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

typo

Guangchuang Yu authored on 21/11/2022 02:56:09
Showing 1 changed files
R/theme.R
History View file @ 6bc28f39
... ... 
@@ -44,7 +44,7 @@ theme_tree <- function(bgcolor="white", ...) {
44 44 
 ##' @importFrom ggplot2 element_text
45 45 
 ##' @author Guangchuang Yu
46 46 
 theme_dendrogram <- function(bgcolor = "white", fgcolor = "black", ...) {
47 
-    list(theme_tree2(bgcolor = bgcolor)
47 
+    list(theme_tree2(bgcolor = bgcolor),
48 48 
         ggfun::theme_noxaxis(color=bgcolor, ...)
49 49 
     )
50 50 
 }
Browse code

update theme_dendrogram

Guangchuang Yu authored on 21/11/2022 02:28:11
Showing 1 changed files
R/theme.R
History View file @ 75079553
... ... 
@@ -44,14 +44,9 @@ theme_tree <- function(bgcolor="white", ...) {
44 44 
 ##' @importFrom ggplot2 element_text
45 45 
 ##' @author Guangchuang Yu
46 46 
 theme_dendrogram <- function(bgcolor = "white", fgcolor = "black", ...) {
47 
-    theme_tree2(bgcolor = bgcolor,
48 
-                axis.line.x = element_blank(),
49 
-                axis.text.x = element_blank(),
50 
-                axis.ticks.x = element_blank(),
51 
-                axis.line.y = element_line(color=fgcolor),
52 
-                axis.text.y = element_text(color=fgcolor),
53 
-                axis.ticks.y = element_line(color=fgcolor),
54 
-                ...)
47 
+    list(theme_tree2(bgcolor = bgcolor)
48 
+        ggfun::theme_noxaxis(color=bgcolor, ...)
49 
+    )
55 50 
 }
56 51
57 52
Browse code

Add outline to nodepies (outline.color and outline.size), remove margins in theme_inset (better display of the inset on the plot)

Léo-Paul Dagallier authored on 07/06/2022 15:35:08
Showing 1 changed files
R/theme.R
History View file @ 5ebd35a4
... ... 
@@ -121,7 +121,7 @@ theme_tree2_internal <- function(bgcolor="white", fgcolor="black",
121 121 
 theme_inset <- function(legend.position =  "none", ...) {
122 122 
     list(xlab(NULL),
123 123 
          ylab(NULL),
124 
-         theme_tree(legend.position = legend.position, ...),
124 
+         theme_tree(legend.position = legend.position, plot.margin = unit(c(0, 0, 0, 0), "lines"), ...),
125 125 
          ggfun::theme_transparent()
126 126 
          )
127 127 
 }
Browse code

Document update

Document update

William Lee authored on 22/03/2022 14:46:29
Showing 1 changed files
R/theme.R
History View file @ 3c7f66c8
... ... 
@@ -1,8 +1,9 @@
1 1 
 ##' tree theme
2 2 
 ##'
3 
+##' 'theme_tree' defines a blank background to display tree
3 4 
 ##'
4 5 
 ##' @title theme_tree
5 
-##' @param bgcolor background color
6 
+##' @param bgcolor set background color, defaults to "white"
6 7 
 ##' @param ... additional parameter
7 8 
 ##' @importFrom ggplot2 theme_void
8 9 
 ##' @importFrom ggplot2 theme
... ... 
@@ -38,7 +39,7 @@ theme_tree <- function(bgcolor="white", ...) {
38 39 
 ##'
39 40 
 ##' @title theme_dendrogram
40 41 
 ##' @inheritParams theme_tree
41 
-##' @param fgcolor color for axis
42 
+##' @param fgcolor set color of axis
42 43 
 ##' @export
43 44 
 ##' @importFrom ggplot2 element_text
44 45 
 ##' @author Guangchuang Yu
... ... 
@@ -56,10 +57,11 @@ theme_dendrogram <- function(bgcolor = "white", fgcolor = "black", ...) {
56 57
57 58 
 ##' tree2 theme
58 59 
 ##'
60 
+##' 'theme_tree2' supports displaying phylogenetic distance by setting x-axis
59 61 
 ##'
60 62 
 ##' @title theme_tree2
61 
-##' @param bgcolor background color
62 
-##' @param fgcolor foreground color
63 
+##' @param bgcolor set background color, defaults to "white"
64 
+##' @param fgcolor set foreground color, defaults to "black"
63 65 
 ##' @param ... additional parameter
64 66 
 ##' @importFrom ggplot2 theme_bw
65 67 
 ##' @importFrom ggplot2 theme
... ... 
@@ -111,7 +113,7 @@ theme_tree2_internal <- function(bgcolor="white", fgcolor="black",
111 113 
 ##'
112 114 
 ##' theme for inset function
113 115 
 ##' @title theme_inset
114 
-##' @param legend.position position of legend
116 
+##' @param legend.position set the position of legend
115 117 
 ##' @param ... additional parameter
116 118 
 ##' @return ggplot object
117 119 
 ##' @export
Browse code

import theme_transparent from ggfun

Bjørn Tore Kopperud authored on 28/01/2022 11:02:50 • GitHub committed on 28/01/2022 11:02:50
Showing 1 changed files
R/theme.R
History View file @ a695ddf7
... ... 
@@ -119,12 +119,7 @@ theme_tree2_internal <- function(bgcolor="white", fgcolor="black",
119 119 
 theme_inset <- function(legend.position =  "none", ...) {
120 120 
     list(xlab(NULL),
121 121 
          ylab(NULL),
122 
-         theme_tree(legend.position = legend.position,
123 
-                    function() theme(panel.background = element_rect(fill = "transparent", colour = NA),
124 
-                                     plot.background = element_rect(fill = "transparent", colour = NA),
125 
-                                     legend.key = element_rect(fill = "transparent", colour = NA),
126 
-                                     legend.background = element_rect(fill = "transparent",colour = NA),
127 
-                                     ...)
128 
-                    )
122 
+         theme_tree(legend.position = legend.position, ...),
123 
+         ggfun::theme_transparent()
129 124 
          )
130 125 
 }
Browse code

remove ggimage dependency for theme

Bjørn Tore Kopperud authored on 19/01/2022 14:32:58 • GitHub committed on 19/01/2022 14:32:58
Showing 1 changed files
R/theme.R
History View file @ 1a0d8747
... ... 
@@ -119,7 +119,12 @@ theme_tree2_internal <- function(bgcolor="white", fgcolor="black",
119 119 
 theme_inset <- function(legend.position =  "none", ...) {
120 120 
     list(xlab(NULL),
121 121 
          ylab(NULL),
122 
-         theme_tree(legend.position =  legend.position, ...),
123 
-         ggimage::theme_transparent()
122 
+         theme_tree(legend.position = legend.position,
123 
+                    function() theme(panel.background = element_rect(fill = "transparent", colour = NA),
124 
+                                     plot.background = element_rect(fill = "transparent", colour = NA),
125 
+                                     legend.key = element_rect(fill = "transparent", colour = NA),
126 
+                                     legend.background = element_rect(fill = "transparent",colour = NA),
127 
+                                     ...)
128 
+                    )
124 129 
          )
125 130 
 }
Browse code

remove legend of theme_inset

Guangchuang Yu authored on 09/08/2019 09:03:30
Showing 1 changed files
R/theme.R
History View file @ dbf4890a
... ... 
@@ -111,14 +111,15 @@ theme_tree2_internal <- function(bgcolor="white", fgcolor="black",
111 111 
 ##'
112 112 
 ##' theme for inset function
113 113 
 ##' @title theme_inset
114 
+##' @param legend.position position of legend
114 115 
 ##' @param ... additional parameter
115 116 
 ##' @return ggplot object
116 117 
 ##' @export
117 118 
 ##' @author Guangchuang Yu
118 
-theme_inset <- function(...) {
119 
+theme_inset <- function(legend.position =  "none", ...) {
119 120 
     list(xlab(NULL),
120 121 
          ylab(NULL),
121 
-         theme_tree(...),
122 
+         theme_tree(legend.position =  legend.position, ...),
122 123 
          ggimage::theme_transparent()
123 124 
          )
124 125 
 }
Browse code

fixed R check of gheatmap and revert theme_tree to based on theme_bw

Guangchuang Yu authored on 06/08/2019 11:27:46
Showing 1 changed files
R/theme.R
History View file @ fd3b93fe
... ... 
@@ -18,19 +18,19 @@
18 18 
 ##' ggtree(tr) + theme_tree()
19 19 
 theme_tree <- function(bgcolor="white", ...) {
20 20
21 
-    ## list(xlab(NULL),
22 
-    ##      ylab(NULL),
23 
-    ##      theme_tree2_internal() +
24 
-    ##      theme(panel.background=element_rect(fill=bgcolor, colour=bgcolor),
25 
-    ##            axis.line.x = element_blank(),
26 
-    ##            axis.text.x = element_blank(),
27 
-    ##            axis.ticks.x = element_blank(),
28 
-    ##            ...)
29 
-    ##      )
30 
-
31 
-    theme_void() +
32 
-    theme(panel.background=element_rect(fill=bgcolor, colour=bgcolor),
33 
-          ...)
21 
+    list(xlab(NULL),
22 
+         ylab(NULL),
23 
+         theme_tree2_internal() +
24 
+         theme(panel.background=element_rect(fill=bgcolor, colour=bgcolor),
25 
+               axis.line.x = element_blank(),
26 
+               axis.text.x = element_blank(),
27 
+               axis.ticks.x = element_blank(),
28 
+               ...)
29 
+         )
30 
+
31 
+    ## theme_void() +
32 
+    ##     theme(panel.background=element_rect(fill=bgcolor, colour=bgcolor),
33 
+    ##           ...)
34 34 
 }
35 35
36 36 
 ##' dendrogram theme
... ... 
@@ -74,10 +74,10 @@ theme_dendrogram <- function(bgcolor = "white", fgcolor = "black", ...) {
74 74 
 ##' tr <- rtree(10)
75 75 
 ##' ggtree(tr) + theme_tree2()
76 76 
 theme_tree2 <- function(bgcolor="white", fgcolor="black", ...) {
77 
-     list(xlab(NULL),
78 
-          ylab(NULL),
79 
-	  theme_tree2_internal(bgcolor, fgcolor, ...)
80 
-	  )
77 
+    list(xlab(NULL),
78 
+         ylab(NULL),
79 
+         theme_tree2_internal(bgcolor, fgcolor, ...)
80 
+         )
81 81 
 }
82 82
83 83 
 ##' @importFrom ggplot2 theme_bw
Browse code

update theme

Guangchuang Yu authored on 05/08/2019 14:34:13
Showing 1 changed files
R/theme.R
History View file @ 827cd9ec
... ... 
@@ -3,9 +3,8 @@
3 3 
 ##'
4 4 
 ##' @title theme_tree
5 5 
 ##' @param bgcolor background color
6 
-##' @param fgcolor foreground color
7 6 
 ##' @param ... additional parameter
8 
-##' @importFrom ggplot2 theme_bw
7 
+##' @importFrom ggplot2 theme_void
9 8 
 ##' @importFrom ggplot2 theme
10 9 
 ##' @importFrom ggplot2 element_blank
11 10 
 ##' @importFrom ggplot2 xlab
... ... 
@@ -17,16 +16,21 @@
17 16 
 ##' require(ape)
18 17 
 ##' tr <- rtree(10)
19 18 
 ##' ggtree(tr) + theme_tree()
20 
-theme_tree <- function(bgcolor="white", fgcolor="black", ...) {
21 
-    list(xlab(NULL),
22 
-         ylab(NULL),
23 
-	 theme_tree2_internal() +
24 
-         theme(panel.background=element_rect(fill=bgcolor, colour=bgcolor),
25 
-               axis.line.x = element_blank(),
26 
-               axis.text.x = element_blank(),
27 
-               axis.ticks.x = element_blank(),
28 
-               ...)
29 
-	 )
19 
+theme_tree <- function(bgcolor="white", ...) {
20 
+
21 
+    ## list(xlab(NULL),
22 
+    ##      ylab(NULL),
23 
+    ##      theme_tree2_internal() +
24 
+    ##      theme(panel.background=element_rect(fill=bgcolor, colour=bgcolor),
25 
+    ##            axis.line.x = element_blank(),
26 
+    ##            axis.text.x = element_blank(),
27 
+    ##            axis.ticks.x = element_blank(),
28 
+    ##            ...)
29 
+    ##      )
30 
+
31 
+    theme_void() +
32 
+    theme(panel.background=element_rect(fill=bgcolor, colour=bgcolor),
33 
+          ...)
30 34 
 }
31 35
32 36 
 ##' dendrogram theme
... ... 
@@ -34,15 +38,19 @@ theme_tree <- function(bgcolor="white", fgcolor="black", ...) {
34 38 
 ##'
35 39 
 ##' @title theme_dendrogram
36 40 
 ##' @inheritParams theme_tree
41 
+##' @param fgcolor color for axis
37 42 
 ##' @export
38 43 
 ##' @importFrom ggplot2 element_text
39 44 
 ##' @author Guangchuang Yu
40 
-theme_dendrogram <- function(bgcolor="white", fgcolor="black", ...) {
41 
-    theme_tree(bgcolor = bgcolor, fgcolor = fgcolor,
42 
-               axis.line.y = element_line(color=fgcolor),
43 
-               axis.text.y = element_text(color=fgcolor),
44 
-               axis.ticks.y = element_line(color=fgcolor),
45 
-               ...)
45 
+theme_dendrogram <- function(bgcolor = "white", fgcolor = "black", ...) {
46 
+    theme_tree2(bgcolor = bgcolor,
47 
+                axis.line.x = element_blank(),
48 
+                axis.text.x = element_blank(),
49 
+                axis.ticks.x = element_blank(),
50 
+                axis.line.y = element_line(color=fgcolor),
51 
+                axis.text.y = element_text(color=fgcolor),
52 
+                axis.ticks.y = element_line(color=fgcolor),
53 
+                ...)
46 54 
 }
47 55
48 56
... ... 
@@ -72,7 +80,7 @@ theme_tree2 <- function(bgcolor="white", fgcolor="black", ...) {
72 80 
 	  )
73 81 
 }
74 82
75 
-##' @importFrom ggplot2 theme_void
83 
+##' @importFrom ggplot2 theme_bw
76 84 
 theme_tree2_internal <- function(bgcolor="white", fgcolor="black",
77 85 
                                  legend.position="right",
78 86 
                                  panel.grid.minor=element_blank(),
... ... 
@@ -83,7 +91,8 @@ theme_tree2_internal <- function(bgcolor="white", fgcolor="black",
83 91 
                                  axis.text.y=element_blank(),...) {
84 92 
     ## need to set axis.line otherwise the setting cannot be inherited.
85 93 
     ## https://github.com/GuangchuangYu/ggtree/issues/218
86 
-    theme_void() +
94 
+
95 
+    theme_bw() +
87 96 
         theme(legend.position=legend.position,
88 97 
               panel.grid.minor=panel.grid.minor,
89 98 
               panel.grid.major=panel.grid.major,
Browse code

update theme

Guangchuang Yu authored on 05/08/2019 13:55:58
Showing 1 changed files
R/theme.R
History View file @ ecf50e8f
... ... 
@@ -72,8 +72,9 @@ theme_tree2 <- function(bgcolor="white", fgcolor="black", ...) {
72 72 
 	  )
73 73 
 }
74 74
75 
+##' @importFrom ggplot2 theme_void
75 76 
 theme_tree2_internal <- function(bgcolor="white", fgcolor="black",
76 
-                                 legend.position="none",
77 
+                                 legend.position="right",
77 78 
                                  panel.grid.minor=element_blank(),
78 79 
                                  panel.grid.major=element_blank(),
79 80 
                                  panel.border=element_blank(),
... ... 
@@ -82,7 +83,7 @@ theme_tree2_internal <- function(bgcolor="white", fgcolor="black",
82 83 
                                  axis.text.y=element_blank(),...) {
83 84 
     ## need to set axis.line otherwise the setting cannot be inherited.
84 85 
     ## https://github.com/GuangchuangYu/ggtree/issues/218
85 
-    theme_bw() +
86 
+    theme_void() +
86 87 
         theme(legend.position=legend.position,
87 88 
               panel.grid.minor=panel.grid.minor,
88 89 
               panel.grid.major=panel.grid.major,
Browse code

tree layout

Guangchuang Yu authored on 24/07/2019 07:38:11
Showing 1 changed files
R/theme.R
History View file @ d3057fa1
... ... 
@@ -12,7 +12,7 @@
12 12 
 ##' @importFrom ggplot2 ylab
13 13 
 ##' @export
14 14 
 ##' @return updated ggplot object with new theme
15 
-##' @author Yu Guangchuang
15 
+##' @author Guangchuang Yu
16 16 
 ##' @examples
17 17 
 ##' require(ape)
18 18 
 ##' tr <- rtree(10)
... ... 
@@ -29,6 +29,23 @@ theme_tree <- function(bgcolor="white", fgcolor="black", ...) {
29 29 
 	 )
30 30 
 }
31 31
32 
+##' dendrogram theme
33 
+##'
34 
+##'
35 
+##' @title theme_dendrogram
36 
+##' @inheritParams theme_tree
37 
+##' @export
38 
+##' @importFrom ggplot2 element_text
39 
+##' @author Guangchuang Yu
40 
+theme_dendrogram <- function(bgcolor="white", fgcolor="black", ...) {
41 
+    theme_tree(bgcolor = bgcolor, fgcolor = fgcolor,
42 
+               axis.line.y = element_line(color=fgcolor),
43 
+               axis.text.y = element_text(color=fgcolor),
44 
+               axis.ticks.y = element_line(color=fgcolor),
45 
+               ...)
46 
+}
47 
+
48 
+
32 49 
 ##' tree2 theme
33 50 
 ##'
34 51 
 ##'
... ... 
@@ -43,7 +60,7 @@ theme_tree <- function(bgcolor="white", fgcolor="black", ...) {
43 60 
 ##' @importFrom ggplot2 element_rect
44 61 
 ##' @export
45 62 
 ##' @return updated ggplot object with new theme
46 
-##' @author Yu Guangchuang
63 
+##' @author Guangchuang Yu
47 64 
 ##' @examples
48 65 
 ##' require(ape)
49 66 
 ##' tr <- rtree(10)
Browse code

typo

Guangchuang Yu authored on 14/01/2019 12:00:44
Showing 1 changed files
R/theme.R
History View file @ 9416b852
... ... 
@@ -63,7 +63,7 @@ theme_tree2_internal <- function(bgcolor="white", fgcolor="black",
63 63 
                                  axis.line.y=element_blank(),
64 64 
                                  axis.ticks.y=element_blank(),
65 65 
                                  axis.text.y=element_blank(),...) {
66 
-    ## need to set axis.line otherwise the the settng cannot be inherited.
66 
+    ## need to set axis.line otherwise the setting cannot be inherited.
67 67 
     ## https://github.com/GuangchuangYu/ggtree/issues/218
68 68 
     theme_bw() +
69 69 
         theme(legend.position=legend.position,
Browse code

bug fixed of theme_tree2(), see also #218

Guangchuang Yu authored on 14/01/2019 02:40:45
Showing 1 changed files
R/theme.R
History View file @ 2b9d5e9d
... ... 
@@ -63,14 +63,16 @@ theme_tree2_internal <- function(bgcolor="white", fgcolor="black",
63 63 
                                  axis.line.y=element_blank(),
64 64 
                                  axis.ticks.y=element_blank(),
65 65 
                                  axis.text.y=element_blank(),...) {
66 
+    ## need to set axis.line otherwise the the settng cannot be inherited.
67 
+    ## https://github.com/GuangchuangYu/ggtree/issues/218
66 68 
     theme_bw() +
67 69 
         theme(legend.position=legend.position,
68 70 
               panel.grid.minor=panel.grid.minor,
69 71 
               panel.grid.major=panel.grid.major,
70 72 
               panel.background=element_rect(fill=bgcolor, colour=bgcolor),
71 73 
               panel.border=panel.border,
72 
-              ## axis.line=element_line(color=fgcolor),
73 
-              axis.line.x=element_line(color=fgcolor),
74 
+              axis.line=element_line(color=fgcolor),
75 
+              ##axis.line.x=element_line(color=fgcolor),
74 76 
               axis.line.y=axis.line.y,
75 77 
               axis.ticks.y=axis.ticks.y,
76 78 
               axis.text.y=axis.text.y,
Browse code

remove theme_transparent

guangchuang yu authored on 04/12/2017 12:41:52
Showing 1 changed files
R/theme.R
History View file @ 9125fc57
... ... 
@@ -77,32 +77,6 @@ theme_tree2_internal <- function(bgcolor="white", fgcolor="black",
77 77 
               ...)
78 78 
 }
79 79
80 
-##' transparent background theme
81 
-##'
82 
-##'
83 
-##' @title theme_transparent
84 
-##' @param ... additional parameter to tweak the theme
85 
-##' @return ggplot object
86 
-##' @importFrom ggplot2 theme
87 
-##' @importFrom ggplot2 element_rect
88 
-##' @export
89 
-##' @author Guangchuang Yu
90 
-theme_transparent <- function(...) {
91 
-    message("this theme was moved to ggimage::theme_transparent and will be removed in next release")
92 
-
93 
-    theme(panel.background = element_rect(
94 
-              fill = "transparent",
95 
-              colour = NA),
96 
-          plot.background = element_rect(
97 
-              fill = "transparent",
98 
-              colour = NA),
99 
-          legend.key = element_rect(
100 
-              fill = "transparent",
101 
-              colour = NA),
102 
-          legend.background = element_rect(
103 
-              fill = "transparent",
104 
-              colour = NA), ...)
105 
-}
106 80
107 81 
 ##' inset theme
108 82 
 ##'
... ... 
@@ -113,10 +87,9 @@ theme_transparent <- function(...) {
113 87 
 ##' @export
114 88 
 ##' @author Guangchuang Yu
115 89 
 theme_inset <- function(...) {
116 
-    message("this theme will be removed in next release")
117 90 
     list(xlab(NULL),
118 91 
          ylab(NULL),
119 92 
          theme_tree(...),
120 
-         theme_transparent()
93 
+         ggimage::theme_transparent()
121 94 
          )
122 95 
 }
Browse code

message for defunct functions

guangchuang yu authored on 23/03/2017 03:40:26
Showing 1 changed files
R/theme.R
History View file @ 62f9f34e
... ... 
@@ -20,7 +20,7 @@
20 20 
 theme_tree <- function(bgcolor="white", fgcolor="black", ...) {
21 21 
     list(xlab(NULL),
22 22 
          ylab(NULL),
23 
-	 theme_tree2_internal() +
23 
+	 theme_tree2_internal() +
24 24 
          theme(panel.background=element_rect(fill=bgcolor, colour=bgcolor),
25 25 
                axis.line.x = element_blank(),
26 26 
                axis.text.x = element_blank(),
... ... 
@@ -63,7 +63,7 @@ theme_tree2_internal <- function(bgcolor="white", fgcolor="black",
63 63 
                                  axis.line.y=element_blank(),
64 64 
                                  axis.ticks.y=element_blank(),
65 65 
                                  axis.text.y=element_blank(),...) {
66 
-    theme_bw() +
66 
+    theme_bw() +
67 67 
         theme(legend.position=legend.position,
68 68 
               panel.grid.minor=panel.grid.minor,
69 69 
               panel.grid.major=panel.grid.major,
... ... 
@@ -88,6 +88,8 @@ theme_tree2_internal <- function(bgcolor="white", fgcolor="black",
88 88 
 ##' @export
89 89 
 ##' @author Guangchuang Yu
90 90 
 theme_transparent <- function(...) {
91 
+    message("this theme was moved to ggimage::theme_transparent and will be removed in next release")
92 
+
91 93 
     theme(panel.background = element_rect(
92 94 
               fill = "transparent",
93 95 
               colour = NA),
... ... 
@@ -95,10 +97,10 @@ theme_transparent <- function(...) {
95 97 
               fill = "transparent",
96 98 
               colour = NA),
97 99 
           legend.key = element_rect(
98 
-              fill = "transparent",
100 
+              fill = "transparent",
99 101 
               colour = NA),
100 102 
           legend.background = element_rect(
101 
-              fill = "transparent",
103 
+              fill = "transparent",
102 104 
               colour = NA), ...)
103 105 
 }
104 106
... ... 
@@ -111,6 +113,7 @@ theme_transparent <- function(...) {
111 113 
 ##' @export
112 114 
 ##' @author Guangchuang Yu
113 115 
 theme_inset <- function(...) {
116 
+    message("this theme will be removed in next release")
114 117 
     list(xlab(NULL),
115 118 
          ylab(NULL),
116 119 
          theme_tree(...),
Browse code

Fix mess with additional parameters

Bisaloo authored on 31/01/2017 08:43:53 • GitHub committed on 31/01/2017 08:43:53
Showing 1 changed files
R/theme.R
History View file @ cd5fb3e0
... ... 
@@ -93,10 +93,10 @@ theme_transparent <- function(...) {
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               colour = NA),
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           plot.background = element_rect(
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               fill = "transparent",
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-              colour = NA), ...),
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+              colour = NA),
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           legend.key = element_rect(
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               fill = "transparent",
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-              colour = NA), ...),
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+              colour = NA),
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           legend.background = element_rect(
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               fill = "transparent",
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               colour = NA), ...)
Browse code

Add missing closing parenthesis

Bisaloo authored on 31/01/2017 08:42:45 • GitHub committed on 31/01/2017 08:42:45
Showing 1 changed files
R/theme.R
History View file @ ced8b06a
... ... 
@@ -96,10 +96,10 @@ theme_transparent <- function(...) {
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               colour = NA), ...),
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           legend.key = element_rect(
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               fill = "transparent",
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-              colour = NA, ...),
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+              colour = NA), ...),
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           legend.background = element_rect(
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               fill = "transparent",
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-              colour = NA, ...)
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+              colour = NA), ...)
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 }
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 ##' inset theme
Browse code

Add legend transparency to theme_transparent

Bisaloo authored on 31/01/2017 08:37:49 • GitHub committed on 31/01/2017 08:37:49
Showing 1 changed files
R/theme.R
History View file @ 225f0e44
... ... 
@@ -93,7 +93,13 @@ theme_transparent <- function(...) {
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               colour = NA),
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           plot.background = element_rect(
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               fill = "transparent",
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-              colour = NA), ...)
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+              colour = NA), ...),
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+          legend.key = element_rect(
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+              fill = "transparent",
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+              colour = NA, ...),
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+          legend.background = element_rect(
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+              fill = "transparent",
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+              colour = NA, ...)
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 }
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99 105 
 ##' inset theme
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/theme.R
History View file @ a92aaed1
... ... 
@@ -8,7 +8,6 @@
8 8 
 ##' @importFrom ggplot2 theme_bw
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 ##' @importFrom ggplot2 theme
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 ##' @importFrom ggplot2 element_blank
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-##' @importFrom ggplot2 %+replace%
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 ##' @importFrom ggplot2 xlab
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 ##' @importFrom ggplot2 ylab
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 ##' @export
... ... 
@@ -21,12 +20,12 @@
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 theme_tree <- function(bgcolor="white", fgcolor="black", ...) {
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     list(xlab(NULL),
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          ylab(NULL),
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-	 theme_tree2_internal() %+replace%
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-            theme(panel.background=element_rect(fill=bgcolor, colour=bgcolor),
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-            axis.line.x = element_blank(),
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-            axis.text.x = element_blank(),
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-            axis.ticks.x = element_blank(),
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-            ...)
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+	 theme_tree2_internal() +
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+         theme(panel.background=element_rect(fill=bgcolor, colour=bgcolor),
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+               axis.line.x = element_blank(),
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+               axis.text.x = element_blank(),
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+               axis.ticks.x = element_blank(),
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+               ...)
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 	 )
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 }
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... ... 
@@ -41,7 +40,6 @@ theme_tree <- function(bgcolor="white", fgcolor="black", ...) {
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 ##' @importFrom ggplot2 theme
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 ##' @importFrom ggplot2 element_blank
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 ##' @importFrom ggplot2 element_line
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-##' @importFrom ggplot2 %+replace%
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 ##' @importFrom ggplot2 element_rect
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 ##' @export
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 ##' @return updated ggplot object with new theme
... ... 
@@ -65,18 +63,18 @@ theme_tree2_internal <- function(bgcolor="white", fgcolor="black",
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                                  axis.line.y=element_blank(),
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                                  axis.ticks.y=element_blank(),
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                                  axis.text.y=element_blank(),...) {
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-    theme_bw() %+replace%
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-    theme(legend.position=legend.position,
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-          panel.grid.minor=panel.grid.minor,
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-          panel.grid.major=panel.grid.major,
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-          panel.background=element_rect(fill=bgcolor, colour=bgcolor),
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-          panel.border=panel.border,
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-          ## axis.line=element_line(color=fgcolor),
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-          axis.line.x=element_line(color=fgcolor),
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-          axis.line.y=axis.line.y,
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-          axis.ticks.y=axis.ticks.y,
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-          axis.text.y=axis.text.y,
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-          ...)
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+    theme_bw() +
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+        theme(legend.position=legend.position,
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+              panel.grid.minor=panel.grid.minor,
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+              panel.grid.major=panel.grid.major,
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+              panel.background=element_rect(fill=bgcolor, colour=bgcolor),
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+              panel.border=panel.border,
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+              ## axis.line=element_line(color=fgcolor),
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+              axis.line.x=element_line(color=fgcolor),
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+              axis.line.y=axis.line.y,
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+              axis.ticks.y=axis.ticks.y,
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+              axis.text.y=axis.text.y,
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+              ...)
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 }
81 79
82 80 
 ##' transparent background theme
Browse code

theme_tree2

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@121780 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 05/10/2016 06:28:50
Showing 1 changed files
R/theme.R
History View file @ e785220c
... ... 
@@ -1,6 +1,6 @@
1 1 
 ##' tree theme
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 ##'
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-##'
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+##'
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 ##' @title theme_tree
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 ##' @param bgcolor background color
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 ##' @param fgcolor foreground color
... ... 
@@ -32,7 +32,7 @@ theme_tree <- function(bgcolor="white", fgcolor="black", ...) {
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 ##' tree2 theme
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 ##'
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-##'
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+##'
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 ##' @title theme_tree2
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 ##' @param bgcolor background color
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 ##' @param fgcolor foreground color
... ... 
@@ -57,24 +57,31 @@ theme_tree2 <- function(bgcolor="white", fgcolor="black", ...) {
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 	  )
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 }
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-theme_tree2_internal <- function(bgcolor="white", fgcolor="black", ...) {
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+theme_tree2_internal <- function(bgcolor="white", fgcolor="black",
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+                                 legend.position="none",
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+                                 panel.grid.minor=element_blank(),
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+                                 panel.grid.major=element_blank(),
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+                                 panel.border=element_blank(),
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+                                 axis.line.y=element_blank(),
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+                                 axis.ticks.y=element_blank(),
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+                                 axis.text.y=element_blank(),...) {
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     theme_bw() %+replace%
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-    theme(legend.position="none",
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-          panel.grid.minor=element_blank(),
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-          panel.grid.major=element_blank(),
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+    theme(legend.position=legend.position,
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+          panel.grid.minor=panel.grid.minor,
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+          panel.grid.major=panel.grid.major,
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           panel.background=element_rect(fill=bgcolor, colour=bgcolor),
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-          panel.border=element_blank(),
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+          panel.border=panel.border,
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           ## axis.line=element_line(color=fgcolor),
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           axis.line.x=element_line(color=fgcolor),
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-          axis.line.y=element_blank(),
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-          axis.ticks.y=element_blank(),
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-          axis.text.y=element_blank(),
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+          axis.line.y=axis.line.y,
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+          axis.ticks.y=axis.ticks.y,
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+          axis.text.y=axis.text.y,
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           ...)
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 }
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 ##' transparent background theme
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 ##'
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-##'
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+##'
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 ##' @title theme_transparent
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 ##' @param ... additional parameter to tweak the theme
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 ##' @return ggplot object
Browse code

typo

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@114268 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 05/03/2016 13:58:18
Showing 1 changed files
R/theme.R
History View file @ d0175637
... ... 
@@ -64,8 +64,8 @@ theme_tree2_internal <- function(bgcolor="white", fgcolor="black", ...) {
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           panel.grid.major=element_blank(),
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           panel.background=element_rect(fill=bgcolor, colour=bgcolor),
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           panel.border=element_blank(),
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-          axis.line=element_line(color=fgcolor),
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-          axis.line.x=element_line(),
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+          ## axis.line=element_line(color=fgcolor),
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+          axis.line.x=element_line(color=fgcolor),
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           axis.line.y=element_blank(),
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           axis.ticks.y=element_blank(),
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           axis.text.y=element_blank(),
Browse code

update theme_tree2

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@114267 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 05/03/2016 13:49:32
Showing 1 changed files
R/theme.R
History View file @ 53eefadd
... ... 
@@ -65,6 +65,7 @@ theme_tree2_internal <- function(bgcolor="white", fgcolor="black", ...) {
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           panel.background=element_rect(fill=bgcolor, colour=bgcolor),
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           panel.border=element_blank(),
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           axis.line=element_line(color=fgcolor),
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+          axis.line.x=element_line(),
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           axis.line.y=element_blank(),
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           axis.ticks.y=element_blank(),
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           axis.text.y=element_blank(),
Browse code

update vignettes

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@112408 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 11/01/2016 04:11:26
Showing 1 changed files
R/theme.R
History View file @ 0ae9e98a
... ... 
@@ -9,6 +9,8 @@
9 9 
 ##' @importFrom ggplot2 theme
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 ##' @importFrom ggplot2 element_blank
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 ##' @importFrom ggplot2 %+replace%
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+##' @importFrom ggplot2 xlab
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+##' @importFrom ggplot2 ylab
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 ##' @export
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 ##' @return updated ggplot object with new theme
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 ##' @author Yu Guangchuang
... ... 
@@ -17,12 +19,15 @@
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 ##' tr <- rtree(10)
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 ##' ggtree(tr) + theme_tree()
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 theme_tree <- function(bgcolor="white", fgcolor="black", ...) {
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-    theme_tree2() %+replace%
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-    theme(panel.background=element_rect(fill=bgcolor, colour=bgcolor),
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-          axis.line.x = element_blank(),
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-          axis.text.x = element_blank(),
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-          axis.ticks.x = element_blank(),
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-          ...)
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+    list(xlab(NULL),
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+         ylab(NULL),
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+	 theme_tree2_internal() %+replace%
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+            theme(panel.background=element_rect(fill=bgcolor, colour=bgcolor),
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+            axis.line.x = element_blank(),
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+            axis.text.x = element_blank(),
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+            axis.ticks.x = element_blank(),
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+            ...)
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+	 )
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 }
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 ##' tree2 theme
... ... 
@@ -46,6 +51,13 @@ theme_tree <- function(bgcolor="white", fgcolor="black", ...) {
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 ##' tr <- rtree(10)
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 ##' ggtree(tr) + theme_tree2()
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 theme_tree2 <- function(bgcolor="white", fgcolor="black", ...) {
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+     list(xlab(NULL),
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+          ylab(NULL),
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+	  theme_tree2_internal(bgcolor, fgcolor, ...)
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+	  )
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+}
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+
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+theme_tree2_internal <- function(bgcolor="white", fgcolor="black", ...) {
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     theme_bw() %+replace%
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     theme(legend.position="none",
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           panel.grid.minor=element_blank(),
Browse code

inset function and update vignette

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@112112 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 04/01/2016 09:56:10
Showing 1 changed files
R/theme.R
History View file @ 245479db
... ... 
@@ -77,3 +77,19 @@ theme_transparent <- function(...) {
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               fill = "transparent",
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               colour = NA), ...)
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 }
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+
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+##' inset theme
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+##'
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+##' theme for inset function
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+##' @title theme_inset
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+##' @param ... additional parameter
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+##' @return ggplot object
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+##' @export
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+##' @author Guangchuang Yu
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+theme_inset <- function(...) {
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+    list(xlab(NULL),
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+         ylab(NULL),
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+         theme_tree(...),
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+         theme_transparent()
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+         )
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+}
Browse code

update vignette

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@111939 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 28/12/2015 11:35:22
Showing 1 changed files
R/theme.R
History View file @ 9f34e866
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,79 @@
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+##' tree theme
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+##'
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+##'
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+##' @title theme_tree
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+##' @param bgcolor background color
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+##' @param fgcolor foreground color
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+##' @param ... additional parameter
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+##' @importFrom ggplot2 theme_bw
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+##' @importFrom ggplot2 theme
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+##' @importFrom ggplot2 element_blank
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+##' @importFrom ggplot2 %+replace%
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+##' @export
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+##' @return updated ggplot object with new theme
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+##' @author Yu Guangchuang
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+##' @examples
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+##' require(ape)
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+##' tr <- rtree(10)
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+##' ggtree(tr) + theme_tree()
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+theme_tree <- function(bgcolor="white", fgcolor="black", ...) {
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+    theme_tree2() %+replace%
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+    theme(panel.background=element_rect(fill=bgcolor, colour=bgcolor),
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+          axis.line.x = element_blank(),
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+          axis.text.x = element_blank(),
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+          axis.ticks.x = element_blank(),
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+          ...)
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+}
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+
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+##' tree2 theme
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+##'
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+##'
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+##' @title theme_tree2
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+##' @param bgcolor background color
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+##' @param fgcolor foreground color
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+##' @param ... additional parameter
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+##' @importFrom ggplot2 theme_bw
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+##' @importFrom ggplot2 theme
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+##' @importFrom ggplot2 element_blank
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+##' @importFrom ggplot2 element_line
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+##' @importFrom ggplot2 %+replace%
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+##' @importFrom ggplot2 element_rect
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+##' @export
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+##' @return updated ggplot object with new theme
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+##' @author Yu Guangchuang
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+##' @examples
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+##' require(ape)
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+##' tr <- rtree(10)
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+##' ggtree(tr) + theme_tree2()
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+theme_tree2 <- function(bgcolor="white", fgcolor="black", ...) {
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+    theme_bw() %+replace%
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+    theme(legend.position="none",
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+          panel.grid.minor=element_blank(),
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+          panel.grid.major=element_blank(),
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+          panel.background=element_rect(fill=bgcolor, colour=bgcolor),
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+          panel.border=element_blank(),
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+          axis.line=element_line(color=fgcolor),
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+          axis.line.y=element_blank(),
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+          axis.ticks.y=element_blank(),
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+          axis.text.y=element_blank(),
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+          ...)
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+}
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+
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+##' transparent background theme
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+##'
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+##'
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+##' @title theme_transparent
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+##' @param ... additional parameter to tweak the theme
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+##' @return ggplot object
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+##' @importFrom ggplot2 theme
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+##' @importFrom ggplot2 element_rect
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+##' @export
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+##' @author Guangchuang Yu
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+theme_transparent <- function(...) {
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+    theme(panel.background = element_rect(
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+              fill = "transparent",
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+              colour = NA),
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+          plot.background = element_rect(
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+              fill = "transparent",
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+              colour = NA), ...)
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+}