Browse code

move scale-color-subtree to ggtreeDendro

Guangchuang Yu authored on 23/09/2022 02:52:18
Showing1 changed files
... ...
@@ -21,7 +21,6 @@ S3method(fortify,treedataList)
21 21
 S3method(fortify,twins)
22 22
 S3method(ggplot_add,cladelab)
23 23
 S3method(ggplot_add,cladelabel)
24
-S3method(ggplot_add,color_subtree)
25 24
 S3method(ggplot_add,facet_plot)
26 25
 S3method(ggplot_add,facet_xlim)
27 26
 S3method(ggplot_add,geom_range)
... ...
@@ -269,8 +268,6 @@ importFrom(rlang,abort)
269 268
 importFrom(rlang,as_name)
270 269
 importFrom(rlang,quo_name)
271 270
 importFrom(scales,alpha)
272
-importFrom(stats,as.hclust)
273
-importFrom(stats,cutree)
274 271
 importFrom(tidyr,gather)
275 272
 importFrom(tidytree,MRCA)
276 273
 importFrom(tidytree,ancestor)
Browse code

linkage support

Guangchuang Yu authored on 11/08/2022 09:03:41
Showing1 changed files
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@@ -7,6 +7,7 @@ S3method(fortify,dendrogram)
7 7
 S3method(fortify,diana)
8 8
 S3method(fortify,hclust)
9 9
 S3method(fortify,igraph)
10
+S3method(fortify,linkage)
10 11
 S3method(fortify,multiPhylo)
11 12
 S3method(fortify,obkData)
12 13
 S3method(fortify,phylo)
... ...
@@ -268,6 +269,8 @@ importFrom(rlang,abort)
268 269
 importFrom(rlang,as_name)
269 270
 importFrom(rlang,quo_name)
270 271
 importFrom(scales,alpha)
272
+importFrom(stats,as.hclust)
273
+importFrom(stats,cutree)
271 274
 importFrom(tidyr,gather)
272 275
 importFrom(tidytree,MRCA)
273 276
 importFrom(tidytree,ancestor)
Browse code

update geom_striplab

xiangpin authored on 22/04/2022 08:27:22
Showing1 changed files
... ...
@@ -29,6 +29,7 @@ S3method(ggplot_add,hilight)
29 29
 S3method(ggplot_add,layout_ggtree)
30 30
 S3method(ggplot_add,range_xaxis)
31 31
 S3method(ggplot_add,scale_ggtree)
32
+S3method(ggplot_add,striplab)
32 33
 S3method(ggplot_add,striplabel)
33 34
 S3method(ggplot_add,taxalink)
34 35
 S3method(ggplot_add,tiplab)
... ...
@@ -82,6 +83,7 @@ export(geom_rootedge)
82 83
 export(geom_rootpoint)
83 84
 export(geom_segment2)
84 85
 export(geom_strip)
86
+export(geom_striplab)
85 87
 export(geom_taxalink)
86 88
 export(geom_text)
87 89
 export(geom_text2)
Browse code

mv identify to ggfun

Guangchuang Yu authored on 01/04/2022 08:21:52
Showing1 changed files
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@@ -37,7 +37,6 @@ S3method(ggplot_add,tree_inset)
37 37
 S3method(ggplot_add,zoom_clade)
38 38
 S3method(groupClade,ggtree)
39 39
 S3method(groupOTU,ggtree)
40
-S3method(identify,gg)
41 40
 S3method(nodeid,ggtree)
42 41
 S3method(nodelab,ggtree)
43 42
 S3method(offspring,ggtree)
... ...
@@ -108,6 +107,7 @@ export(groupOTU)
108 107
 export(guide_legend)
109 108
 export(gzoom)
110 109
 export(hexpand)
110
+export(identify)
111 111
 export(inset)
112 112
 export(label_pad)
113 113
 export(layout_circular)
... ...
@@ -173,6 +173,7 @@ importFrom(dplyr,mutate)
173 173
 importFrom(dplyr,rename)
174 174
 importFrom(dplyr,select)
175 175
 importFrom(ggfun,get_aes_var)
176
+importFrom(ggfun,identify)
176 177
 importFrom(ggplot2,Geom)
177 178
 importFrom(ggplot2,GeomLabel)
178 179
 importFrom(ggplot2,GeomPoint)
... ...
@@ -241,16 +242,11 @@ importFrom(ggplot2,xlab)
241 242
 importFrom(ggplot2,xlim)
242 243
 importFrom(ggplot2,ylab)
243 244
 importFrom(ggplot2,ylim)
244
-importFrom(graphics,identify)
245 245
 importFrom(grid,arrow)
246
-importFrom(grid,convertX)
247
-importFrom(grid,convertY)
248 246
 importFrom(grid,curveGrob)
249
-importFrom(grid,dataViewport)
250 247
 importFrom(grid,gTree)
251 248
 importFrom(grid,gpar)
252 249
 importFrom(grid,grid.layout)
253
-importFrom(grid,grid.locator)
254 250
 importFrom(grid,grid.newpage)
255 251
 importFrom(grid,grobTree)
256 252
 importFrom(grid,pushViewport)
Browse code

update man files and fixed R check

Guangchuang Yu authored on 23/03/2022 04:13:34
Showing1 changed files
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@@ -123,6 +123,7 @@ export(nodeid)
123 123
 export(nodelab)
124 124
 export(nodepie)
125 125
 export(open_tree)
126
+export(plot_list)
126 127
 export(range_format)
127 128
 export(read.tree)
128 129
 export(revts)
... ...
@@ -136,6 +137,7 @@ export(scale_color_subtree)
136 137
 export(scale_colour_manual)
137 138
 export(scale_colour_subtree)
138 139
 export(scale_fill_manual)
140
+export(scale_x_continuous)
139 141
 export(scale_x_ggtree)
140 142
 export(scale_x_range)
141 143
 export(set_hilight_legend)
... ...
@@ -161,6 +163,7 @@ importFrom(ape,ladderize)
161 163
 importFrom(ape,read.tree)
162 164
 importFrom(ape,reorder.phylo)
163 165
 importFrom(ape,rtree)
166
+importFrom(aplot,plot_list)
164 167
 importFrom(aplot,xrange)
165 168
 importFrom(dplyr,collapse)
166 169
 importFrom(dplyr,filter)
... ...
@@ -262,7 +265,6 @@ importFrom(methods,is)
262 265
 importFrom(methods,missingArg)
263 266
 importFrom(methods,setGeneric)
264 267
 importFrom(methods,setOldClass)
265
-importFrom(pillar,style_subtle)
266 268
 importFrom(rlang,.data)
267 269
 importFrom(rlang,abort)
268 270
 importFrom(rlang,as_name)
Browse code

update citation

xiangpin authored on 01/03/2022 07:37:15
Showing1 changed files
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@@ -262,6 +262,7 @@ importFrom(methods,is)
262 262
 importFrom(methods,missingArg)
263 263
 importFrom(methods,setGeneric)
264 264
 importFrom(methods,setOldClass)
265
+importFrom(pillar,style_subtle)
265 266
 importFrom(rlang,.data)
266 267
 importFrom(rlang,abort)
267 268
 importFrom(rlang,as_name)
Browse code

scale_color_subtree

Guangchuang Yu authored on 01/12/2021 08:14:20
Showing1 changed files
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@@ -20,6 +20,7 @@ S3method(fortify,treedataList)
20 20
 S3method(fortify,twins)
21 21
 S3method(ggplot_add,cladelab)
22 22
 S3method(ggplot_add,cladelabel)
23
+S3method(ggplot_add,color_subtree)
23 24
 S3method(ggplot_add,facet_plot)
24 25
 S3method(ggplot_add,facet_xlim)
25 26
 S3method(ggplot_add,geom_range)
... ...
@@ -131,7 +132,9 @@ export(rtree)
131 132
 export(scaleClade)
132 133
 export(scale_color)
133 134
 export(scale_color_manual)
135
+export(scale_color_subtree)
134 136
 export(scale_colour_manual)
137
+export(scale_colour_subtree)
135 138
 export(scale_fill_manual)
136 139
 export(scale_x_ggtree)
137 140
 export(scale_x_range)
Browse code

remove rvcheck depend

xiangpin authored on 18/08/2021 06:27:37
Showing1 changed files
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@@ -166,6 +166,7 @@ importFrom(dplyr,left_join)
166 166
 importFrom(dplyr,mutate)
167 167
 importFrom(dplyr,rename)
168 168
 importFrom(dplyr,select)
169
+importFrom(ggfun,get_aes_var)
169 170
 importFrom(ggplot2,Geom)
170 171
 importFrom(ggplot2,GeomLabel)
171 172
 importFrom(ggplot2,GeomPoint)
... ...
@@ -262,8 +263,6 @@ importFrom(rlang,.data)
262 263
 importFrom(rlang,abort)
263 264
 importFrom(rlang,as_name)
264 265
 importFrom(rlang,quo_name)
265
-importFrom(rvcheck,get_aes_var)
266
-importFrom(rvcheck,get_fun_from_pkg)
267 266
 importFrom(scales,alpha)
268 267
 importFrom(tidyr,gather)
269 268
 importFrom(tidytree,MRCA)
... ...
@@ -284,3 +283,4 @@ importFrom(utils,getFromNamespace)
284 283
 importFrom(utils,modifyList)
285 284
 importFrom(utils,packageDescription)
286 285
 importFrom(utils,packageVersion)
286
+importFrom(yulab.utils,get_fun_from_pkg)
Browse code

add td_mutate and hilight or cladelab supporting fuction data

xiangpin authored on 27/07/2021 09:34:30
Showing1 changed files
... ...
@@ -137,6 +137,7 @@ export(scale_x_ggtree)
137 137
 export(scale_x_range)
138 138
 export(set_hilight_legend)
139 139
 export(td_filter)
140
+export(td_mutate)
140 141
 export(td_unnest)
141 142
 export(theme)
142 143
 export(theme_dendrogram)
Browse code

label_pad

Guangchuang Yu authored on 09/10/2020 15:27:38
Showing1 changed files
... ...
@@ -108,6 +108,7 @@ export(guide_legend)
108 108
 export(gzoom)
109 109
 export(hexpand)
110 110
 export(inset)
111
+export(label_pad)
111 112
 export(layout_circular)
112 113
 export(layout_dendrogram)
113 114
 export(layout_fan)
Browse code

fortify method for treedataList

Guangchuang Yu authored on 20/09/2020 06:49:31
Showing1 changed files
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@@ -16,6 +16,7 @@ S3method(fortify,phylog)
16 16
 S3method(fortify,phyloseq)
17 17
 S3method(fortify,pvclust)
18 18
 S3method(fortify,treedata)
19
+S3method(fortify,treedataList)
19 20
 S3method(fortify,twins)
20 21
 S3method(ggplot_add,cladelab)
21 22
 S3method(ggplot_add,cladelabel)
Browse code

ggexpand

Guangchuang Yu authored on 18/09/2020 08:19:27
Showing1 changed files
... ...
@@ -22,7 +22,7 @@ S3method(ggplot_add,cladelabel)
22 22
 S3method(ggplot_add,facet_plot)
23 23
 S3method(ggplot_add,facet_xlim)
24 24
 S3method(ggplot_add,geom_range)
25
-S3method(ggplot_add,hexpand)
25
+S3method(ggplot_add,ggexpand)
26 26
 S3method(ggplot_add,hilight)
27 27
 S3method(ggplot_add,layout_ggtree)
28 28
 S3method(ggplot_add,range_xaxis)
... ...
@@ -96,6 +96,7 @@ export(get_clade_position)
96 96
 export(get_heatmap_column_position)
97 97
 export(get_taxa_name)
98 98
 export(ggdensitree)
99
+export(ggexpand)
99 100
 export(ggplot)
100 101
 export(ggsave)
101 102
 export(ggtree)
... ...
@@ -141,6 +142,7 @@ export(theme_inset)
141 142
 export(theme_tree)
142 143
 export(theme_tree2)
143 144
 export(unit)
145
+export(vexpand)
144 146
 export(viewClade)
145 147
 export(xlim)
146 148
 export(xlim_expand)
Browse code

remove shadowtext

xiangpin authored on 16/09/2020 07:03:32
Showing1 changed files
... ...
@@ -260,7 +260,6 @@ importFrom(rlang,quo_name)
260 260
 importFrom(rvcheck,get_aes_var)
261 261
 importFrom(rvcheck,get_fun_from_pkg)
262 262
 importFrom(scales,alpha)
263
-importFrom(shadowtext,geom_shadowtext)
264 263
 importFrom(tidyr,gather)
265 264
 importFrom(tidytree,MRCA)
266 265
 importFrom(tidytree,ancestor)
Browse code

new export

xiangpin authored on 15/09/2020 14:01:20
Showing1 changed files
... ...
@@ -17,6 +17,7 @@ S3method(fortify,phyloseq)
17 17
 S3method(fortify,pvclust)
18 18
 S3method(fortify,treedata)
19 19
 S3method(fortify,twins)
20
+S3method(ggplot_add,cladelab)
20 21
 S3method(ggplot_add,cladelabel)
21 22
 S3method(ggplot_add,facet_plot)
22 23
 S3method(ggplot_add,facet_xlim)
... ...
@@ -60,6 +61,7 @@ export(flip)
60 61
 export(fortify)
61 62
 export(geom_aline)
62 63
 export(geom_balance)
64
+export(geom_cladelab)
63 65
 export(geom_cladelabel)
64 66
 export(geom_cladelabel2)
65 67
 export(geom_facet)
... ...
@@ -258,6 +260,7 @@ importFrom(rlang,quo_name)
258 260
 importFrom(rvcheck,get_aes_var)
259 261
 importFrom(rvcheck,get_fun_from_pkg)
260 262
 importFrom(scales,alpha)
263
+importFrom(shadowtext,geom_shadowtext)
261 264
 importFrom(tidyr,gather)
262 265
 importFrom(tidytree,MRCA)
263 266
 importFrom(tidytree,ancestor)
Browse code

td_unnest

Guangchuang Yu authored on 14/09/2020 02:14:03
Showing1 changed files
... ...
@@ -131,12 +131,13 @@ export(scale_fill_manual)
131 131
 export(scale_x_ggtree)
132 132
 export(scale_x_range)
133 133
 export(set_hilight_legend)
134
+export(td_filter)
135
+export(td_unnest)
134 136
 export(theme)
135 137
 export(theme_dendrogram)
136 138
 export(theme_inset)
137 139
 export(theme_tree)
138 140
 export(theme_tree2)
139
-export(tree_filter)
140 141
 export(unit)
141 142
 export(viewClade)
142 143
 export(xlim)
Browse code

tree_filter

Guangchuang Yu authored on 29/08/2020 05:49:35
Showing1 changed files
... ...
@@ -136,6 +136,7 @@ export(theme_dendrogram)
136 136
 export(theme_inset)
137 137
 export(theme_tree)
138 138
 export(theme_tree2)
139
+export(tree_filter)
139 140
 export(unit)
140 141
 export(viewClade)
141 142
 export(xlim)
... ...
@@ -153,6 +154,7 @@ importFrom(aplot,xrange)
153 154
 importFrom(dplyr,collapse)
154 155
 importFrom(dplyr,filter)
155 156
 importFrom(dplyr,full_join)
157
+importFrom(dplyr,left_join)
156 158
 importFrom(dplyr,mutate)
157 159
 importFrom(dplyr,rename)
158 160
 importFrom(dplyr,select)
Browse code

update %<+%

xiangpin authored on 25/08/2020 01:42:18
Showing1 changed files
... ...
@@ -153,7 +153,6 @@ importFrom(aplot,xrange)
153 153
 importFrom(dplyr,collapse)
154 154
 importFrom(dplyr,filter)
155 155
 importFrom(dplyr,full_join)
156
-importFrom(dplyr,left_join)
157 156
 importFrom(dplyr,mutate)
158 157
 importFrom(dplyr,rename)
159 158
 importFrom(dplyr,select)
Browse code

zoomClade and geom_zoom_clade

Guangchuang Yu authored on 03/08/2020 16:21:17
Showing1 changed files
... ...
@@ -31,6 +31,7 @@ S3method(ggplot_add,taxalink)
31 31
 S3method(ggplot_add,tiplab)
32 32
 S3method(ggplot_add,tiplab_ylab)
33 33
 S3method(ggplot_add,tree_inset)
34
+S3method(ggplot_add,zoom_clade)
34 35
 S3method(groupClade,ggtree)
35 36
 S3method(groupOTU,ggtree)
36 37
 S3method(identify,gg)
... ...
@@ -87,6 +88,7 @@ export(geom_tippoint)
87 88
 export(geom_tree)
88 89
 export(geom_tree2)
89 90
 export(geom_treescale)
91
+export(geom_zoom_clade)
90 92
 export(get.path)
91 93
 export(get_clade_position)
92 94
 export(get_heatmap_column_position)
... ...
@@ -139,6 +141,7 @@ export(viewClade)
139 141
 export(xlim)
140 142
 export(xlim_expand)
141 143
 export(xlim_tree)
144
+export(zoomClade)
142 145
 exportMethods(gzoom)
143 146
 exportMethods(scale_color)
144 147
 importFrom(ape,di2multi)
Browse code

fixed R check

Guangchuang Yu authored on 28/07/2020 08:46:58
Showing1 changed files
... ...
@@ -167,6 +167,7 @@ importFrom(ggplot2,aes_)
167 167
 importFrom(ggplot2,aes_string)
168 168
 importFrom(ggplot2,annotate)
169 169
 importFrom(ggplot2,annotation_custom)
170
+importFrom(ggplot2,as_labeller)
170 171
 importFrom(ggplot2,coord_cartesian)
171 172
 importFrom(ggplot2,coord_flip)
172 173
 importFrom(ggplot2,coord_polar)
... ...
@@ -199,7 +200,6 @@ importFrom(ggplot2,ggproto)
199 200
 importFrom(ggplot2,ggsave)
200 201
 importFrom(ggplot2,guide_legend)
201 202
 importFrom(ggplot2,guides)
202
-importFrom(ggplot2,labeller)
203 203
 importFrom(ggplot2,last_plot)
204 204
 importFrom(ggplot2,layer)
205 205
 importFrom(ggplot2,margin)
Browse code

remove functions

Guangchuang Yu authored on 28/07/2020 07:02:57
Showing1 changed files
... ...
@@ -46,7 +46,6 @@ export(MRCA)
46 46
 export(StatBalance)
47 47
 export(add_colorbar)
48 48
 export(aes)
49
-export(annotation_image)
50 49
 export(arrow)
51 50
 export(as.polytomy)
52 51
 export(collapse)
... ...
@@ -116,7 +115,6 @@ export(nodeid)
116 115
 export(nodelab)
117 116
 export(nodepie)
118 117
 export(open_tree)
119
-export(phylopic)
120 118
 export(range_format)
121 119
 export(read.tree)
122 120
 export(revts)
... ...
@@ -131,7 +129,6 @@ export(scale_fill_manual)
131 129
 export(scale_x_ggtree)
132 130
 export(scale_x_range)
133 131
 export(set_hilight_legend)
134
-export(subview)
135 132
 export(theme)
136 133
 export(theme_dendrogram)
137 134
 export(theme_inset)
... ...
@@ -238,7 +235,6 @@ importFrom(grid,grid.locator)
238 235
 importFrom(grid,grid.newpage)
239 236
 importFrom(grid,grobTree)
240 237
 importFrom(grid,pushViewport)
241
-importFrom(grid,rasterGrob)
242 238
 importFrom(grid,rectGrob)
243 239
 importFrom(grid,unit)
244 240
 importFrom(grid,viewport)
Browse code

as_ylab in geom_tiplab()

Guangchuang Yu authored on 28/07/2020 06:04:40
Showing1 changed files
... ...
@@ -29,6 +29,7 @@ S3method(ggplot_add,scale_ggtree)
29 29
 S3method(ggplot_add,striplabel)
30 30
 S3method(ggplot_add,taxalink)
31 31
 S3method(ggplot_add,tiplab)
32
+S3method(ggplot_add,tiplab_ylab)
32 33
 S3method(ggplot_add,tree_inset)
33 34
 S3method(groupClade,ggtree)
34 35
 S3method(groupOTU,ggtree)
Browse code

hexpand

Guangchuang Yu authored on 27/07/2020 11:40:01
Showing1 changed files
... ...
@@ -21,6 +21,7 @@ S3method(ggplot_add,cladelabel)
21 21
 S3method(ggplot_add,facet_plot)
22 22
 S3method(ggplot_add,facet_xlim)
23 23
 S3method(ggplot_add,geom_range)
24
+S3method(ggplot_add,hexpand)
24 25
 S3method(ggplot_add,hilight)
25 26
 S3method(ggplot_add,layout_ggtree)
26 27
 S3method(ggplot_add,range_xaxis)
... ...
@@ -99,6 +100,7 @@ export(groupClade)
99 100
 export(groupOTU)
100 101
 export(guide_legend)
101 102
 export(gzoom)
103
+export(hexpand)
102 104
 export(inset)
103 105
 export(layout_circular)
104 106
 export(layout_dendrogram)
Browse code

update export

xiangpin authored on 23/07/2020 06:31:31
Showing1 changed files
... ...
@@ -22,7 +22,6 @@ S3method(ggplot_add,facet_plot)
22 22
 S3method(ggplot_add,facet_xlim)
23 23
 S3method(ggplot_add,geom_range)
24 24
 S3method(ggplot_add,hilight)
25
-S3method(ggplot_add,hilight2)
26 25
 S3method(ggplot_add,layout_ggtree)
27 26
 S3method(ggplot_add,range_xaxis)
28 27
 S3method(ggplot_add,scale_ggtree)
... ...
@@ -41,10 +40,8 @@ export("%<%")
41 40
 export("%<+%")
42 41
 export("%>%")
43 42
 export(Date2decimal)
44
-export(GeomHilight)
45 43
 export(MRCA)
46 44
 export(StatBalance)
47
-export(StatHilight)
48 45
 export(add_colorbar)
49 46
 export(aes)
50 47
 export(annotation_image)
... ...
@@ -66,8 +63,6 @@ export(geom_cladelabel2)
66 63
 export(geom_facet)
67 64
 export(geom_highlight)
68 65
 export(geom_hilight)
69
-export(geom_hilight2)
70
-export(geom_hilight_encircle)
71 66
 export(geom_inset)
72 67
 export(geom_label)
73 68
 export(geom_label2)
... ...
@@ -133,7 +128,6 @@ export(scale_fill_manual)
133 128
 export(scale_x_ggtree)
134 129
 export(scale_x_range)
135 130
 export(set_hilight_legend)
136
-export(stat_hilight)
137 131
 export(subview)
138 132
 export(theme)
139 133
 export(theme_dendrogram)
Browse code

new export and importFrom

xiangpin authored on 22/07/2020 06:19:44
Showing1 changed files
... ...
@@ -22,6 +22,7 @@ S3method(ggplot_add,facet_plot)
22 22
 S3method(ggplot_add,facet_xlim)
23 23
 S3method(ggplot_add,geom_range)
24 24
 S3method(ggplot_add,hilight)
25
+S3method(ggplot_add,hilight2)
25 26
 S3method(ggplot_add,layout_ggtree)
26 27
 S3method(ggplot_add,range_xaxis)
27 28
 S3method(ggplot_add,scale_ggtree)
... ...
@@ -65,6 +66,7 @@ export(geom_cladelabel2)
65 66
 export(geom_facet)
66 67
 export(geom_highlight)
67 68
 export(geom_hilight)
69
+export(geom_hilight2)
68 70
 export(geom_hilight_encircle)
69 71
 export(geom_inset)
70 72
 export(geom_label)
... ...
@@ -161,6 +163,7 @@ importFrom(dplyr,select)
161 163
 importFrom(ggplot2,Geom)
162 164
 importFrom(ggplot2,GeomLabel)
163 165
 importFrom(ggplot2,GeomPoint)
166
+importFrom(ggplot2,GeomPolygon)
164 167
 importFrom(ggplot2,GeomRect)
165 168
 importFrom(ggplot2,GeomSegment)
166 169
 importFrom(ggplot2,GeomText)
... ...
@@ -175,6 +178,7 @@ importFrom(ggplot2,coord_flip)
175 178
 importFrom(ggplot2,coord_polar)
176 179
 importFrom(ggplot2,draw_key_path)
177 180
 importFrom(ggplot2,draw_key_point)
181
+importFrom(ggplot2,draw_key_polygon)
178 182
 importFrom(ggplot2,draw_key_text)
179 183
 importFrom(ggplot2,element_blank)
180 184
 importFrom(ggplot2,element_line)
... ...
@@ -218,6 +222,7 @@ importFrom(ggplot2,scale_y_continuous)
218 222
 importFrom(ggplot2,theme)
219 223
 importFrom(ggplot2,theme_bw)
220 224
 importFrom(ggplot2,theme_void)
225
+importFrom(ggplot2,vars)
221 226
 importFrom(ggplot2,waiver)
222 227
 importFrom(ggplot2,xlab)
223 228
 importFrom(ggplot2,xlim)
Browse code

geom_taxalink supports aes mapping

Guangchuang Yu authored on 20/07/2020 14:59:17
Showing1 changed files
... ...
@@ -81,7 +81,6 @@ export(geom_rootpoint)
81 81
 export(geom_segment2)
82 82
 export(geom_strip)
83 83
 export(geom_taxalink)
84
-export(geom_taxalink2)
85 84
 export(geom_text)
86 85
 export(geom_text2)
87 86
 export(geom_tiplab)
Browse code

new export

xiangpin authored on 19/07/2020 08:02:43
Showing1 changed files
... ...
@@ -26,6 +26,7 @@ S3method(ggplot_add,layout_ggtree)
26 26
 S3method(ggplot_add,range_xaxis)
27 27
 S3method(ggplot_add,scale_ggtree)
28 28
 S3method(ggplot_add,striplabel)
29
+S3method(ggplot_add,taxalink)
29 30
 S3method(ggplot_add,tiplab)
30 31
 S3method(ggplot_add,tree_inset)
31 32
 S3method(groupClade,ggtree)
... ...
@@ -80,6 +81,7 @@ export(geom_rootpoint)
80 81
 export(geom_segment2)
81 82
 export(geom_strip)
82 83
 export(geom_taxalink)
84
+export(geom_taxalink2)
83 85
 export(geom_text)
84 86
 export(geom_text2)
85 87
 export(geom_tiplab)
... ...
@@ -248,6 +250,8 @@ importFrom(methods,missingArg)
248 250
 importFrom(methods,setGeneric)
249 251
 importFrom(methods,setOldClass)
250 252
 importFrom(rlang,.data)
253
+importFrom(rlang,abort)
254
+importFrom(rlang,as_name)
251 255
 importFrom(rlang,quo_name)
252 256
 importFrom(rvcheck,get_aes_var)
253 257
 importFrom(rvcheck,get_fun_from_pkg)
Browse code

layout_inward_circular

Guangchuang Yu authored on 16/07/2020 10:30:54
Showing1 changed files
... ...
@@ -105,6 +105,7 @@ export(inset)
105 105
 export(layout_circular)
106 106
 export(layout_dendrogram)
107 107
 export(layout_fan)
108
+export(layout_inward_circular)
108 109
 export(layout_rectangular)
109 110
 export(margin)
110 111
 export(msaplot)
Browse code

import alpha from scales

xiangpin authored on 16/07/2020 03:30:45
Showing1 changed files
... ...
@@ -250,6 +250,7 @@ importFrom(rlang,.data)
250 250
 importFrom(rlang,quo_name)
251 251
 importFrom(rvcheck,get_aes_var)
252 252
 importFrom(rvcheck,get_fun_from_pkg)
253
+importFrom(scales,alpha)
253 254
 importFrom(tidyr,gather)
254 255
 importFrom(tidytree,MRCA)
255 256
 importFrom(tidytree,ancestor)
Browse code

new import

xiangpin authored on 13/07/2020 03:04:43
Showing1 changed files
... ...
@@ -157,7 +157,6 @@ importFrom(dplyr,mutate)
157 157
 importFrom(dplyr,rename)
158 158
 importFrom(dplyr,select)
159 159
 importFrom(ggplot2,Geom)
160
-importFrom(ggplot2,GeomCurve)
161 160
 importFrom(ggplot2,GeomLabel)
162 161
 importFrom(ggplot2,GeomPoint)
163 162
 importFrom(ggplot2,GeomRect)
... ...
@@ -226,7 +225,9 @@ importFrom(graphics,identify)
226 225
 importFrom(grid,arrow)
227 226
 importFrom(grid,convertX)
228 227
 importFrom(grid,convertY)
228
+importFrom(grid,curveGrob)
229 229
 importFrom(grid,dataViewport)
230
+importFrom(grid,gTree)
230 231
 importFrom(grid,gpar)
231 232
 importFrom(grid,grid.layout)
232 233
 importFrom(grid,grid.locator)
Browse code

fortify method for pvclust

Guangchuang Yu authored on 22/06/2020 02:48:45
Showing1 changed files
... ...
@@ -14,6 +14,7 @@ S3method(fortify,phylo4)
14 14
 S3method(fortify,phylo4d)
15 15
 S3method(fortify,phylog)
16 16
 S3method(fortify,phyloseq)
17
+S3method(fortify,pvclust)
17 18
 S3method(fortify,treedata)
18 19
 S3method(fortify,twins)
19 20
 S3method(ggplot_add,cladelabel)
Browse code

add dot parameter for geom_rect and more details of warnings of extendto

xiangpin authored on 16/06/2020 12:53:34
Showing1 changed files
... ...
@@ -263,6 +263,7 @@ importFrom(treeio,Ntip)
263 263
 importFrom(treeio,as.phylo)
264 264
 importFrom(treeio,as.treedata)
265 265
 importFrom(treeio,read.fasta)
266
+importFrom(utils,getFromNamespace)
266 267
 importFrom(utils,modifyList)
267 268
 importFrom(utils,packageDescription)
268 269
 importFrom(utils,packageVersion)
Browse code

import xrange from aplot

Guangchuang Yu authored on 07/04/2020 09:39:43
Showing1 changed files
... ...
@@ -142,12 +142,12 @@ export(xlim_expand)
142 142
 export(xlim_tree)
143 143
 exportMethods(gzoom)
144 144
 exportMethods(scale_color)
145
-import(aplot)
146 145
 importFrom(ape,di2multi)
147 146
 importFrom(ape,ladderize)
148 147
 importFrom(ape,read.tree)
149 148
 importFrom(ape,reorder.phylo)
150 149
 importFrom(ape,rtree)
150
+importFrom(aplot,xrange)
151 151
 importFrom(dplyr,collapse)
152 152
 importFrom(dplyr,filter)
153 153
 importFrom(dplyr,full_join)
Browse code

import aplot

Guangchuang Yu authored on 07/04/2020 09:02:46
Showing1 changed files
... ...
@@ -142,6 +142,7 @@ export(xlim_expand)
142 142
 export(xlim_tree)
143 143
 exportMethods(gzoom)
144 144
 exportMethods(scale_color)
145
+import(aplot)
145 146
 importFrom(ape,di2multi)
146 147
 importFrom(ape,ladderize)
147 148
 importFrom(ape,read.tree)
Guangchuang Yu authored on 31/03/2020 04:16:05
Showing1 changed files
... ...
@@ -16,7 +16,6 @@ S3method(fortify,phylog)
16 16
 S3method(fortify,phyloseq)
17 17
 S3method(fortify,treedata)
18 18
 S3method(fortify,twins)
19
-S3method(ggplot_add,axisAlign)
20 19
 S3method(ggplot_add,cladelabel)
21 20
 S3method(ggplot_add,facet_plot)
22 21
 S3method(ggplot_add,facet_xlim)
... ...
@@ -139,10 +138,8 @@ export(theme_tree2)
139 138
 export(unit)
140 139
 export(viewClade)
141 140
 export(xlim)
142
-export(xlim2)
143 141
 export(xlim_expand)
144 142
 export(xlim_tree)
145
-export(ylim2)
146 143
 exportMethods(gzoom)
147 144
 exportMethods(scale_color)
148 145
 importFrom(ape,di2multi)
... ...
@@ -204,7 +201,6 @@ importFrom(ggplot2,guides)
204 201
 importFrom(ggplot2,labeller)
205 202
 importFrom(ggplot2,last_plot)
206 203
 importFrom(ggplot2,layer)
207
-importFrom(ggplot2,layer_scales)
208 204
 importFrom(ggplot2,margin)
209 205
 importFrom(ggplot2,position_nudge)
210 206
 importFrom(ggplot2,scale_color_manual)
... ...
@@ -214,10 +210,8 @@ importFrom(ggplot2,scale_fill_gradient)
214 210
 importFrom(ggplot2,scale_fill_manual)
215 211
 importFrom(ggplot2,scale_x_continuous)
216 212
 importFrom(ggplot2,scale_x_date)
217
-importFrom(ggplot2,scale_x_discrete)
218 213
 importFrom(ggplot2,scale_x_reverse)
219 214
 importFrom(ggplot2,scale_y_continuous)
220
-importFrom(ggplot2,scale_y_discrete)
221 215
 importFrom(ggplot2,theme)
222 216
 importFrom(ggplot2,theme_bw)
223 217
 importFrom(ggplot2,theme_void)
Browse code

remove mutate_

Guangchuang Yu authored on 25/03/2020 03:58:15
Showing1 changed files
... ...
@@ -154,7 +154,7 @@ importFrom(dplyr,collapse)
154 154
 importFrom(dplyr,filter)
155 155
 importFrom(dplyr,full_join)
156 156
 importFrom(dplyr,left_join)
157
-importFrom(dplyr,mutate_)
157
+importFrom(dplyr,mutate)
158 158
 importFrom(dplyr,rename)
159 159
 importFrom(dplyr,select)
160 160
 importFrom(ggplot2,Geom)
Browse code

import expansion

Guangchuang Yu authored on 12/03/2020 09:27:40
Showing1 changed files
... ...
@@ -180,7 +180,7 @@ importFrom(ggplot2,element_blank)
180 180
 importFrom(ggplot2,element_line)
181 181
 importFrom(ggplot2,element_rect)
182 182
 importFrom(ggplot2,element_text)
183
-importFrom(ggplot2,expand_scale)
183
+importFrom(ggplot2,expansion)
184 184
 importFrom(ggplot2,facet_grid)
185 185
 importFrom(ggplot2,fortify)
186 186
 importFrom(ggplot2,geom_bar)
Browse code

geom_highlight

Guangchuang Yu authored on 08/01/2020 02:55:39
Showing1 changed files
... ...
@@ -62,6 +62,7 @@ export(geom_balance)
62 62
 export(geom_cladelabel)
63 63
 export(geom_cladelabel2)
64 64
 export(geom_facet)
65
+export(geom_highlight)
65 66
 export(geom_hilight)
66 67
 export(geom_hilight_encircle)
67 68
 export(geom_inset)
Browse code

fixed warnings

Guangchuang Yu authored on 29/11/2019 07:47:41
Showing1 changed files
... ...
@@ -98,12 +98,14 @@ export(ggtree)
98 98
 export(gheatmap)
99 99
 export(groupClade)
100 100
 export(groupOTU)
101
+export(guide_legend)
101 102
 export(gzoom)
102 103
 export(inset)
103 104
 export(layout_circular)
104 105
 export(layout_dendrogram)
105 106
 export(layout_fan)
106 107
 export(layout_rectangular)
108
+export(margin)
107 109
 export(msaplot)
108 110
 export(multiplot)
109 111
 export(nodebar)
... ...
@@ -120,6 +122,9 @@ export(rotate_tree)
120 122
 export(rtree)
121 123
 export(scaleClade)
122 124
 export(scale_color)
125
+export(scale_color_manual)
126
+export(scale_colour_manual)
127
+export(scale_fill_manual)
123 128
 export(scale_x_ggtree)
124 129
 export(scale_x_range)
125 130
 export(set_hilight_legend)
... ...
@@ -199,8 +204,10 @@ importFrom(ggplot2,labeller)
199 204
 importFrom(ggplot2,last_plot)
200 205
 importFrom(ggplot2,layer)
201 206
 importFrom(ggplot2,layer_scales)
207
+importFrom(ggplot2,margin)
202 208
 importFrom(ggplot2,position_nudge)
203 209
 importFrom(ggplot2,scale_color_manual)
210
+importFrom(ggplot2,scale_colour_manual)
204 211
 importFrom(ggplot2,scale_fill_discrete)
205 212
 importFrom(ggplot2,scale_fill_gradient)
206 213
 importFrom(ggplot2,scale_fill_manual)
Browse code

offspring method for ggtree object

Guangchuang Yu authored on 21/11/2019 08:13:29
Showing1 changed files
... ...
@@ -33,6 +33,7 @@ S3method(groupOTU,ggtree)
33 33
 S3method(identify,gg)
34 34
 S3method(nodeid,ggtree)
35 35
 S3method(nodelab,ggtree)
36
+S3method(offspring,ggtree)
36 37
 export("%+>%")
37 38
 export("%<%")
38 39
 export("%<+%")
Browse code

rm .()

Guangchuang Yu authored on 02/11/2019 08:54:12
Showing1 changed files
... ...
@@ -37,7 +37,6 @@ export("%+>%")
37 37
 export("%<%")
38 38
 export("%<+%")
39 39
 export("%>%")
40
-export(.)
41 40
 export(Date2decimal)
42 41
 export(GeomHilight)
43 42
 export(MRCA)
Browse code

extend `xlim2` and `ylim2` to support discrete scale.

Guangchuang Yu authored on 01/11/2019 09:06:55
Showing1 changed files
... ...
@@ -198,6 +198,7 @@ importFrom(ggplot2,guides)
198 198
 importFrom(ggplot2,labeller)
199 199
 importFrom(ggplot2,last_plot)
200 200
 importFrom(ggplot2,layer)
201
+importFrom(ggplot2,layer_scales)
201 202
 importFrom(ggplot2,position_nudge)
202 203
 importFrom(ggplot2,scale_color_manual)
203 204
 importFrom(ggplot2,scale_fill_discrete)
... ...
@@ -205,8 +206,10 @@ importFrom(ggplot2,scale_fill_gradient)
205 206
 importFrom(ggplot2,scale_fill_manual)
206 207
 importFrom(ggplot2,scale_x_continuous)
207 208
 importFrom(ggplot2,scale_x_date)
209
+importFrom(ggplot2,scale_x_discrete)
208 210
 importFrom(ggplot2,scale_x_reverse)
209 211
 importFrom(ggplot2,scale_y_continuous)
212
+importFrom(ggplot2,scale_y_discrete)
210 213
 importFrom(ggplot2,theme)
211 214
 importFrom(ggplot2,theme_bw)
212 215
 importFrom(ggplot2,theme_void)
Browse code

xlim2 and ylim2

Guangchuang Yu authored on 01/11/2019 05:57:59
Showing1 changed files
... ...
@@ -133,10 +133,10 @@ export(theme_tree2)
133 133
 export(unit)
134 134
 export(viewClade)
135 135
 export(xlim)
136
-export(xlim_align)
136
+export(xlim2)
137 137
 export(xlim_expand)
138 138
 export(xlim_tree)
139
-export(ylim_align)
139
+export(ylim2)
140 140
 exportMethods(gzoom)
141 141
 exportMethods(scale_color)
142 142
 importFrom(ape,di2multi)
Browse code

roxygen2md

Guangchuang Yu authored on 01/11/2019 04:24:00
Showing1 changed files
... ...
@@ -16,7 +16,7 @@ S3method(fortify,phylog)
16 16
 S3method(fortify,phyloseq)
17 17
 S3method(fortify,treedata)
18 18
 S3method(fortify,twins)
19
-S3method(ggplot_add,align_axis)
19
+S3method(ggplot_add,axisAlign)
20 20
 S3method(ggplot_add,cladelabel)
21 21
 S3method(ggplot_add,facet_plot)
22 22
 S3method(ggplot_add,facet_xlim)
... ...
@@ -45,8 +45,6 @@ export(StatBalance)
45 45
 export(StatHilight)
46 46
 export(add_colorbar)
47 47
 export(aes)
48
-export(align_x)
49
-export(align_y)
50 48
 export(annotation_image)
51 49
 export(arrow)
52 50
 export(as.polytomy)
... ...
@@ -135,8 +133,10 @@ export(theme_tree2)
135 133
 export(unit)
136 134
 export(viewClade)
137 135
 export(xlim)
136
+export(xlim_align)
138 137
 export(xlim_expand)
139 138
 export(xlim_tree)
139
+export(ylim_align)
140 140
 exportMethods(gzoom)
141 141
 exportMethods(scale_color)
142 142
 importFrom(ape,di2multi)
Browse code

align_x and align_y

Guangchuang Yu authored on 31/10/2019 09:28:27
Showing1 changed files
... ...
@@ -16,6 +16,7 @@ S3method(fortify,phylog)
16 16
 S3method(fortify,phyloseq)
17 17
 S3method(fortify,treedata)
18 18
 S3method(fortify,twins)
19
+S3method(ggplot_add,align_axis)
19 20
 S3method(ggplot_add,cladelabel)
20 21
 S3method(ggplot_add,facet_plot)
21 22
 S3method(ggplot_add,facet_xlim)
... ...
@@ -27,7 +28,6 @@ S3method(ggplot_add,scale_ggtree)
27 28
 S3method(ggplot_add,striplabel)
28 29
 S3method(ggplot_add,tiplab)
29 30
 S3method(ggplot_add,tree_inset)
30
-S3method(ggplot_add,ylim_ggtree)
31 31
 S3method(groupClade,ggtree)
32 32
 S3method(groupOTU,ggtree)
33 33
 S3method(identify,gg)
... ...
@@ -45,6 +45,8 @@ export(StatBalance)
45 45
 export(StatHilight)
46 46
 export(add_colorbar)
47 47
 export(aes)
48
+export(align_x)
49
+export(align_y)
48 50
 export(annotation_image)
49 51
 export(arrow)
50 52
 export(as.polytomy)
... ...
@@ -135,7 +137,6 @@ export(viewClade)
135 137
 export(xlim)
136 138
 export(xlim_expand)
137 139
 export(xlim_tree)
138
-export(ylim_ggtree)
139 140
 exportMethods(gzoom)
140 141
 exportMethods(scale_color)
141 142
 importFrom(ape,di2multi)
Browse code

ylim_ggtree

Guangchuang Yu authored on 31/10/2019 07:16:49
Showing1 changed files
... ...
@@ -27,6 +27,7 @@ S3method(ggplot_add,scale_ggtree)
27 27
 S3method(ggplot_add,striplabel)
28 28
 S3method(ggplot_add,tiplab)
29 29
 S3method(ggplot_add,tree_inset)
30
+S3method(ggplot_add,ylim_ggtree)
30 31
 S3method(groupClade,ggtree)
31 32
 S3method(groupOTU,ggtree)
32 33
 S3method(identify,gg)
... ...
@@ -134,6 +135,7 @@ export(viewClade)
134 135
 export(xlim)
135 136
 export(xlim_expand)
136 137
 export(xlim_tree)
138
+export(ylim_ggtree)
137 139
 exportMethods(gzoom)
138 140
 exportMethods(scale_color)
139 141
 importFrom(ape,di2multi)
... ...
@@ -171,6 +173,7 @@ importFrom(ggplot2,element_blank)
171 173
 importFrom(ggplot2,element_line)
172 174
 importFrom(ggplot2,element_rect)
173 175
 importFrom(ggplot2,element_text)
176
+importFrom(ggplot2,expand_scale)
174 177
 importFrom(ggplot2,facet_grid)
175 178
 importFrom(ggplot2,fortify)
176 179
 importFrom(ggplot2,geom_bar)
Browse code

reexport arrow and unit

Guangchuang Yu authored on 28/09/2019 10:22:18
Showing1 changed files
... ...
@@ -45,6 +45,7 @@ export(StatHilight)
45 45
 export(add_colorbar)
46 46
 export(aes)
47 47
 export(annotation_image)
48
+export(arrow)
48 49
 export(as.polytomy)
49 50
 export(collapse)
50 51
 export(decimal2Date)
... ...
@@ -128,6 +129,7 @@ export(theme_dendrogram)
128 129
 export(theme_inset)
129 130
 export(theme_tree)
130 131
 export(theme_tree2)
132
+export(unit)
131 133
 export(viewClade)
132 134
 export(xlim)
133 135
 export(xlim_expand)
... ...
@@ -210,6 +212,7 @@ importFrom(ggplot2,xlim)
210 212
 importFrom(ggplot2,ylab)
211 213
 importFrom(ggplot2,ylim)
212 214
 importFrom(graphics,identify)
215
+importFrom(grid,arrow)
213 216
 importFrom(grid,convertX)
214 217
 importFrom(grid,convertY)
215 218
 importFrom(grid,dataViewport)
Browse code

fortify for tree graph

Guangchuang Yu authored on 28/09/2019 09:25:27
Showing1 changed files
... ...
@@ -6,6 +6,7 @@ S3method(fortify,agnes)
6 6
 S3method(fortify,dendrogram)
7 7
 S3method(fortify,diana)
8 8
 S3method(fortify,hclust)
9
+S3method(fortify,igraph)
9 10
 S3method(fortify,multiPhylo)
10 11
 S3method(fortify,obkData)
11 12
 S3method(fortify,phylo)
Browse code

Added ggdensitree method ggdensitree can plot lists of phylogenetic trees (or list of treedata) such that - tips are aligned in the y axis and - tips can optionally (actually default) be aligned in the x axis - colouring of edges can be match to an aesthetic/scale Node and tip labelling can only be done on the first tree in the list

brj1 authored on 10/09/2019 22:31:48
Showing1 changed files
... ...
@@ -88,6 +88,7 @@ export(get.path)
88 88
 export(get_clade_position)
89 89
 export(get_heatmap_column_position)
90 90
 export(get_taxa_name)
91
+export(ggdensitree)
91 92
 export(ggplot)
92 93
 export(ggsave)
93 94
 export(ggtree)
... ...
@@ -223,6 +224,7 @@ importFrom(grid,unit)
223 224
 importFrom(grid,viewport)
224 225
 importFrom(magrittr,"%<>%")
225 226
 importFrom(magrittr,"%>%")
227
+importFrom(magrittr,add)
226 228
 importFrom(magrittr,equals)
227 229
 importFrom(methods,is)
228 230
 importFrom(methods,missingArg)
Browse code

fortify methods for agnes, diana and twins

Guangchuang Yu authored on 30/08/2019 05:01:11
Showing1 changed files
... ...
@@ -1,8 +1,10 @@
1 1
 # Generated by roxygen2: do not edit by hand
2 2
 
3
-S3method(MRCA,gg)
3
+S3method(MRCA,ggtree)
4 4
 S3method(collapse,ggtree)
5
+S3method(fortify,agnes)
5 6
 S3method(fortify,dendrogram)
7
+S3method(fortify,diana)
6 8
 S3method(fortify,hclust)
7 9
 S3method(fortify,multiPhylo)
8 10
 S3method(fortify,obkData)
... ...
@@ -12,6 +14,7 @@ S3method(fortify,phylo4d)
12 14
 S3method(fortify,phylog)
13 15
 S3method(fortify,phyloseq)
14 16
 S3method(fortify,treedata)
17
+S3method(fortify,twins)
15 18
 S3method(ggplot_add,cladelabel)
16 19
 S3method(ggplot_add,facet_plot)
17 20
 S3method(ggplot_add,facet_xlim)
Browse code

update layouts

Guangchuang Yu authored on 29/08/2019 16:24:50
Showing1 changed files
... ...
@@ -17,8 +17,7 @@ S3method(ggplot_add,facet_plot)
17 17
 S3method(ggplot_add,facet_xlim)
18 18
 S3method(ggplot_add,geom_range)
19 19
 S3method(ggplot_add,hilight)
20
-S3method(ggplot_add,layout_dendrogram)
21
-S3method(ggplot_add,layout_fan)
20
+S3method(ggplot_add,layout_ggtree)
22 21
 S3method(ggplot_add,range_xaxis)
23 22
 S3method(ggplot_add,scale_ggtree)
24 23
 S3method(ggplot_add,striplabel)
Browse code

geom-hilight

Guangchuang Yu authored on 28/08/2019 08:27:43
Showing1 changed files
... ...
@@ -16,6 +16,7 @@ S3method(ggplot_add,cladelabel)
16 16
 S3method(ggplot_add,facet_plot)
17 17
 S3method(ggplot_add,facet_xlim)
18 18
 S3method(ggplot_add,geom_range)
19
+S3method(ggplot_add,hilight)
19 20
 S3method(ggplot_add,layout_dendrogram)
20 21
 S3method(ggplot_add,layout_fan)
21 22
 S3method(ggplot_add,range_xaxis)
Browse code

geom_strip

Guangchuang Yu authored on 27/08/2019 05:12:46
Showing1 changed files
... ...
@@ -20,6 +20,7 @@ S3method(ggplot_add,layout_dendrogram)
20 20
 S3method(ggplot_add,layout_fan)
21 21
 S3method(ggplot_add,range_xaxis)
22 22
 S3method(ggplot_add,scale_ggtree)
23
+S3method(ggplot_add,striplabel)
23 24
 S3method(ggplot_add,tiplab)
24 25
 S3method(ggplot_add,tree_inset)
25 26
 S3method(groupClade,ggtree)
Browse code

support phylog

Guangchuang Yu authored on 21/08/2019 05:59:44
Showing1 changed files
... ...
@@ -9,6 +9,7 @@ S3method(fortify,obkData)
9 9
 S3method(fortify,phylo)
10 10
 S3method(fortify,phylo4)
11 11
 S3method(fortify,phylo4d)
12
+S3method(fortify,phylog)
12 13
 S3method(fortify,phyloseq)
13 14
 S3method(fortify,treedata)
14 15
 S3method(ggplot_add,cladelabel)
... ...
@@ -33,6 +34,7 @@ export("%>%")
33 34
 export(.)
34 35
 export(Date2decimal)
35 36
 export(GeomHilight)
37
+export(MRCA)
36 38
 export(StatBalance)
37 39
 export(StatHilight)
38 40
 export(add_colorbar)
Browse code

update geom_balance

Guangchuang Yu authored on 14/08/2019 08:10:10
Showing1 changed files
... ...
@@ -79,7 +79,6 @@ export(geom_tree)
79 79
 export(geom_tree2)
80 80
 export(geom_treescale)
81 81
 export(get.path)
82
-export(get_balance_position)
83 82
 export(get_clade_position)
84 83
 export(get_heatmap_column_position)
85 84
 export(get_taxa_name)
... ...
@@ -114,7 +113,6 @@ export(scale_color)
114 113
 export(scale_x_ggtree)
115 114
 export(scale_x_range)
116 115
 export(set_hilight_legend)
117
-export(stat_balance)
118 116
 export(stat_hilight)
119 117
 export(subview)
120 118
 export(theme)
Browse code

geom_cladelabel now supports unrooted tree

Guangchuang Yu authored on 13/08/2019 16:09:40
Showing1 changed files
... ...
@@ -11,6 +11,7 @@ S3method(fortify,phylo4)
11 11
 S3method(fortify,phylo4d)
12 12
 S3method(fortify,phyloseq)
13 13
 S3method(fortify,treedata)
14
+S3method(ggplot_add,cladelabel)
14 15
 S3method(ggplot_add,facet_plot)
15 16
 S3method(ggplot_add,facet_xlim)
16 17
 S3method(ggplot_add,geom_range)
Browse code

upgrade nodeid and define nodelab methods

Guangchuang Yu authored on 09/08/2019 03:15:25
Showing1 changed files
... ...
@@ -23,6 +23,8 @@ S3method(ggplot_add,tree_inset)
23 23
 S3method(groupClade,ggtree)
24 24
 S3method(groupOTU,ggtree)
25 25
 S3method(identify,gg)
26
+S3method(nodeid,ggtree)
27
+S3method(nodelab,ggtree)
26 28
 export("%+>%")
27 29
 export("%<%")
28 30
 export("%<+%")
... ...
@@ -96,6 +98,7 @@ export(msaplot)
96 98
 export(multiplot)
97 99
 export(nodebar)
98 100
 export(nodeid)
101
+export(nodelab)
99 102
 export(nodepie)
100 103
 export(open_tree)
101 104
 export(phylopic)
... ...
@@ -230,6 +233,8 @@ importFrom(tidytree,ancestor)
230 233
 importFrom(tidytree,as_tibble)
231 234
 importFrom(tidytree,groupClade)
232 235
 importFrom(tidytree,groupOTU)
236
+importFrom(tidytree,nodeid)
237
+importFrom(tidytree,nodelab)
233 238
 importFrom(tidytree,offspring)
234 239
 importFrom(tidytree,parent)
235 240
 importFrom(treeio,Nnode)
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
Showing1 changed files
... ...
@@ -130,10 +130,12 @@ importFrom(ape,read.tree)
130 130
 importFrom(ape,reorder.phylo)
131 131
 importFrom(ape,rtree)
132 132
 importFrom(dplyr,collapse)
133
+importFrom(dplyr,filter)
133 134
 importFrom(dplyr,full_join)
134 135
 importFrom(dplyr,left_join)
135 136
 importFrom(dplyr,mutate_)
136 137
 importFrom(dplyr,rename)
138
+importFrom(dplyr,select)
137 139
 importFrom(ggplot2,Geom)
138 140
 importFrom(ggplot2,GeomCurve)
139 141
 importFrom(ggplot2,GeomLabel)
Browse code

update theme

Guangchuang Yu authored on 05/08/2019 13:55:58
Showing1 changed files
... ...
@@ -191,6 +191,7 @@ importFrom(ggplot2,scale_x_reverse)
191 191
 importFrom(ggplot2,scale_y_continuous)
192 192
 importFrom(ggplot2,theme)
193 193
 importFrom(ggplot2,theme_bw)
194
+importFrom(ggplot2,theme_void)
194 195
 importFrom(ggplot2,waiver)
195 196
 importFrom(ggplot2,xlab)
196 197
 importFrom(ggplot2,xlim)
Browse code

support of dendrogram

Guangchuang Yu authored on 31/07/2019 02:21:33
Showing1 changed files
... ...
@@ -2,6 +2,8 @@
2 2
 
3 3
 S3method(MRCA,gg)
4 4
 S3method(collapse,ggtree)
5
+S3method(fortify,dendrogram)
6
+S3method(fortify,hclust)
5 7
 S3method(fortify,multiPhylo)
6 8
 S3method(fortify,obkData)
7 9
 S3method(fortify,phylo)
Browse code

tree layout

Guangchuang Yu authored on 24/07/2019 07:38:11
Showing1 changed files
... ...
@@ -12,6 +12,8 @@ S3method(fortify,treedata)
12 12
 S3method(ggplot_add,facet_plot)
13 13
 S3method(ggplot_add,facet_xlim)
14 14
 S3method(ggplot_add,geom_range)
15
+S3method(ggplot_add,layout_dendrogram)
16
+S3method(ggplot_add,layout_fan)
15 17
 S3method(ggplot_add,range_xaxis)
16 18
 S3method(ggplot_add,scale_ggtree)
17 19
 S3method(ggplot_add,tiplab)
... ...
@@ -84,6 +86,10 @@ export(groupClade)
84 86
 export(groupOTU)
85 87
 export(gzoom)
86 88
 export(inset)
89
+export(layout_circular)
90
+export(layout_dendrogram)
91
+export(layout_fan)
92
+export(layout_rectangular)
87 93
 export(msaplot)
88 94
 export(multiplot)
89 95
 export(nodebar)
... ...
@@ -92,23 +98,6 @@ export(nodepie)
92 98
 export(open_tree)
93 99
 export(phylopic)
94 100
 export(range_format)
95
-export(read.astral)
96
-export(read.beast)
97
-export(read.codeml)
98
-export(read.codeml_mlc)
99
-export(read.hyphy)
100
-export(read.iqtree)
101
-export(read.jplace)
102
-export(read.jtree)
103
-export(read.mrbayes)
104
-export(read.newick)
105
-export(read.nexus)
106
-export(read.nhx)
107
-export(read.paml_rst)
108
-export(read.phylip)
109
-export(read.phyloT)
110
-export(read.r8s)
111
-export(read.raxml)
112 101
 export(read.tree)
113 102
 export(revts)
114 103
 export(rotate)
... ...
@@ -123,6 +112,7 @@ export(stat_balance)
123 112
 export(stat_hilight)
124 113
 export(subview)
125 114
 export(theme)
115
+export(theme_dendrogram)
126 116
 export(theme_inset)
127 117
 export(theme_tree)
128 118
 export(theme_tree2)
... ...
@@ -134,7 +124,6 @@ exportMethods(gzoom)
134 124
 exportMethods(scale_color)
135 125
 importFrom(ape,di2multi)
136 126
 importFrom(ape,ladderize)
137
-importFrom(ape,read.nexus)
138 127
 importFrom(ape,read.tree)
139 128
 importFrom(ape,reorder.phylo)
140 129
 importFrom(ape,rtree)
... ...
@@ -165,6 +154,7 @@ importFrom(ggplot2,draw_key_text)
165 154
 importFrom(ggplot2,element_blank)
166 155
 importFrom(ggplot2,element_line)
167 156
 importFrom(ggplot2,element_rect)
157
+importFrom(ggplot2,element_text)
168 158
 importFrom(ggplot2,facet_grid)
169 159
 importFrom(ggplot2,fortify)
170 160
 importFrom(ggplot2,geom_bar)
... ...
@@ -241,23 +231,7 @@ importFrom(treeio,Nnode)
241 231
 importFrom(treeio,Ntip)
242 232
 importFrom(treeio,as.phylo)
243 233
 importFrom(treeio,as.treedata)
244
-importFrom(treeio,read.astral)
245
-importFrom(treeio,read.beast)
246
-importFrom(treeio,read.codeml)
247
-importFrom(treeio,read.codeml_mlc)
248 234
 importFrom(treeio,read.fasta)
249
-importFrom(treeio,read.hyphy)
250
-importFrom(treeio,read.iqtree)
251
-importFrom(treeio,read.jplace)
252
-importFrom(treeio,read.jtree)
253
-importFrom(treeio,read.mrbayes)
254
-importFrom(treeio,read.newick)
255
-importFrom(treeio,read.nhx)
256
-importFrom(treeio,read.paml_rst)
257
-importFrom(treeio,read.phylip)
258
-importFrom(treeio,read.phyloT)
259
-importFrom(treeio,read.r8s)
260
-importFrom(treeio,read.raxml)
261 235
 importFrom(utils,modifyList)
262 236
 importFrom(utils,packageDescription)
263 237
 importFrom(utils,packageVersion)
Browse code

update geom_range and scale_x_range

Guangchuang Yu authored on 24/07/2019 04:28:47
Showing1 changed files
... ...
@@ -11,6 +11,7 @@ S3method(fortify,phyloseq)
11 11
 S3method(fortify,treedata)
12 12
 S3method(ggplot_add,facet_plot)
13 13
 S3method(ggplot_add,facet_xlim)
14
+S3method(ggplot_add,geom_range)
14 15
 S3method(ggplot_add,range_xaxis)
15 16
 S3method(ggplot_add,scale_ggtree)
16 17
 S3method(ggplot_add,tiplab)
Browse code

geom_range

Guangchuang Yu authored on 23/07/2019 16:25:05
Showing1 changed files
... ...
@@ -11,6 +11,7 @@ S3method(fortify,phyloseq)
11 11
 S3method(fortify,treedata)
12 12
 S3method(ggplot_add,facet_plot)
13 13
 S3method(ggplot_add,facet_xlim)
14
+S3method(ggplot_add,range_xaxis)
14 15
 S3method(ggplot_add,scale_ggtree)
15 16
 S3method(ggplot_add,tiplab)
16 17
 S3method(ggplot_add,tree_inset)
... ...
@@ -115,6 +116,7 @@ export(rtree)
115 116
 export(scaleClade)
116 117
 export(scale_color)
117 118
 export(scale_x_ggtree)
119
+export(scale_x_range)
118 120
 export(set_hilight_legend)
119 121
 export(stat_balance)
120 122
 export(stat_hilight)
Browse code

mode paramter in collapse

Guangchuang Yu authored on 11/07/2019 05:43:27
Showing1 changed files
... ...
@@ -168,6 +168,7 @@ importFrom(ggplot2,geom_bar)
168 168
 importFrom(ggplot2,geom_blank)
169 169
 importFrom(ggplot2,geom_label)
170 170
 importFrom(ggplot2,geom_point)
171
+importFrom(ggplot2,geom_polygon)
171 172
 importFrom(ggplot2,geom_rect)
172 173
 importFrom(ggplot2,geom_segment)
173 174
 importFrom(ggplot2,geom_text)
Browse code

geom_tiplab

Guangchuang Yu authored on 05/07/2019 06:39:00
Showing1 changed files
... ...
@@ -12,6 +12,7 @@ S3method(fortify,treedata)
12 12
 S3method(ggplot_add,facet_plot)
13 13
 S3method(ggplot_add,facet_xlim)
14 14
 S3method(ggplot_add,scale_ggtree)
15
+S3method(ggplot_add,tiplab)
15 16
 S3method(ggplot_add,tree_inset)
16 17
 S3method(groupClade,ggtree)
17 18
 S3method(groupOTU,ggtree)
Browse code

geom_inset

Guangchuang Yu authored on 05/07/2019 05:46:17
Showing1 changed files
... ...
@@ -12,6 +12,7 @@ S3method(fortify,treedata)
12 12
 S3method(ggplot_add,facet_plot)
13 13
 S3method(ggplot_add,facet_xlim)
14 14
 S3method(ggplot_add,scale_ggtree)
15
+S3method(ggplot_add,tree_inset)
15 16
 S3method(groupClade,ggtree)
16 17
 S3method(groupOTU,ggtree)
17 18
 S3method(identify,gg)
... ...
@@ -44,6 +45,7 @@ export(geom_cladelabel2)
44 45
 export(geom_facet)
45 46
 export(geom_hilight)
46 47
 export(geom_hilight_encircle)
48
+export(geom_inset)
47 49
 export(geom_label)
48 50
 export(geom_label2)
49 51
 export(geom_motif)
Browse code

facet_data

Guangchuang Yu authored on 02/07/2019 05:39:32
Showing1 changed files
... ...
@@ -31,6 +31,7 @@ export(as.polytomy)
31 31
 export(collapse)
32 32
 export(decimal2Date)
33 33
 export(expand)
34
+export(facet_data)
34 35
 export(facet_labeller)
35 36
 export(facet_plot)
36 37
 export(facet_widths)
Browse code

fixed #237

Guangchuang Yu authored on 28/06/2019 06:37:27
Showing1 changed files
... ...
@@ -133,7 +133,9 @@ importFrom(ape,reorder.phylo)
133 133
 importFrom(ape,rtree)
134 134
 importFrom(dplyr,collapse)
135 135
 importFrom(dplyr,full_join)
136
+importFrom(dplyr,left_join)
136 137
 importFrom(dplyr,mutate_)
138
+importFrom(dplyr,rename)
137 139
 importFrom(ggplot2,Geom)
138 140
 importFrom(ggplot2,GeomCurve)
139 141
 importFrom(ggplot2,GeomLabel)
Browse code

geom_facet

Guangchuang Yu authored on 23/05/2019 06:56:06
Showing1 changed files
... ...
@@ -9,6 +9,7 @@ S3method(fortify,phylo4)
9 9
 S3method(fortify,phylo4d)
10 10
 S3method(fortify,phyloseq)
11 11
 S3method(fortify,treedata)
12
+S3method(ggplot_add,facet_plot)
12 13
 S3method(ggplot_add,facet_xlim)
13 14
 S3method(ggplot_add,scale_ggtree)
14 15
 S3method(groupClade,ggtree)
... ...
@@ -39,6 +40,7 @@ export(geom_aline)
39 40
 export(geom_balance)
40 41
 export(geom_cladelabel)
41 42
 export(geom_cladelabel2)
43
+export(geom_facet)
42 44
 export(geom_hilight)
43 45
 export(geom_hilight_encircle)
44 46
 export(geom_label)
Browse code

update namespace

Guangchuang Yu authored on 23/05/2019 02:36:37
Showing1 changed files
... ...
@@ -209,7 +209,6 @@ importFrom(grid,viewport)
209 209
 importFrom(magrittr,"%<>%")
210 210
 importFrom(magrittr,"%>%")
211 211
 importFrom(magrittr,equals)
212
-importFrom(magrittr,extract)
213 212
 importFrom(methods,is)
214 213
 importFrom(methods,missingArg)
215 214
 importFrom(methods,setGeneric)
Browse code

update scale_x_ggtree

Guangchuang Yu authored on 22/05/2019 14:09:37
Showing1 changed files
... ...
@@ -10,6 +10,7 @@ S3method(fortify,phylo4d)
10 10
 S3method(fortify,phyloseq)
11 11
 S3method(fortify,treedata)
12 12
 S3method(ggplot_add,facet_xlim)
13
+S3method(ggplot_add,scale_ggtree)
13 14
 S3method(groupClade,ggtree)
14 15
 S3method(groupOTU,ggtree)
15 16
 S3method(identify,gg)
... ...
@@ -186,6 +187,7 @@ importFrom(ggplot2,scale_x_reverse)
186 187
 importFrom(ggplot2,scale_y_continuous)
187 188
 importFrom(ggplot2,theme)
188 189
 importFrom(ggplot2,theme_bw)
190
+importFrom(ggplot2,waiver)
189 191
 importFrom(ggplot2,xlab)
190 192
 importFrom(ggplot2,xlim)
191 193
 importFrom(ggplot2,ylab)
Browse code

xlim-expand supports ggplot2

Guangchuang Yu authored on 21/05/2019 10:32:17
Showing1 changed files
... ...
@@ -9,6 +9,7 @@ S3method(fortify,phylo4)
9 9
 S3method(fortify,phylo4d)
10 10
 S3method(fortify,phyloseq)
11 11
 S3method(fortify,treedata)
12
+S3method(ggplot_add,facet_xlim)
12 13
 S3method(groupClade,ggtree)
13 14
 S3method(groupOTU,ggtree)
14 15
 S3method(identify,gg)
... ...
@@ -164,6 +165,7 @@ importFrom(ggplot2,geom_text)
164 165
 importFrom(ggplot2,geom_tile)
165 166
 importFrom(ggplot2,ggplot)
166 167
 importFrom(ggplot2,ggplotGrob)
168
+importFrom(ggplot2,ggplot_add)
167 169
 importFrom(ggplot2,ggplot_build)
168 170
 importFrom(ggplot2,ggplot_gtable)
169 171
 importFrom(ggplot2,ggproto)
... ...
@@ -205,11 +207,13 @@ importFrom(grid,viewport)
205 207
 importFrom(magrittr,"%<>%")
206 208
 importFrom(magrittr,"%>%")
207 209
 importFrom(magrittr,equals)
210
+importFrom(magrittr,extract)
208 211
 importFrom(methods,is)
209 212
 importFrom(methods,missingArg)
210 213
 importFrom(methods,setGeneric)
211 214
 importFrom(methods,setOldClass)
212 215
 importFrom(rlang,.data)
216
+importFrom(rlang,quo_name)
213 217
 importFrom(rvcheck,get_aes_var)
214 218
 importFrom(rvcheck,get_fun_from_pkg)
215 219
 importFrom(tidyr,gather)
Browse code

clean up code

Guangchuang Yu authored on 30/01/2019 12:53:00
Showing1 changed files
... ...
@@ -214,10 +214,12 @@ importFrom(rvcheck,get_aes_var)
214 214
 importFrom(rvcheck,get_fun_from_pkg)
215 215
 importFrom(tidyr,gather)
216 216
 importFrom(tidytree,MRCA)
217
+importFrom(tidytree,ancestor)
217 218
 importFrom(tidytree,as_tibble)
218 219
 importFrom(tidytree,groupClade)
219 220
 importFrom(tidytree,groupOTU)
220 221
 importFrom(tidytree,offspring)
222
+importFrom(tidytree,parent)
221 223
 importFrom(treeio,Nnode)
222 224
 importFrom(treeio,Ntip)
223 225
 importFrom(treeio,as.phylo)
Browse code

fixed R check

Guangchuang Yu authored on 28/01/2019 09:40:56
Showing1 changed files
... ...
@@ -211,6 +211,7 @@ importFrom(methods,setGeneric)
211 211
 importFrom(methods,setOldClass)
212 212
 importFrom(rlang,.data)
213 213
 importFrom(rvcheck,get_aes_var)
214
+importFrom(rvcheck,get_fun_from_pkg)
214 215
 importFrom(tidyr,gather)
215 216
 importFrom(tidytree,MRCA)
216 217
 importFrom(tidytree,as_tibble)
Browse code

remove get.offspring.df & get.offspring.tip

Guangchuang Yu authored on 28/01/2019 09:12:15
Showing1 changed files
... ...
@@ -61,7 +61,6 @@ export(geom_tippoint)
61 61
 export(geom_tree)
62 62
 export(geom_tree2)
63 63
 export(geom_treescale)
64
-export(get.offspring.tip)
65 64
 export(get.path)
66 65
 export(get_balance_position)
67 66
 export(get_clade_position)
... ...
@@ -123,7 +122,6 @@ export(xlim_tree)
123 122
 exportMethods(gzoom)
124 123
 exportMethods(scale_color)
125 124
 importFrom(ape,di2multi)
126
-importFrom(ape,extract.clade)
127 125
 importFrom(ape,ladderize)
128 126
 importFrom(ape,read.nexus)
129 127
 importFrom(ape,read.tree)
... ...
@@ -218,6 +216,7 @@ importFrom(tidytree,MRCA)
218 216
 importFrom(tidytree,as_tibble)
219 217
 importFrom(tidytree,groupClade)
220 218
 importFrom(tidytree,groupOTU)
219
+importFrom(tidytree,offspring)
221 220
 importFrom(treeio,Nnode)
222 221
 importFrom(treeio,Ntip)
223 222
 importFrom(treeio,as.phylo)
Browse code

reduce dependency

Guangchuang Yu authored on 27/01/2019 23:14:00
Showing1 changed files
... ...
@@ -190,7 +190,6 @@ importFrom(ggplot2,xlab)
190 190
 importFrom(ggplot2,xlim)
191 191
 importFrom(ggplot2,ylab)
192 192
 importFrom(ggplot2,ylim)
193
-importFrom(grDevices,colorRampPalette)
194 193
 importFrom(graphics,identify)
195 194
 importFrom(grid,convertX)
196 195
 importFrom(grid,convertY)
... ...
@@ -214,9 +213,6 @@ importFrom(methods,setGeneric)
214 213
 importFrom(methods,setOldClass)
215 214
 importFrom(rlang,.data)
216 215
 importFrom(rvcheck,get_aes_var)
217
-importFrom(rvcheck,get_fun_from_pkg)
218
-importFrom(scales,alpha)
219
-importFrom(tibble,data_frame)
220 216
 importFrom(tidyr,gather)
221 217
 importFrom(tidytree,MRCA)
222 218
 importFrom(tidytree,as_tibble)
Browse code

facet_widths

Guangchuang Yu authored on 27/01/2019 16:59:37
Showing1 changed files
... ...
@@ -30,6 +30,7 @@ export(decimal2Date)
30 30
 export(expand)
31 31
 export(facet_labeller)
32 32
 export(facet_plot)
33
+export(facet_widths)
33 34
 export(flip)
34 35
 export(fortify)
35 36
 export(geom_aline)
... ...
@@ -166,6 +167,7 @@ importFrom(ggplot2,geom_tile)
166 167
 importFrom(ggplot2,ggplot)
167 168
 importFrom(ggplot2,ggplotGrob)
168 169
 importFrom(ggplot2,ggplot_build)
170
+importFrom(ggplot2,ggplot_gtable)
169 171
 importFrom(ggplot2,ggproto)
170 172
 importFrom(ggplot2,ggsave)
171 173
 importFrom(ggplot2,guide_legend)
Browse code

mv rescale_tree to treeio

Guangchuang Yu authored on 11/01/2019 11:16:48
Showing1 changed files
... ...
@@ -100,7 +100,6 @@ export(read.phyloT)
100 100
 export(read.r8s)
101 101
 export(read.raxml)
102 102
 export(read.tree)
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-export(rescale_tree)
104 103
 export(revts)
105 104
 export(rotate)
106 105
 export(rotate_tree)
... ...
@@ -219,7 +218,6 @@ importFrom(tibble,data_frame)
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 importFrom(tidyr,gather)
220 219
 importFrom(tidytree,MRCA)
221 220
 importFrom(tidytree,as_tibble)
222
-importFrom(tidytree,get_tree_data)
223 221
 importFrom(tidytree,groupClade)
224 222
 importFrom(tidytree,groupOTU)
225 223
 importFrom(treeio,Nnode)
Browse code

new MRCA methods

Guangchuang Yu authored on 10/01/2019 13:18:05
Showing1 changed files
... ...
@@ -1,5 +1,6 @@
1 1
 # Generated by roxygen2: do not edit by hand
2 2
 
3
+S3method(MRCA,gg)
3 4
 S3method(collapse,ggtree)
4 5
 S3method(fortify,multiPhylo)
5