one of 'text', 'label', 'shadowtext', 'image' and 'phylopic'}
33 33
Browse code

update man files and fixed R check

Guangchuang Yu authored on 23/03/2022 04:13:34
Showing 1 changed files
man/geom_tiplab.Rd
History View file @ fbeaa25d
... ... 
@@ -19,20 +19,23 @@ geom_tiplab(
19 19 
 \arguments{
20 20 
 \item{mapping}{aes mapping}
21 21
22 
-\item{hjust}{horizontal adjustment}
22 
+\item{hjust}{horizontal adjustment, defaults to 0}
23 23
24 
-\item{align}{align tip lab or not, logical}
24 
+\item{align}{if TRUE, align all tip labels to the longest tip by adding padding characters
25 
+to the left side of tip labels, defaults to "FALSE"
26 
+with a line connecting each tip and its corresponding label, defaults to "FALSE"}
25 27
26 
-\item{linetype}{linetype for adding line if align = TRUE}
28 
+\item{linetype}{set linetype of the line if align = TRUE, defaults to "dotted"}
27 29
28 
-\item{linesize}{line size of line if align = TRUE}
30 
+\item{linesize}{set line size of the line if align = TRUE, defaults to 0.5}
29 31
30 32 
 \item{geom}{one of 'text', 'label', 'shadowtext', 'image' and 'phylopic'}
31 33
32 34 
 \item{offset}{tiplab offset, horizontal
33 
-adjustment to nudge tip labels, default is 0.}
35 
+adjustment to nudge tip labels, defaults to 0}
34 36
35 
-\item{as_ylab}{display tip labels as y-axis label, only works for rectangular and dendrogram layouts}
37 
+\item{as_ylab}{display tip labels as y-axis label,
38 
+only works for rectangular and dendrogram layouts, defaults to "FALSE"}
36 39
37 40 
 \item{...}{additional parameter
38 41
... ... 
@@ -40,17 +43,17 @@ additional parameters can refer the following parameters.
40 43
41 44 
 The following parameters for geom="text".
42 45 
 \itemize{
43 
-\item \code{size} control the size of tip labels, default is 3.88.
44 
-\item \code{colour} control the colour of tip labels, default is "black".
45 
-\item \code{angle} control the angle of tip labels, default is 0.
46 
-\item \code{vjust} A numeric vector specifying vertical justification, default is 0.5.
47 
-\item \code{alpha} the transparency of text, default is NA.
48 
-\item \code{family} the family of text, default is 'sans'.
49 
-\item \code{fontface} the font face of text, default is 1 (plain), others are
46 
+\item \code{size} control the size of tip labels, defaults to 3.88.
47 
+\item \code{colour} control the colour of tip labels, defaults to "black".
48 
+\item \code{angle} control the angle of tip labels, defaults to 0.
49 
+\item \code{vjust} A numeric vector specifying vertical justification, defaults to 0.5.
50 
+\item \code{alpha} the transparency of text, defaults to NA.
51 
+\item \code{family} the family of text, defaults to 'sans'.
52 
+\item \code{fontface} the font face of text, defaults to 1 (plain), others are
50 53 
 2 (bold), 3 (italic), 4 (bold.italic).
51 
-\item \code{lineheight} The height of a line as a multiple of the size of text, default is 1.2 .
52 
-\item \code{nudge_x} horizontal adjustment to nudge labels, default is 0.
53 
-\item \code{nudge_y}  vertical adjustment to nudge labels, default is 0.
54 
+\item \code{lineheight} The height of a line as a multiple of the size of text, defaults to 1.2 .
55 
+\item \code{nudge_x} horizontal adjustment to nudge labels, defaults to 0.
56 
+\item \code{nudge_y}  vertical adjustment to nudge labels, defaults to 0.
54 57 
 \item \code{check.overlap} if TRUE, text that overlaps previous text in the same layer
55 58 
 will not be plotted.
56 59 
 \item \code{parse} if TRUE, the labels will be parsed into expressions, if it is 'emoji', the labels
... ... 
@@ -59,62 +62,75 @@ will be parsed into emojifont.
59 62
60 63 
 The following parameters for geom="label".
61 64 
 \itemize{
62 
-\item \code{size} the size of tip labels, default is 3.88.
63 
-\item \code{colour} the colour of tip labels, default is "black".
64 
-\item \code{fill} the colour of rectangular box of labels, default is "white".
65 
-\item \code{vjust} numeric vector specifying vertical justification, default is 0.5.
66 
-\item \code{alpha} the transparency of labels, default is NA.
67 
-\item \code{family} the family of text, default is 'sans'.
68 
-\item \code{fontface} the font face of text, default is 1 (plain), others are
65 
+\item \code{size} the size of tip labels, defaults to 3.88.
66 
+\item \code{colour} the colour of tip labels, defaults to "black".
67 
+\item \code{fill} the colour of rectangular box of labels, defaults to "white".
68 
+\item \code{vjust} numeric vector specifying vertical justification, defaults to 0.5.
69 
+\item \code{alpha} the transparency of labels, defaults to NA.
70 
+\item \code{family} the family of text, defaults to 'sans'.
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+\item \code{fontface} the font face of text, defaults to 1 (plain), others are
69 72 
 2 (bold), 3 (italic), 4 (bold.italic).
70 
-\item \code{lineheight} The height of a line as a multiple of the size of text, default is 1.2.
71 
-\item \code{nudge_x} horizontal adjustment to nudge labels, default is 0.
72 
-\item \code{nudge_y}  vertical adjustment, default is 0.
73 
+\item \code{lineheight} The height of a line as a multiple of the size of text, defaults to 1.2.
74 
+\item \code{nudge_x} horizontal adjustment to nudge labels, defaults to 0.
75 
+\item \code{nudge_y}  vertical adjustment, defaults to 0.
73 76 
 \item \code{check.overlap} if TRUE, text that overlaps previous text in the same layer
74 77 
 will not be plotted.
75 78 
 \item \code{parse} if TRUE, the labels will be parsed into expressions, if it is 'emoji', the labels
76 79 
 will be parsed into emojifont.
77 
-\item \code{label.padding} Amount of padding around label, default is 'unit(0.25, "lines")'.
78 
-\item \code{label.r} Radius of rounded corners, default is 'unit(0.15, "lines")'.
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-\item \code{label.size} Size of label border, in mm, default is 0.25.
80 
+\item \code{label.padding} Amount of padding around label, defaults to 'unit(0.25, "lines")'.
81 
+\item \code{label.r} Radius of rounded corners, defaults to 'unit(0.15, "lines")'.
82 
+\item \code{label.size} Size of label border, in mm, defaults to 0.25.
80 83 
 }
81 84
82 85 
 The following parameters for geom="shadowtext", some parameters are like to geom="text".
83 86 
 \itemize{
84 
-\item \code{bg.colour} the background colour of text, default is "black".
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-\item \code{bg.r} the width of background of text, default is 0.1 .
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+\item \code{bg.colour} the background colour of text, defaults to "black".
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+\item \code{bg.r} the width of background of text, defaults to 0.1 .
86 89 
 }
87 90
88 91 
 The following parameters for geom="image" or geom="phylopic".
89 92 
 \itemize{
90 93 
 \item \code{image} the image file path for geom='image', but when geom='phylopic',
91 94 
 it should be the uid of phylopic databases.
92 
-\item \code{size} the image size, default is 0.05.
93 
-\item \code{colour} the color of image, default is NULL.
94 
-\item \code{alpha} the transparency of image, default is 0.8.
95 
+\item \code{size} the image size, defaults to 0.05.
96 
+\item \code{colour} the color of image, defaults to NULL.
97 
+\item \code{alpha} the transparency of image, defaults to 0.8.
95 98 
 }
96 99
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 The following parameters for the line when align = TRUE.
98 101 
 \itemize{
99 
-\item \code{colour} the colour of line, default is 'black'.
100 
-\item \code{alpha} the transparency of line, default is NA.
102 
+\item \code{colour} the colour of line, defaults to 'black'.
103 
+\item \code{alpha} the transparency of line, defaults to NA.
101 104 
 \item \code{arrow} specification for arrow heads,
102 
-as created by arrow(), default is NULL.
105 
+as created by arrow(), defaults to NULL.
103 106 
 \item \code{arrow.fill} fill color to usse for the arrow head (if closed),
104 
-default is 'NULL', meaning use 'colour' aesthetic.
107 
+defaults to 'NULL', meaning use 'colour' aesthetic.
105 108 
 }}
106 109 
 }
107 110 
 \value{
108 111 
 tip label layer
109 112 
 }
110 113 
 \description{
111 
-add tip label layer
114 
+add tip label layer for a tree
115 
+}
116 
+\details{
117 
+'geom_tiplab' not only supports using text or label geom to display tip labels,
118 
+but also supports image geom to label tip with image files or phylopics.
119 
+
120 
+For adding tip labels to a tree with circular layout, 'geom_tiplab' will
121 
+automatically adjust the angle of the tip labels to the tree by
122 
+internally calling 'geom_tiplab2'.
112 123 
 }
113 124 
 \examples{
114 125 
 require(ape)
115 126 
 tr <- rtree(10)
116 127 
 ggtree(tr) + geom_tiplab()
117 128 
 }
129 
+\references{
130 
+For more detailed demonstration, please refer to chapter 4.3.3 of
131 
+\emph{Data Integration, Manipulation and Visualization of Phylogenetic Trees}
132 
+\url{http://yulab-smu.top/treedata-book/index.html} by Guangchuang Yu.
133 
+}
118 134 
 \author{
119 135 
 Guangchuang Yu
120 136 
 }
Browse code

nudge_x can also work like offset

xiangpin authored on 19/04/2021 01:50:12
Showing 1 changed files
man/geom_tiplab.Rd
History View file @ 66052971
... ... 
@@ -29,7 +29,8 @@ geom_tiplab(
29 29
30 30 
 \item{geom}{one of 'text', 'label', 'shadowtext', 'image' and 'phylopic'}
31 31
32 
-\item{offset}{tiplab offset}
32 
+\item{offset}{tiplab offset, horizontal
33 
+adjustment to nudge tip labels, default is 0.}
33 34
34 35 
 \item{as_ylab}{display tip labels as y-axis label, only works for rectangular and dendrogram layouts}
35 36
... ... 
@@ -48,8 +49,8 @@ The following parameters for geom="text".
48 49 
 \item \code{fontface} the font face of text, default is 1 (plain), others are
49 50 
 2 (bold), 3 (italic), 4 (bold.italic).
50 51 
 \item \code{lineheight} The height of a line as a multiple of the size of text, default is 1.2 .
51 
-\item \code{nudge_x} horizontal adjustment, default is 0.
52 
-\item \code{nudge_y}  vertical adjustment, default is 0.
52 
+\item \code{nudge_x} horizontal adjustment to nudge labels, default is 0.
53 
+\item \code{nudge_y}  vertical adjustment to nudge labels, default is 0.
53 54 
 \item \code{check.overlap} if TRUE, text that overlaps previous text in the same layer
54 55 
 will not be plotted.
55 56 
 \item \code{parse} if TRUE, the labels will be parsed into expressions, if it is 'emoji', the labels
... ... 
@@ -67,7 +68,7 @@ The following parameters for geom="label".
67 68 
 \item \code{fontface} the font face of text, default is 1 (plain), others are
68 69 
 2 (bold), 3 (italic), 4 (bold.italic).
69 70 
 \item \code{lineheight} The height of a line as a multiple of the size of text, default is 1.2.
70 
-\item \code{nudge_x} horizontal adjustment, default is 0.
71 
+\item \code{nudge_x} horizontal adjustment to nudge labels, default is 0.
71 72 
 \item \code{nudge_y}  vertical adjustment, default is 0.
72 73 
 \item \code{check.overlap} if TRUE, text that overlaps previous text in the same layer
73 74 
 will not be plotted.
Browse code

update the man of geom_tiplab

xiangpin authored on 14/04/2021 04:24:24
Showing 1 changed files
man/geom_tiplab.Rd
History View file @ d8c602e2
... ... 
@@ -33,7 +33,75 @@ geom_tiplab(
33 33
34 34 
 \item{as_ylab}{display tip labels as y-axis label, only works for rectangular and dendrogram layouts}
35 35
36 
-\item{...}{additional parameter}
36 
+\item{...}{additional parameter
37 
+
38 
+additional parameters can refer the following parameters.
39 
+
40 
+The following parameters for geom="text".
41 
+\itemize{
42 
+\item \code{size} control the size of tip labels, default is 3.88.
43 
+\item \code{colour} control the colour of tip labels, default is "black".
44 
+\item \code{angle} control the angle of tip labels, default is 0.
45 
+\item \code{vjust} A numeric vector specifying vertical justification, default is 0.5.
46 
+\item \code{alpha} the transparency of text, default is NA.
47 
+\item \code{family} the family of text, default is 'sans'.
48 
+\item \code{fontface} the font face of text, default is 1 (plain), others are
49 
+2 (bold), 3 (italic), 4 (bold.italic).
50 
+\item \code{lineheight} The height of a line as a multiple of the size of text, default is 1.2 .
51 
+\item \code{nudge_x} horizontal adjustment, default is 0.
52 
+\item \code{nudge_y}  vertical adjustment, default is 0.
53 
+\item \code{check.overlap} if TRUE, text that overlaps previous text in the same layer
54 
+will not be plotted.
55 
+\item \code{parse} if TRUE, the labels will be parsed into expressions, if it is 'emoji', the labels
56 
+will be parsed into emojifont.
57 
+}
58 
+
59 
+The following parameters for geom="label".
60 
+\itemize{
61 
+\item \code{size} the size of tip labels, default is 3.88.
62 
+\item \code{colour} the colour of tip labels, default is "black".
63 
+\item \code{fill} the colour of rectangular box of labels, default is "white".
64 
+\item \code{vjust} numeric vector specifying vertical justification, default is 0.5.
65 
+\item \code{alpha} the transparency of labels, default is NA.
66 
+\item \code{family} the family of text, default is 'sans'.
67 
+\item \code{fontface} the font face of text, default is 1 (plain), others are
68 
+2 (bold), 3 (italic), 4 (bold.italic).
69 
+\item \code{lineheight} The height of a line as a multiple of the size of text, default is 1.2.
70 
+\item \code{nudge_x} horizontal adjustment, default is 0.
71 
+\item \code{nudge_y}  vertical adjustment, default is 0.
72 
+\item \code{check.overlap} if TRUE, text that overlaps previous text in the same layer
73 
+will not be plotted.
74 
+\item \code{parse} if TRUE, the labels will be parsed into expressions, if it is 'emoji', the labels
75 
+will be parsed into emojifont.
76 
+\item \code{label.padding} Amount of padding around label, default is 'unit(0.25, "lines")'.
77 
+\item \code{label.r} Radius of rounded corners, default is 'unit(0.15, "lines")'.
78 
+\item \code{label.size} Size of label border, in mm, default is 0.25.
79 
+}
80 
+
81 
+The following parameters for geom="shadowtext", some parameters are like to geom="text".
82 
+\itemize{
83 
+\item \code{bg.colour} the background colour of text, default is "black".
84 
+\item \code{bg.r} the width of background of text, default is 0.1 .
85 
+}
86 
+
87 
+The following parameters for geom="image" or geom="phylopic".
88 
+\itemize{
89 
+\item \code{image} the image file path for geom='image', but when geom='phylopic',
90 
+it should be the uid of phylopic databases.
91 
+\item \code{size} the image size, default is 0.05.
92 
+\item \code{colour} the color of image, default is NULL.
93 
+\item \code{alpha} the transparency of image, default is 0.8.
94 
+}
95 
+
96 
+The following parameters for the line when align = TRUE.
97 
+\itemize{
98 
+\item \code{colour} the colour of line, default is 'black'.
99 
+\item \code{alpha} the transparency of line, default is NA.
100 
+\item \code{arrow} specification for arrow heads,
101 
+as created by arrow(), default is NULL.
102 
+\item \code{arrow.fill} fill color to usse for the arrow head (if closed),
103 
+default is 'NULL', meaning use 'colour' aesthetic.
104 
+}}
37 105 
 }
38 106 
 \value{
39 107 
 tip label layer
Browse code

shadowtext

Guangchuang Yu authored on 02/09/2020 08:44:40
Showing 1 changed files
man/geom_tiplab.Rd
History View file @ 11cd1cce
... ... 
@@ -27,7 +27,7 @@ geom_tiplab(
27 27
28 28 
 \item{linesize}{line size of line if align = TRUE}
29 29
30 
-\item{geom}{one of 'text', 'label', 'image' and 'phylopic'}
30 
+\item{geom}{one of 'text', 'label', 'shadowtext', 'image' and 'phylopic'}
31 31
32 32 
 \item{offset}{tiplab offset}
33 33
Browse code

as_ylab in geom_tiplab()

Guangchuang Yu authored on 28/07/2020 06:36:51
Showing 1 changed files
man/geom_tiplab.Rd
History View file @ 59c29a00
... ... 
@@ -31,7 +31,7 @@ geom_tiplab(
31 31
32 32 
 \item{offset}{tiplab offset}
33 33
34 
-\item{as_ylab}{display tip labels as y-axis label, only works for rectangular layout}
34 
+\item{as_ylab}{display tip labels as y-axis label, only works for rectangular and dendrogram layouts}
35 35
36 36 
 \item{...}{additional parameter}
37 37 
 }
Browse code

as_ylab in geom_tiplab()

Guangchuang Yu authored on 28/07/2020 06:04:40
Showing 1 changed files
man/geom_tiplab.Rd
History View file @ cbd57123
... ... 
@@ -12,6 +12,7 @@ geom_tiplab(
12 12 
   linesize = 0.5,
13 13 
   geom = "text",
14 14 
   offset = 0,
15 
+  as_ylab = FALSE,
15 16 
   ...
16 17 
 )
17 18 
 }
... ... 
@@ -30,6 +31,8 @@ geom_tiplab(
30 31
31 32 
 \item{offset}{tiplab offset}
32 33
34 
+\item{as_ylab}{display tip labels as y-axis label, only works for rectangular layout}
35 
+
33 36 
 \item{...}{additional parameter}
34 37 
 }
35 38 
 \value{
Browse code

clip="off" and update docs

Guangchuang Yu authored on 06/12/2019 03:01:17
Showing 1 changed files
man/geom_tiplab.Rd
History View file @ fb0a330e
... ... 
@@ -4,9 +4,16 @@
4 4 
 \alias{geom_tiplab}
5 5 
 \title{geom_tiplab}
6 6 
 \usage{
7 
-geom_tiplab(mapping = NULL, hjust = 0, align = FALSE,
8 
-  linetype = "dotted", linesize = 0.5, geom = "text", offset = 0,
9 
-  ...)
7 
+geom_tiplab(
8 
+  mapping = NULL,
9 
+  hjust = 0,
10 
+  align = FALSE,
11 
+  linetype = "dotted",
12 
+  linesize = 0.5,
13 
+  geom = "text",
14 
+  offset = 0,
15 
+  ...
16 
+)
10 17 
 }
11 18 
 \arguments{
12 19 
 \item{mapping}{aes mapping}
Browse code

geom_tiplab

Guangchuang Yu authored on 05/07/2019 06:39:00
Showing 1 changed files
man/geom_tiplab.Rd
History View file @ 585c3bd9
... ... 
@@ -36,9 +36,6 @@ require(ape)
36 36 
 tr <- rtree(10)
37 37 
 ggtree(tr) + geom_tiplab()
38 38 
 }
39 
-\seealso{
40 
-\link{geom_tiplab2}
41 
-}
42 39 
 \author{
43 40 
 Guangchuang Yu
44 41 
 }
Browse code

Cross link geom_tiplab and geom_tiplab2

Hugo Gruson authored on 26/06/2019 12:54:53
Showing 1 changed files
man/geom_tiplab.Rd
History View file @ 6dc7c898
... ... 
@@ -36,6 +36,9 @@ require(ape)
36 36 
 tr <- rtree(10)
37 37 
 ggtree(tr) + geom_tiplab()
38 38 
 }
39 
+\seealso{
40 
+\link{geom_tiplab2}
41 
+}
39 42 
 \author{
40 43 
 Guangchuang Yu
41 44 
 }
Browse code

bug fixed of viewClade

Guangchuang Yu authored on 07/08/2018 12:07:15
Showing 1 changed files
man/geom_tiplab.Rd
History View file @ c3727414
... ... 
@@ -5,7 +5,8 @@
5 5 
 \title{geom_tiplab}
6 6 
 \usage{
7 7 
 geom_tiplab(mapping = NULL, hjust = 0, align = FALSE,
8 
-  linetype = "dotted", linesize = 0.5, geom = "text", offset = 0, ...)
8 
+  linetype = "dotted", linesize = 0.5, geom = "text", offset = 0,
9 
+  ...)
9 10 
 }
10 11 
 \arguments{
11 12 
 \item{mapping}{aes mapping}
Browse code

compatible with ggplot2 v2.2.1 & 2.2.2

guangchuang yu authored on 25/06/2018 07:19:15
Showing 1 changed files
man/geom_tiplab.Rd
History View file @ 5ae49127
... ... 
@@ -36,5 +36,5 @@ tr <- rtree(10)
36 36 
 ggtree(tr) + geom_tiplab()
37 37 
 }
38 38 
 \author{
39 
-Yu Guangchuang
39 
+Guangchuang Yu
40 40 
 }
Browse code

ggtree with image files

guangchuang yu authored on 04/12/2017 11:45:07
Showing 1 changed files
man/geom_tiplab.Rd
History View file @ ea38627a
... ... 
@@ -18,7 +18,7 @@ geom_tiplab(mapping = NULL, hjust = 0, align = FALSE,
18 18
19 19 
 \item{linesize}{line size of line if align = TRUE}
20 20
21 
-\item{geom}{one of 'text' and 'label'}
21 
+\item{geom}{one of 'text', 'label', 'image' and 'phylopic'}
22 22
23 23 
 \item{offset}{tiplab offset}
24 24
Browse code

geom_tiplab enhancement

guangchuang yu authored on 20/11/2017 13:20:02
Showing 1 changed files
man/geom_tiplab.Rd
History View file @ d50bc7b6
... ... 
@@ -5,7 +5,7 @@
5 5 
 \title{geom_tiplab}
6 6 
 \usage{
7 7 
 geom_tiplab(mapping = NULL, hjust = 0, align = FALSE,
8 
-  linetype = "dotted", linesize = 1, geom = "text", offset = 0, ...)
8 
+  linetype = "dotted", linesize = 0.5, geom = "text", offset = 0, ...)
9 9 
 }
10 10 
 \arguments{
11 11 
 \item{mapping}{aes mapping}
Browse code

geom_motif #148

guangchuang yu authored on 22/08/2017 08:22:37
Showing 1 changed files
man/geom_tiplab.Rd
History View file @ 363c0555
... ... 
@@ -38,4 +38,3 @@ ggtree(tr) + geom_tiplab()
38 38 
 \author{
39 39 
 Yu Guangchuang
40 40 
 }
41 
-
Browse code

update docs

guangchuang yu authored on 16/08/2017 02:36:13
Showing 1 changed files
man/geom_tiplab.Rd
History View file @ f0e199ad
... ... 
@@ -38,3 +38,4 @@ ggtree(tr) + geom_tiplab()
38 38 
 \author{
39 39 
 Yu Guangchuang
40 40 
 }
41 
+
Browse code

add extend parameter in geom_cladelabel

guangchuang yu authored on 26/07/2017 02:13:53
Showing 1 changed files
man/geom_tiplab.Rd
History View file @ 353dfa09
... ... 
@@ -38,4 +38,3 @@ ggtree(tr) + geom_tiplab()
38 38 
 \author{
39 39 
 Yu Guangchuang
40 40 
 }
41 
-
Browse code

facet_plot

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@120776 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 07/09/2016 01:36:05
Showing 1 changed files
man/geom_tiplab.Rd
History View file @ 1652e9e8
... ... 
@@ -5,7 +5,7 @@
5 5 
 \title{geom_tiplab}
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 \usage{
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 geom_tiplab(mapping = NULL, hjust = 0, align = FALSE,
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-  linetype = "dotted", linesize = 1, geom = "text", ...)
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+  linetype = "dotted", linesize = 1, geom = "text", offset = 0, ...)
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 }
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 \arguments{
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 \item{mapping}{aes mapping}
... ... 
@@ -20,6 +20,8 @@ geom_tiplab(mapping = NULL, hjust = 0, align = FALSE,
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 \item{geom}{one of 'text' and 'label'}
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+\item{offset}{tiplab offset}
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+
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 \item{...}{additional parameter}
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 }
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 \value{
Browse code

geom_label2

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@115937 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 07/04/2016 04:02:44
Showing 1 changed files
man/geom_tiplab.Rd
History View file @ 7d9641c6
... ... 
@@ -5,7 +5,7 @@
5 5 
 \title{geom_tiplab}
6 6 
 \usage{
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 geom_tiplab(mapping = NULL, hjust = 0, align = FALSE,
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-  linetype = "dotted", linesize = 1, ...)
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+  linetype = "dotted", linesize = 1, geom = "text", ...)
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 }
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 \arguments{
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 \item{mapping}{aes mapping}
... ... 
@@ -18,6 +18,8 @@ geom_tiplab(mapping = NULL, hjust = 0, align = FALSE,
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 \item{linesize}{line size of line if align = TRUE}
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+\item{geom}{one of 'text' and 'label'}
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+
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 \item{...}{additional parameter}
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 }
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 \value{
Browse code

lots updates

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

Guangchuang Yu authored on 22/12/2015 04:08:02
Showing 1 changed files
man/geom_tiplab.Rd
History View file @ 6c9cd355
... ... 
@@ -1,4 +1,4 @@
1 
-% Generated by roxygen2 (4.1.1): do not edit by hand
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+% Generated by roxygen2: do not edit by hand
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 % Please edit documentation in R/geom_tiplab.R
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 \name{geom_tiplab}
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 \alias{geom_tiplab}
Browse code

update according to changes of ggplot2

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107869 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 28/08/2015 13:39:22
Showing 1 changed files
man/geom_tiplab.Rd
History View file @ 1d4d6914
... ... 
@@ -1,5 +1,5 @@
1 1 
 % Generated by roxygen2 (4.1.1): do not edit by hand
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-% Please edit documentation in R/ggtree.R
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+% Please edit documentation in R/geom_tiplab.R
3 3 
 \name{geom_tiplab}
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 \alias{geom_tiplab}
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 \title{geom_tiplab}
Browse code

annotation_image

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@106969 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 01/08/2015 13:12:53
Showing 1 changed files
man/geom_tiplab.Rd
History View file @ 5cfb0ffa
... ... 
@@ -5,7 +5,7 @@
5 5 
 \title{geom_tiplab}
6 6 
 \usage{
7 7 
 geom_tiplab(mapping = NULL, hjust = 0, align = FALSE,
8 
-  linetype = "dotted", line.size = 1, ...)
8 
+  linetype = "dotted", linesize = 1, ...)
9 9 
 }
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 \arguments{
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 \item{mapping}{aes mapping}
... ... 
@@ -16,7 +16,7 @@ geom_tiplab(mapping = NULL, hjust = 0, align = FALSE,
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 \item{linetype}{linetype for adding line if align = TRUE}
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-\item{line.size}{line size of line if align = TRUE}
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+\item{linesize}{line size of line if align = TRUE}
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 \item{...}{additional parameter}
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 }
Browse code

group_name parameter of groupOTU/groupClade and new geom_tiplab

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@106964 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 01/08/2015 08:58:16
Showing 1 changed files
man/geom_tiplab.Rd
History View file @ 68c7ac99
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@@ -4,13 +4,20 @@
4 4 
 \alias{geom_tiplab}
5 5 
 \title{geom_tiplab}
6 6 
 \usage{
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-geom_tiplab(align = FALSE, hjust = 0, ...)
7 
+geom_tiplab(mapping = NULL, hjust = 0, align = FALSE,
8 
+  linetype = "dotted", line.size = 1, ...)
8 9 
 }
9 10 
 \arguments{
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-\item{align}{align tip lab or not, logical}
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+\item{mapping}{aes mapping}
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 \item{hjust}{horizontal adjustment}
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+\item{align}{align tip lab or not, logical}
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+
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+\item{linetype}{linetype for adding line if align = TRUE}
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+
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+\item{line.size}{line size of line if align = TRUE}
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+
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 \item{...}{additional parameter}
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 }
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 \value{
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: ca17acc22b608158936b9c2790bff2f7504f38d9

add author



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@103112 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 27/04/2015 03:15:40
Showing 1 changed files
man/geom_tiplab.Rd
History View file @ b893400f
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@@ -1,4 +1,4 @@
1 
-% Generated by roxygen2 (4.1.0): do not edit by hand
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+% Generated by roxygen2 (4.1.1): do not edit by hand
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 % Please edit documentation in R/ggtree.R
3 3 
 \name{geom_tiplab}
4 4 
 \alias{geom_tiplab}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 4c62d2f58238f5534a0dcd8df6c6a884c0e141be

better geom_tiplab



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@101639 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 31/03/2015 10:30:58
Showing 1 changed files
man/geom_tiplab.Rd
History View file @ ca45db4f
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@@ -4,7 +4,7 @@
4 4 
 \alias{geom_tiplab}
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 \title{geom_tiplab}
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 \usage{
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-geom_tiplab(align = FALSE, hjust = -0.25, ...)
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+geom_tiplab(align = FALSE, hjust = 0, ...)
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 }
9 9 
 \arguments{
10 10 
 \item{align}{align tip lab or not, logical}
Browse code

Adds ggtree/ seq2pathway/ sidap/ to the repos.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@98340 bc3139a8-67e5-0310-9ffc-ced21a209358

Marc Carlson authored on 14/01/2015 21:22:07
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man/geom_tiplab.Rd
History View file @ 0c8aaf33
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new file mode 100644
... ... 
@@ -0,0 +1,30 @@
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+% Generated by roxygen2 (4.1.0): do not edit by hand
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+% Please edit documentation in R/ggtree.R
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+\name{geom_tiplab}
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+\alias{geom_tiplab}
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+\title{geom_tiplab}
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+\usage{
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+geom_tiplab(align = FALSE, hjust = -0.25, ...)
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+}
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+\arguments{
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+\item{align}{align tip lab or not, logical}
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+
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+\item{hjust}{horizontal adjustment}
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+
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+\item{...}{additional parameter}
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+}
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+\value{
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+tip label layer
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+}
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+\description{
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+add tip label layer
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+}
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+\examples{
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+require(ape)
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+tr <- rtree(10)
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+ggtree(tr) + geom_tiplab()
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+}
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+\author{
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+Yu Guangchuang
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+}
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+