1. ggtree
  2. NAMESPACE
Browse code

ggtree supports dendro object

Guangchuang Yu authored on 02/03/2023 02:23:07
Showing 1 changed files
NAMESPACE
History View file @ 2bbee05b
... ... 
@@ -3,6 +3,7 @@
3 3 
 S3method(MRCA,ggtree)
4 4 
 S3method(collapse,ggtree)
5 5 
 S3method(fortify,agnes)
6 
+S3method(fortify,dendro)
6 7 
 S3method(fortify,dendrogram)
7 8 
 S3method(fortify,diana)
8 9 
 S3method(fortify,hclust)
Browse code

relace warning_wrap with cli package

xiangpin authored on 09/11/2022 13:34:24
Showing 1 changed files
NAMESPACE
History View file @ c3621530
... ... 
@@ -167,6 +167,7 @@ importFrom(ape,reorder.phylo)
167 167 
 importFrom(ape,rtree)
168 168 
 importFrom(aplot,plot_list)
169 169 
 importFrom(aplot,xrange)
170 
+importFrom(cli,cli_alert_warning)
170 171 
 importFrom(dplyr,collapse)
171 172 
 importFrom(dplyr,filter)
172 173 
 importFrom(dplyr,full_join)
Browse code

move scale-color-subtree to ggtreeDendro

Guangchuang Yu authored on 23/09/2022 02:52:18
Showing 1 changed files
NAMESPACE
History View file @ bf457df7
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ ab464358
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 2d64d4bb
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 7e05bcf0
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ fbeaa25d
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ f1d8298d
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ e005bd2c
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 99b0a413
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 8da1b32d
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 12f3dc39
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 6ae936b0
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 29b07526
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 3f5542c6
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 76cf32fe
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 38a7d6f4
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 256e2fec
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 6f1fd621
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 764fb630
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ e0663b6e
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ b62eb8c8
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ cbd57123
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 3ac084ba
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 01337f66
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 46df22c8
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 9541f27d
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 3856fee3
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 3c271402
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 0fa9bd58
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ c29f9927
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 3a653ad1
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 87299539
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ e5fdd3b3
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 71f958df
... ... 
@@ -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)
Browse code

aplot

Guangchuang Yu authored on 31/03/2020 04:16:05
Showing 1 changed files
NAMESPACE
History View file @ 670ec6af
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ f3952913
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 210d5a66
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ d903c8a1
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ d14c7a71
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 2dcbd9e0
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ fbbd0f08
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ e6e8f4be
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 79e93b9f
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 1540db03
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 06f952f0
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 6e77743a
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ b22e59a5
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 81382246
... ... 
@@ -6,6 +6,7 @@ S3method(fortify,agnes)
6 6 
 S3method(fortify,dendrogram)
7 7 
 S3method(fortify,diana)
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 S3method(fortify,hclust)
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+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
Showing 1 changed files
NAMESPACE
History View file @ a88f71ef
... ... 
@@ -88,6 +88,7 @@ export(get.path)
88 88 
 export(get_clade_position)
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 export(get_heatmap_column_position)
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 export(get_taxa_name)
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+export(ggdensitree)
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 export(ggplot)
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 export(ggsave)
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 export(ggtree)
... ... 
@@ -223,6 +224,7 @@ importFrom(grid,unit)
223 224 
 importFrom(grid,viewport)
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 importFrom(magrittr,"%<>%")
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 importFrom(magrittr,"%>%")
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+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
Showing 1 changed files
NAMESPACE
History View file @ dce1205a
... ... 
@@ -1,8 +1,10 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
-S3method(MRCA,gg)
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+S3method(MRCA,ggtree)
4 4 
 S3method(collapse,ggtree)
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+S3method(fortify,agnes)
5 6 
 S3method(fortify,dendrogram)
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+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)