1. ggtree
  2. Commit deef58153b6b4212a5d92f60898d8265dfe40db5
Browse code

unit test of groupOTU & groupClade

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@121230 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 22/09/2016 05:42:40
Showing 4 changed files
NEWS
History View file @ deef581
... ... 
@@ -1,10 +1,12 @@
1 1 
 CHANGES IN VERSION 1.5.14
2 2 
 ------------------------
3 
+ o unit test for groupOTU and groupClade <2016-09-22, Thu>
4 
+ o groupOTU label groups by input group names (when input is a named list) <2016-09-22, Thu>
3 5 
  o update angle calculation for geom_tiplab <2016-09-13, Thu>
4 6 
  o as.polytomy to collapse binary tree to polytomy by applying 'fun' to selected 'feature' (e.g. bootstrap value less than 70). <2016-09-13, Tue>
5 7 
    + currently only phylo object supported.
6 8 
    + add test for as.polytomy
7 
-
9 
+
8 10 
 CHANGES IN VERSION 1.5.13
9 11 
 ------------------------
10 12 
  o facet_plot for plotting data with tree <2016-09-06, Tue>
... ... 
@@ -14,12 +16,12 @@ CHANGES IN VERSION 1.5.13
14 16 
    + colnames_offset_y
15 17 
    + hjust
16 18 
  o offset parameter in geom_tiplab and geom_tiplab2 <2016-09-05, Mon>
17 
-
19 
+
18 20 
 CHANGES IN VERSION 1.5.12
19 21 
 ------------------------
20 22 
  o use data in all layers instead of the base layer for coordination calculation in subview <2016-09-01, Thu>
21 23 
  o bug fixed in subview, width & height should be width/2 & height/2 <2016-09-01, Thu>
22 
-
24 
+
23 25 
 CHANGES IN VERSION 1.5.11
24 26 
 ------------------------
25 27 
  o gheatmap works with matrix <2016-08-28, Sun>
... ... 
@@ -28,27 +30,27 @@ CHANGES IN VERSION 1.5.11
28 30 
  o bug fixed in geom_tiplab <2016-08-17, Wed>
29 31 
    + https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/Tm9ULK7hd9E/HviXEh3CBwAJ
30 32 
  o update citation info, add doi. <2016-08-16, Tue>
31 
-
33 
+
32 34 
 CHANGES IN VERSION 1.5.10
33 35 
 ------------------------
34 36 
  o fixed issue #72 for label of geom_treescale not displayed <2016-08-16, Tue>
35 37 
    + https://github.com/GuangchuangYu/ggtree/issues/72
36 
-
38 
+
37 39 
 CHANGES IN VERSION 1.5.9
38 40 
 ------------------------
39 41 
  o update citation info <2016-08-12, Fri>
40 
-
42 
+
41 43 
 CHANGES IN VERSION 1.5.8
42 44 
 ------------------------
43 45 
  o add color parameter in geom_cladelabel, color should be of length 1 or 2 <2016-08-11, Thu>
44 46 
  o geom_cladelabel support parsing expression <2016-08-11, Thu>
45 
-
47 
+
46 48 
 CHANGES IN VERSION 1.5.7
47 49 
 ------------------------
48 50 
  o geom_strip can accept taxa name as input but labeling strip will not supported.
49 51 
    To support labeling strip, user need to input node id  <2016-07-27, Wed>
50 
- o nodeid function for converting node label(s) to node id(s) <2016-07-27, Wed>
51 
-
52 
+ o nodeid function for converting node label(s) to node id(s) <2016-07-27, Wed>
53 
+
52 54 
 CHANGES IN VERSION 1.5.6
53 55 
 ------------------------
54 56 
  o remove dependency of Biostring for installing ggtree <2016-07-21, Thu>
... ... 
@@ -69,7 +71,7 @@ CHANGES IN VERSION 1.5.5
69 71 
  o bug fixed if time-scaled tree extend into the BCE. <2016-06-02, Thu>
70 72 
    + as.Date won't work for BCE time.
71 73 
    + as.Date=FALSE by default in fortify method, just use the time in decimal format (real number, not Date object).
72 
-
74 
+
73 75 
 CHANGES IN VERSION 1.5.4
74 76 
 ------------------------
75 77 
  o reroot method for raxml object <2016-05-22, Sun>
... ... 
@@ -77,7 +79,7 @@ CHANGES IN VERSION 1.5.4
77 79 
  o bug fixed in collapse <2016-05-20, Fri>
78 80 
    + if user collapse a node that is an offspring of a collapsed node, print warning msg and return the tree directly
79 81 
  o use byte compiler <2016-05-18, Wed>
80 
- o change any(is.na()) to anyNA() which is more efficient <2016-05-18, Wed>
82 
+ o change any(is.na()) to anyNA() which is more efficient <2016-05-18, Wed>
81 83 
  o https://github.com/Bioconductor-mirror/ggtree/commit/559548c66b51253e8ccb983d353385838a81f106
82 84
83 85 
 CHANGES IN VERSION 1.5.3
... ... 
@@ -86,9 +88,9 @@ CHANGES IN VERSION 1.5.3
86 88 
    + add fan layout example in treeVisualization vignette
87 89 
    + add open_tree and rotate_tree example in treeManipulation vignette
88 90 
  o add angle in ggtree function, fan layout supported <2016-05-12, Thu>
89 
- o rotate_tree and open_tree function <2016-05-12, Thu>
91 
+ o rotate_tree and open_tree function <2016-05-12, Thu>
90 92 
  o support reading BEAST MCC trees (multiple trees in one file) via the read.beast function <2016-05-12, Thu>
91 
- o https://github.com/Bioconductor-mirror/ggtree/commit/51eec4721595c274c24dc4df2f1fdf40700cb1a5
93 
+ o https://github.com/Bioconductor-mirror/ggtree/commit/51eec4721595c274c24dc4df2f1fdf40700cb1a5
92 94
93 95 
 CHANGES IN VERSION 1.5.2
94 96 
 ------------------------
... ... 
@@ -101,7 +103,7 @@ CHANGES IN VERSION 1.5.2
101 103 
    + https://github.com/GuangchuangYu/ggtree/issues/40
102 104 
  o supports phylo4d object <2016-05-10, Tue>
103 105 
    + https://github.com/GuangchuangYu/ggtree/issues/47
104 
-
106 
+
105 107 
 CHANGES IN VERSION 1.5.1
106 108 
 ------------------------
107 109 
  o update vignettes <2016-05-10, Tue>
... ... 
@@ -113,11 +115,11 @@ CHANGES IN VERSION 1.5.1
113 115 
    + https://github.com/GuangchuangYu/ggtree/pull/57
114 116 
  o geom_strip for associated taxa <2016-05-09, Mon>
115 117 
    + https://github.com/GuangchuangYu/ggtree/issues/52
116 
-
118 
+
117 119 
 CHANGES IN VERSION 1.4.0
118 120 
 ------------------------
119 121 
  o BioC 3.3 released <2016-05-05, Thu>
120 
-
122 
+
121 123 
 CHANGES IN VERSION 1.3.16
122 124 
 ------------------------
123 125 
  o geom_treescale() supports family argument <2016-04-27, Wed>
... ... 
@@ -127,7 +129,7 @@ CHANGES IN VERSION 1.3.16
127 129 
  o support passing textConnection(text_string) as a file <2016-04-21, Thu>
128 130 
    + contributed by Casey Dunn <casey_dunn@brown.edu>
129 131 
    + https://github.com/GuangchuangYu/ggtree/pull/55#issuecomment-212859693
130 
-
132 
+
131 133 
 CHANGES IN VERSION 1.3.15
132 134 
 ------------------------
133 135 
  o geom_tiplab2 supports parameter hjust <2016-04-18, Mon>
... ... 
@@ -135,9 +137,9 @@ CHANGES IN VERSION 1.3.15
135 137 
  o geom_label2 that support subsetting <2016-04-07, Thu>
136 138 
  o geom_tiplab2 for adding tip label of circular layout <2016-04-06, Wed>
137 139 
  o use plot$plot_env to access ggplot2 parameter <2016-04-06, Wed>
138 
- o geom_taxalink for connecting related taxa <2016-04-01, Fri>
140 
+ o geom_taxalink for connecting related taxa <2016-04-01, Fri>
139 141 
  o geom_range for adding range of HPD to present uncertainty of evolutionary inference <2016-04-01, Fri>
140 
-
142 
+
141 143 
 CHANGES IN VERSION 1.3.14
142 144 
 ------------------------
143 145 
  o geom_tiplab works with NA values, compatible with collapse <2016-03-05, Sat>
... ... 
@@ -145,12 +147,12 @@ CHANGES IN VERSION 1.3.14
145 147 
  o offset works in `align=FFALSE` with `annotation_image` function <2016-02-23, Tue>
146 148 
    + see https://github.com/GuangchuangYu/ggtree/issues/46
147 149 
  o subview and inset now supports annotating with img files <2016-02-23, Tue>
148 
-
150 
+
149 151 
 CHANGES IN VERSION 1.3.13
150 152 
 ------------------------
151 153 
  o add example of rescale_tree function in treeAnnotation.Rmd <2016-02-07, Sun>
152 154 
  o geom_cladelabel works with collapse <2016-02-07, Sun>
153 
-   + see https://github.com/GuangchuangYu/ggtree/issues/38
155 
+   + see https://github.com/GuangchuangYu/ggtree/issues/38
154 156
155 157 
 CHANGES IN VERSION 1.3.12
156 158 
 ------------------------
... ... 
@@ -158,8 +160,8 @@ CHANGES IN VERSION 1.3.12
158 160 
  o solved issues of geom_tree2 <2016-01-25, Mon>
159 161 
    + https://github.com/hadley/ggplot2/issues/1512
160 162 
  o colnames_level parameter in gheatmap <2016-01-25, Mon>
161 
- o raxml2nwk function for converting raxml bootstrap tree to newick format <2016-01-25, Mon>
162 
-
163 
+ o raxml2nwk function for converting raxml bootstrap tree to newick format <2016-01-25, Mon>
164 
+
163 165 
 CHANGES IN VERSION 1.3.11
164 166 
 ------------------------
165 167 
  o solved issues of geom_tree2 <2016-01-25, Mon>
... ... 
@@ -171,7 +173,7 @@ CHANGES IN VERSION 1.3.11
171 173 
  o implement geom_tree2 layer that support duplicated node records via the setup_tree_data function <2016-01-21, Thu>
172 174 
  o rescale_tree function for rescaling branch length of tree object <2016-01-20, Wed>
173 175 
  o upgrade set_branch_length, now branch can be rescaled using feature in extraInfo slot <2016-01-20, Wed>
174 
-
176 
+
175 177 
 CHANGES IN VERSION 1.3.10
176 178 
 ------------------------
177 179 
  o remove dependency of gridExtra by implementing multiplot function instead of using grid.arrange <2016-01-20, Wed>
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@@ -185,7 +187,7 @@ CHANGES IN VERSION 1.3.9
185 187 
  o viewClade, scaleClade, collapse, expand, rotate, flip, get_taxa_name and scale_x_ggtree accepts input tree_view=NULL.
186 188 
    these function will access the last plot if tree_view=NULL. <2016-01-13, Wed>
187 189 
    + > ggtree(rtree(30)); viewClade(node=35) works. no need to pipe.
188 
-
190 
+
189 191 
 CHANGES IN VERSION 1.3.8
190 192 
 ------------------------
191 193 
  o add example of viewClade in 'Tree Manipulation' vignette <2016-01-13, Wed>
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@@ -195,7 +197,7 @@ CHANGES IN VERSION 1.3.8
195 197 
  o 05 advance tree annotation vignette <2016-01-04, Mon>
196 198 
  o export theme_inset <2016-01-04, Mon>
197 199 
  o inset, nodebar, nodepie functions <2015-12-31, Thu>
198 
-
200 
+
199 201 
 CHANGES IN VERSION 1.3.7
200 202 
 ------------------------
201 203 
  o split the long vignette to several vignettes
... ... 
@@ -204,14 +206,14 @@ CHANGES IN VERSION 1.3.7
204 206 
    + 02 tree visualization <2015-12-28, Mon>
205 207 
    + 03 tree manipulation <2015-12-28, Mon>
206 208 
    + 04 tree annotation <2015-12-29, Tue>
207 
-
209 
+
208 210 
 CHANGES IN VERSION 1.3.6
209 211 
 ------------------------
210 212 
  o MRCA function for finding Most Recent Common Ancestor among a vector of tips <2015-12-22, Tue>
211 213 
  o geom_cladelabel: add bar and label to annotate a clade <2015-12-21, Mon>
212 214 
    - remove annotation_clade and annotation_clade2 functions.
213 215 
  o geom_treescale: tree scale layer. (add_legend was removed) <2015-12-21, Mon>
214 
-
216 
+
215 217 
 CHANGES IN VERSION 1.3.5
216 218 
 ------------------------
217 219 
  o bug fixed, read.nhx now works with scientific notation <2015-11-30, Mon>
... ... 
@@ -226,12 +228,12 @@ CHANGES IN VERSION 1.3.4
226 228 
    + see https://github.com/GuangchuangYu/ggtree/issues/26
227 229 
  o support NHX (New Hampshire X) format via read.nhx function <2015-11-17, Tue>
228 230 
  o bug fixed in extract.treeinfo.jplace <2015-11-17, Thu>
229 
-
231 
+
230 232 
 CHANGES IN VERSION 1.3.3
231 233 
 ------------------------
232 234 
  o support color=NULL in gheatmap, then no colored line will draw within the heatmap <2015-10-30, Fri>
233 235 
  o add `angle` for also rectangular, so that it will be available for layout='rectangular' following by coord_polar() <2015-10-27, Tue>
234 
-
236 
+
235 237 
 CHANGES IN VERSION 1.3.2
236 238 
 ------------------------
237 239 
  o update vignette, add example of ape bootstrap and phangorn ancestral sequences <2015-10-26, Mon>
... ... 
@@ -239,7 +241,7 @@ CHANGES IN VERSION 1.3.2
239 241 
    see https://github.com/GuangchuangYu/ggtree/issues/20
240 242 
  o add support of ancestral sequences inferred by phangorn <2015-10-26, Mon>
241 243 
    see https://github.com/GuangchuangYu/ggtree/issues/21
242 
-
244 
+
243 245 
 CHANGES IN VERSION 1.3.1
244 246 
 ------------------------
245 247 
  o change angle to angle + 90, so that label will in radial direction <2015-10-22, Thu>
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@@ -247,17 +249,17 @@ CHANGES IN VERSION 1.3.1
247 249 
  o na.rm should be always passed to layer(), fixed it in geom_hilight and geom_text2 <2015-10-21, Wed>
248 250 
    + see https://github.com/hadley/ggplot2/issues/1380
249 251 
  o matching beast stats with tree using internal node number instead of label <2015-10-20, Tue>
250 
-
252 
+
251 253 
 CHANGES IN VERSION 1.2.0
252 254 
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253 255 
  o BioC 3.2 released
254 
-
256 
+
255 257 
 CHANGES IN VERSION 1.1.21
256 258 
 ------------------------
257 259 
  o support hyphy output of ancestral sequences that is in phylip sequential format (no TAXALABELS block available) <2015-10-07, Wed>
258 260 
  o fixed bug in geom_tiplab when x contains NA (eg, removing by collapse function) <2015-10-01, Thu>
259 261 
  o new implementation of geom_hilight, a truly geom layer function <2015-09-10, Thu>
260 
-
262 
+
261 263 
 CHANGES IN VERSION 1.1.20
262 264 
 ------------------------
263 265 
  o bug fixed in %add2%, if node available use node, otherwise use label <2015-09-04, Fri>
... ... 
@@ -268,7 +270,7 @@ CHANGES IN VERSION 1.1.20
268 270 
    + read.r8s, parser function
269 271 
    + fortify method
270 272 
    + plot, get.tree, get.fields, groupOTU, groupClade, scale_color, gzoom and show methods
271 
- o bug fixed in fortify.multiPhylo, convert df$.id to factor of levels=names(multiPhylo_object) <2015-09-02, Wed>
273 
+ o bug fixed in fortify.multiPhylo, convert df$.id to factor of levels=names(multiPhylo_object) <2015-09-02, Wed>
272 274 
  o update scale_x_ggtree to support Date as x-axis <2015-09-01, Tue>
273 275 
  o add mrsd parameter for user to specify 'most recent sampling date' for time tree <2015-09-01, Tue>
274 276 
    - remove 'time_scale' parameter.
... ... 
@@ -278,15 +280,15 @@ CHANGES IN VERSION 1.1.20
278 280 
    + plot, get.tree, get.fields, groupOTU, groupClade, scale_color, gzoom and show methods
279 281 
    + fortify.raxml method
280 282 
  o bug fixed in edgeNum2nodeNum for jplace parsing jplace file <2015-09-01, Tue>
281 
-
283 
+
282 284 
 CHANGES IN VERSION 1.1.19
283 285 
 ------------------------
284 
- o use fortify instead of fortify.phylo in fortify.multiPhylo,
286 
+ o use fortify instead of fortify.phylo in fortify.multiPhylo,
285 287 
    so that multiPhylo can be a list of beast/codeml or other supported objects. <2015-08-31, Mon>
286 288 
  o support multiPhylo object, should use + facet_wrap or + facet_grid <2015-08-31, Mon>
287 289 
  o remove dependency of EBImage and phytools to speedup the installation process of ggtree <2015-08-31, Mon>
288 290 
    + these two packages is not commonly used, and will be loaded automatically when needed.
289 
-
291 
+
290 292 
 CHANGES IN VERSION 1.1.18
291 293 
 ------------------------
292 294 
  o layout name change to 'rectangular', 'slanted', 'circular'/'fan' for phylogram and cladogram (if branch.length = 'none')
... ... 
@@ -294,37 +296,37 @@ CHANGES IN VERSION 1.1.18
294 296 
  o implement geom_point2, geom_text2, geom_segment2 to support subsetting <2015-08-28, Fri>
295 297 
      see https://github.com/hadley/ggplot2/issues/1295
296 298 
  o update geom_tiplab according to geom_text2 and geom_segment2 <2015-08-28, Fri>
297 
- o add geom_tippoint, geom_nodepoint and geom_rootpoint <2015-08-28, Fri>
298 
-
299 
+ o add geom_tippoint, geom_nodepoint and geom_rootpoint <2015-08-28, Fri>
300 
+
299 301 
 CHANGES IN VERSION 1.1.17
300 302 
 ------------------------
301 303 
  o bug fixed in rm.singleton.newick by adding support of scientific notation in branch length <2015-08-27, Thu>
302 304 
  o bug fixed in gheatmap, remove inherit aes from ggtree <2015-08-27, Thu>
303 305 
  o add 'width' parameter to add_legend, now user can specify the width of legend bar <2015-08-27, Thu>
304 
- o add 'colnames_position' parameter to gheatmap, now colnames can be display on the top of heatmap <2015-08-27, Thu>
306 
+ o add 'colnames_position' parameter to gheatmap, now colnames can be display on the top of heatmap <2015-08-27, Thu>
305 307 
  o theme_transparent to make background transparent <2015-08-27, Thu>
306 
- o subview for adding ggplot object (subview) to another ggplot object (mainview) <2015-08-27, Thu>
307 
-
308 
+ o subview for adding ggplot object (subview) to another ggplot object (mainview) <2015-08-27, Thu>
309 
+
308 310 
 CHANGES IN VERSION 1.1.16
309 311 
 ------------------------
310 312 
  o update citation <2015-08-17, Mon>
311 
-
313 
+
312 314 
 CHANGES IN VERSION 1.1.15
313 315 
 ------------------------
314 316 
  o open text angle parameter for annotation_clade/annotation_clade2 <2015-08-13, Thu>
315 317 
  o support changing size of add_legend <2015-08-13, Thu>
316 318 
  o reroot methods for phylo and beast <2015-08-07, Fri>
317 
-
319 
+
318 320 
 CHANGES IN VERSION 1.1.14
319 321 
 ------------------------
320 322 
  o update paml_rst to compatible with only marginal ancestral sequence or joint ancestral sequence available <2015-08-07, Fri>
321 
-
323 
+
322 324 
 CHANGES IN VERSION 1.1.13
323 325 
 ------------------------
324 326 
  o implement annotation_image <2015-08-01, Sat>
325 327 
  o better implementation of geom_tiplab for accepting aes mapping and auto add align dotted line <2015-08-01, Sat>
326 328 
  o open group_name parameter of groupOTU/groupClade to user <2015-08-01, Sat>
327 
-
329 
+
328 330 
 CHANGES IN VERSION 1.1.12
329 331 
 ------------------------
330 332 
  o update vignette according to the changes <2015-07-31, Fri>
... ... 
@@ -332,14 +334,14 @@ CHANGES IN VERSION 1.1.12
332 334 
  o extend groupClade to support operating on tree view <2015-07-31, Fri>
333 335 
  o extend groupOTU to support operating on tree view <2015-07-31, Fri>
334 336 
  o new implementation of groupClade & groupOTU <2015-07-31, Fri>
335 
-
337 
+
336 338 
 CHANGES IN VERSION 1.1.11
337 339 
 ------------------------
338 340 
  o annotation_clade and annotation_clade2 functions. <2015-07-30, Thu>
339 341 
  o better add_legend implementation. <2015-07-30, Thu>
340 342 
  o add ... in theme_tree & theme_tree2 for accepting additional parameter. <2015-07-30, Thu>
341 343 
  o better geom_tree implementation. Now we can scale the tree with aes(color=numVar). <2015-07-30, Thu>
342 
-
344 
+
343 345 
 CHANGES IN VERSION 1.1.10
344 346 
 ------------------------
345 347 
  o solve overlapping branches for layout = "fan" || "radial",
... ... 
@@ -355,32 +357,32 @@ CHANGES IN VERSION 1.1.9
355 357 
  o get_taxa_name function will return taxa name vector of a selected clade <2015-06-30, Tue>
356 358 
  o add example of flip function in vignette <2015-06-30, Tue>
357 359 
  o flip function for exchanging positions of two selected branches <2015-06-30, Tue>
358 
-
360 
+
359 361 
 CHANGES IN VERSION 1.1.8
360 362 
 ------------------------
361 363 
  o update get.placement <2015-06-05, Fri>
362 364 
  o edgeNum2nodeNum for converting edge number to node number for EPA/pplacer output <2015-06-04, Thu>
363 365 
  o mv scale_x_gheatmap to scale_x_ggtree, which also support msaplot <2015-06-02, Tue>
364 366 
  o add mask function <2015-06-02, Tue>
365 
-
367 
+
366 368 
 CHANGES IN VERSION 1.1.7
367 369 
 ------------------------
368 370 
  o add example of msaplot in vignette <2015-05-22, Fri>
369 371 
  o msaplot for adding multiple sequence alignment <2015-05-22, Fri>
370 
-
372 
+
371 373 
 CHANGES IN VERSION 1.1.6
372 374 
 ------------------------
373 375 
  o add vertical_only parameter to scaleClade and set to TRUE by default.
374 376 
    only vertical will be scaled by default. <2015-05-22, Fri>
375 377 
  o update add_colorbar & add_legend <2015-05-21, Thu>
376 
- o add example of add_legend and gheatmap in vignette <2015-05-18, Mon>
378 
+ o add example of add_legend and gheatmap in vignette <2015-05-18, Mon>
377 379 
  o gheatmap implementation of gplot <2015-05-18, Mon>
378 380 
  o add_legend for adding evolution distance legend <2015-05-18, Mon>
379 
-
381 
+
380 382 
 CHANGES IN VERSION 1.1.5
381 383 
 ------------------------
382 384 
  o implement scaleClade <2015-05-12, Tue>
383 
-
385 
+
384 386 
 CHANGES IN VERSION 1.1.4
385 387 
 ------------------------
386 388 
  o better performance of parsing beast tree  <2015-05-11, Mon>
... ... 
@@ -388,13 +390,13 @@ CHANGES IN VERSION 1.1.4
388 390 
    + support file that only contains one evidence for some of the nodes/tips
389 391 
  o update add_colorbar to auto determine the position <2015-05-04, Mon>
390 392 
  o add_colorbar function <2015-04-30, Thu>
391 
-
393 
+
392 394 
 CHANGES IN VERSION 1.1.3
393 395 
 ------------------------
394 396 
  o add space between residue substitution (e.g. K123R / E155D) <2015-04-30, Thu>
395 397 
  o remove slash line in heatmap legend <2015-04-30, Thu>
396 398 
  o update vignette to add example of merge_tree <2015-04-29, Wed>
397 
-
399 
+
398 400 
 CHANGES IN VERSION 1.1.2
399 401 
 ------------------------
400 402 
  o in addition to parsing beast time scale tree in XXX_year[\\.\\d]*, now supports XXX/year[\\.\\d]* <2015-04-29, Wed>
... ... 
@@ -409,17 +411,17 @@ CHANGES IN VERSION 1.1.2
409 411 
  o extend get.fields methods to support additional fields <2015-04-28, Tue>
410 412 
  o extend tree class to support additional info by merging two tree <2015-04-28, Tue>
411 413 
  o implement merge_tree function to merge two tree objects into one <2015-04-28, Tue>
412 
-
414 
+
413 415 
 CHANGES IN VERSION 1.1.1
414 416 
 ------------------------
415 417 
  o minor bug fixed in extracting node ID of rst file <2015-04-27, Mon>
416 418 
  o update parsing beast time scale tree to support _year (originally supports _year.\\d+) <2015-04-27, Mon>
417 419 
  o add Tommy in author <2015-04-27, Mon>
418 
-
420 
+
419 421 
 CHANGES IN VERSION 0.99.28
420 422 
 ------------------------
421 423 
  o update vignette with floating table of content <2015-04-08, Wed>
422 
-
424 
+
423 425 
 CHANGES IN VERSION 0.99.27
424 426 
 ------------------------
425 427 
  o bug fixed, see https://github.com/GuangchuangYu/ggtree/issues/4 <2015-03-07, Tue>
... ... 
@@ -428,42 +430,42 @@ CHANGES IN VERSION 0.99.26
428 430 
 ------------------------
429 431 
  o update geom_tiplab <2015-03-31, Tue>
430 432 
  o update plot method of beast <2015-03-17, Tue>
431 
-
433 
+
432 434 
 CHANGES IN VERSION 0.99.25
433 435 
 ------------------------
434 436 
  o implement groupClade <2015-03-13, Fri>
435 
-
437 
+
436 438 
 CHANGES IN VERSION 0.99.24
437 439 
 ------------------------
438 440 
  o use "round" segment end, look very better <2015-03-12, Thu>
439 441 
  o update vignett <2015-03-11, Wed>
440 
-
442 
+
441 443 
 CHANGES IN VERSION 0.99.23
442 444 
 ------------------------
443 445 
  o mv geom_hilight to hilight <2015-03-11, Wed>
444 446 
  o mv geom_phylopic to phylopic <2015-03-11, Wed>
445 
- o implement collapse and expand for collapse and expand a selected clade <2015-03-11, Wed>
446 
-
447 
+ o implement collapse and expand for collapse and expand a selected clade <2015-03-11, Wed>
448 
+
447 449 
 CHANGES IN VERSION 0.99.22
448 450 
 ------------------------
449 451 
  o remove quote in beast tip/node labels <2015-03-10, Tue>
450 
-
452 
+
451 453 
 CHANGES IN VERSION 0.99.21
452 454 
 ------------------------
453 455 
  o fixed downloading png file in Windows platform, should explicitly setting mode="wb". <2015-03-03, Tue>
454 
-
456 
+
455 457 
 CHANGES IN VERSION 0.99.19
456 458 
 ------------------------
457 459 
  o for time scale tree inferred by BEAST, now user can use time_scale=TRUE parameter in ggtree function <2015-02-12, Thu>
458 
-
460 
+
459 461 
 CHANGES IN VERSION 0.99.18
460 462 
 ------------------------
461 463 
  o bug fixed in reorder the labels in gplot.heatmap <2015-02-12, Thu>
462 
-
464 
+
463 465 
 CHANGES IN VERSION 0.99.17
464 466 
 ------------------------
465 467 
  o add angle and branch.y variable in cladogram layout <2015-02-10, Tue>
466 
-
468 
+
467 469 
 CHANGES IN VERSION 0.99.16
468 470 
 ------------------------
469 471 
  o correct typo in vignette <2015-02-10, Tue>
... ... 
@@ -471,7 +473,7 @@ CHANGES IN VERSION 0.99.16
471 473 
 CHANGES IN VERSION 0.99.15
472 474 
 ------------------------
473 475 
  o fully support of replace operator, %<% <2015-02-09, Mon>
474 
-
476 
+
475 477 
 CHANGES IN VERSION 0.99.14
476 478 
 ------------------------
477 479 
  o add example in groupOTU for adding legend manually <2015-02-09, Mon>.
... ... 
@@ -479,13 +481,13 @@ CHANGES IN VERSION 0.99.14
479 481 
 CHANGES IN VERSION 0.99.13
480 482 
 ------------------------
481 483 
  o two dimensional tree <2015-02-06, Fri>
482 
-
484 
+
483 485 
 CHANGES IN VERSION 0.99.12
484 486 
 ------------------------
485 487 
  o update vignette <2015-02-04, Wed>
486 488 
  o gzoom methods that supports all tree objects <2015-02-04, Wed>
487 
- o geom_hilight layer for highlighting clade <2015-02-04, Wed>
488 
-
489 
+ o geom_hilight layer for highlighting clade <2015-02-04, Wed>
490 
+
489 491 
 CHANGES IN VERSION 0.99.11
490 492 
 ------------------------
491 493 
  o add scale_color to support colored lines and text based on numerical values and update vignette <2015-02-04, Wed>
... ... 
@@ -499,12 +501,12 @@ CHANGES IN VERSION 0.99.10
499 501 
 CHANGES IN VERSION 0.99.9
500 502 
 ------------------------
501 503 
  o update vignette <2015-02-02, Mon>
502 
-
504 
+
503 505 
 CHANGES IN VERSION 0.99.8
504 506 
 ------------------------
505 507 
  o add get.phylopic function to read the online phylo pic and convert it to grob object,
506 508 
    which can be use to annotate ggplot figure using annotation_custom <2015-01-30, Fri>
507 
-
509 
+
508 510 
 CHANGES IN VERSION 0.99.7
509 511 
 ------------------------
510 512 
  o add angle information for 'fan' & 'unrooted' layout <2015-01-29, Thu>
... ... 
@@ -513,7 +515,7 @@ CHANGES IN VERSION 0.99.6
513 515 
 ------------------------
514 516 
  o read.beast now supports support values of sets such as {x, y, z} <2015-01-19, Mon>
515 517 
  o now read.beast supports characters in support values <2015-01-18, Sun>
516 
- o add example of gzoom and groupOTU in vignette <2015-01-14, Wed>
518 
+ o add example of gzoom and groupOTU in vignette <2015-01-14, Wed>
517 519 
  o implement groupOTU methods <2015-01-14, Wed>
518 520 
  o export get.offspring.tip <2015-01-14, Wed>
519 521
... ... 
@@ -524,7 +526,7 @@ CHANGES IN VERSION 0.99.5
524 526 
  o add gzoom function, similar to zoom function in ape <2015-01-07, Wed>
525 527 
  o add examples in man pages of %<% and %<+% operators <2015-01-06, Tue>
526 528 
  o remove <<- and update vignette <2015-01-06, Tue>
527 
- o update vignette and use BibTex and CSL for references <2015-01-05, Mon>
529 
+ o update vignette and use BibTex and CSL for references <2015-01-05, Mon>
528 530 
  o update cladogram layout <2015-01-05, Mon>
529 531 
  o read.baseml function and update vignette with baseml example <2015-01-04, Sun>
530 532 
  o plot method for hyphy and hyphy example in vignette <2015-01-04, Sun>
... ... 
@@ -532,9 +534,9 @@ CHANGES IN VERSION 0.99.5
532 534
533 535 
 CHANGES IN VERSION 0.99.4
534 536 
 ------------------------
535 
- o ggtree now support branch.length = "none" to only draw tree topology <2015-01-03, Sat>
537 
+ o ggtree now support branch.length = "none" to only draw tree topology <2015-01-03, Sat>
536 538 
  o get.subs method for hyphy object <2015-01-03, Sat>
537 
- o show, get.tree and get.subs methods of hyphy <2015-01-02, Fri>
539 
+ o show, get.tree and get.subs methods of hyphy <2015-01-02, Fri>
538 540 
  o export read.hyphy <2015-01-02, Fri>
539 541 
  o export hyphy class <2015-01-01, Thu>
540 542 
  o plot method for beast class and get.tree method for codeml class <2014-12-31, Wed>
... ... 
@@ -547,7 +549,7 @@ CHANGES IN VERSION 0.99.4
547 549 
  o update man file and add example file of beast output <2014-12-26, Fri>
548 550 
  o get.tree and get.fileds methods of beast class <2014-12-26, Fri>
549 551 
  o read.beast <2014-12-26, Fri>
550 
- o beast class and show method <2014-12-26, Fri>
552 
+ o beast class and show method <2014-12-26, Fri>
551 553 
  o coplot prototype<2014-12-24, Wed>
552 554 
  o parse translation matrix in beast nexus <2014-12-24, Wed>
553 555 
  o extract beast stats info <2014-12-23, Tue>
... ... 
@@ -560,7 +562,7 @@ CHANGES IN VERSION 0.99.3
560 562 
  o write.jplace and fully supports of jplace by ggtree. <2014-12-21, Sun>
561 563 
  o support unrooted layout in ggplot. <2014-12-21, Sun>
562 564 
  o support fan, radial, dendrogram layout in geom_tree. <2014-12-21, Sun>
563 
-
565 
+
564 566 
 CHANGES IN VERSION 0.99.2
565 567 
 ------------------------
566 568 
  o layout of unrooted tree, implemented equal-angle algorithm that described in Chapter 34
R/method-groupOTU.R
History View file @ deef581
... ... 
@@ -90,7 +90,7 @@ setMethod("groupOTU", signature(object="paml_rst"),
90 90
91 91 
 ##' group tree based on selected OTU, will traceback to MRCA
92 92 
 ##'
93 
-##'
93 
+##'
94 94 
 ##' @rdname groupOTU-methods
95 95 
 ##' @exportMethod groupOTU
96 96 
 setMethod("groupOTU", signature(object="phylo"),
... ... 
@@ -111,21 +111,26 @@ setMethod("groupOTU", signature(object="r8s"),
111 111
112 112
113 113 
 ##' @importFrom ape which.edge
114 
-gfocus <- function(phy, focus, group_name) {
114 
+gfocus <- function(phy, focus, group_name, focus_label=NULL) {
115 115 
     if (is.character(focus)) {
116 116 
         focus <- which(phy$tip.label %in% focus)
117 117 
     }
118 
-
118 
+
119 119 
     n <- getNodeNum(phy)
120 120 
     if (is.null(attr(phy, group_name))) {
121 121 
         foc <- rep(0, n)
122 122 
     } else {
123 123 
         foc <- attr(phy, group_name)
124 124 
     }
125 
-    i <- max(foc) + 1
125 
+    i <- max(suppressWarnings(as.numeric(foc)), na.rm=TRUE) + 1
126 126 
     ## sn <- phy$edge[which.edge(phy, focus),] %>% as.vector %>% unique
127 127 
     sn <- unique(as.vector(phy$edge[which.edge(phy, focus),]))
128 
-    foc[sn] <- i
128 
+    if (is.null(focus_label)) {
129 
+        foc[sn] <- i
130 
+    } else {
131 
+        foc[sn] <- focus_label
132 
+    }
133 
+
129 134 
     attr(phy, group_name) <- foc
130 135 
     phy
131 136 
 }
... ... 
@@ -133,7 +138,7 @@ gfocus <- function(phy, focus, group_name) {
133 138
134 139 
 ##' group OTU
135 140 
 ##'
136 
-##'
141 
+##'
137 142 
 ##' @title groupOTU.phylo
138 143 
 ##' @param phy tree object
139 144 
 ##' @param focus tip list
... ... 
@@ -144,8 +149,8 @@ groupOTU.phylo <- function(phy, focus, group_name="group") {
144 149 
     attr(phy, group_name) <- NULL
145 150 
     if ( is(focus, "list") ) {
146 151 
         for (i in 1:length(focus)) {
147 
-            phy <- gfocus(phy, focus[[i]], group_name)
148 
-        }
152 
+            phy <- gfocus(phy, focus[[i]], group_name, names(focus)[i])
153 
+        }
149 154 
     } else {
150 155 
         phy <- gfocus(phy, focus, group_name)
151 156 
     }
... ... 
@@ -167,14 +172,14 @@ groupOTU.ggplot <- function(object, focus, group_name) {
167 172 
     df <- object$data
168 173 
     df[, group_name] <- 0
169 174 
     object$data <- groupOTU.df(df, focus, group_name)
170 
-    return(object)
175 
+    return(object)
171 176 
 }
172 177
173 178
174 
-groupOTU.df <- function(df, focus, group_name) {
179 
+groupOTU.df <- function(df, focus, group_name) {
175 180 
     if (is(focus, "list")) {
176 181 
         for (i in 1:length(focus)) {
177 
-            df <- gfocus.df(df, focus[[i]], group_name)
182 
+            df <- gfocus.df(df, focus[[i]], group_name, names(focus)[i])
178 183 
         }
179 184 
     } else {
180 185 
         df <- gfocus.df(df, focus, group_name)
... ... 
@@ -183,13 +188,16 @@ groupOTU.df <- function(df, focus, group_name) {
183 188 
     return(df)
184 189 
 }
185 190
186 
-gfocus.df <- function(df, focus, group_name) {
191 
+gfocus.df <- function(df, focus, group_name, focus_label=NULL) {
187 192 
     focus <- df$node[which(df$label %in% focus)]
193 
+    if (is.null(focus_label))
194 
+        focus_label <- max(suppressWarnings(as.numeric(df[, group_name])), na.rm=TRUE) + 1
195 
+
188 196 
     if (length(focus) == 1) {
189 
-        df[match(focus, df$node), group_name] <- max(df(df[, group_name])) + 1
197 
+        df[match(focus, df$node), group_name] <-focus_label
190 198 
         return(df)
191 199 
     }
192 
-
200 
+
193 201 
     anc <- getAncestor.df(df, focus[1])
194 202 
     foc <- c(focus[1], anc)
195 203 
     for (j in 2:length(focus)) {
... ... 
@@ -200,7 +208,7 @@ gfocus.df <- function(df, focus, group_name) {
200 208 
         foc <- c(foc, comAnc[1])
201 209 
     }
202 210 
     idx <- match(foc, df$node)
203 
-    df[idx, group_name] <- max(df[, group_name]) + 1
211 
+    df[idx, group_name] <- focus_label
204 212 
     return(df)
205 213 
 }
206 214
README.md
History View file @ deef581
... ... 
@@ -3,7 +3,7 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with
3 3
4 4 
 [![releaseVersion](https://img.shields.io/badge/release%20version-1.4.20-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.5.14-green.svg?style=flat)](https://github.com/GuangchuangYu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![total](https://img.shields.io/badge/downloads-13439/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1122/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
5 5
6 
-[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2016--09--21-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
6 
+[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2016--09--22-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
7 7
8 8 
 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-green.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html)
9 9
tests/testthat/test-group.R
History View file @ deef581
10 10 
new file mode 100644
... ... 
@@ -0,0 +1,35 @@
1 
+context('groupOTU')
2 
+
3 
+test_that('groupOTU', {
4 
+    nwk <- system.file("extdata", "sample.nwk", package="ggtree")
5 
+    tree <- read.tree(nwk)
6 
+    focus <- c("D", "E", "F", "G")
7 
+    df <- fortify(groupOTU(tree, focus=focus))
8 
+    expect_true(all(df$group[df$label %in% focus] == 1))
9 
+
10 
+    cls <- list(c1=c("A", "B", "C", "D", "E"),
11 
+                c2=c("F", "G", "H"),
12 
+                c3=c("L", "K", "I", "J"),
13 
+                c4="M")
14 
+    df <- fortify(groupOTU(tree, cls))
15 
+    for (i in seq_along(cls)) {
16 
+        expect_true(all(df$group[df$label %in% cls[[i]]] == names(cls)[i]))
17 
+    }
18 
+})
19 
+
20 
+
21 
+context('groupClade')
22 
+
23 
+test_that('groupClade', {
24 
+    nwk <- system.file("extdata", "sample.nwk", package="ggtree")
25 
+    tree <- read.tree(nwk)
26 
+    focus <- c("D", "E", "F", "G")
27 
+    nodes <- c(21, 17)
28 
+    df <- fortify(groupClade(tree, node=nodes))
29 
+
30 
+    for (i in seq_along(nodes)) {
31 
+        expect_true(all(df$group[df$node %in% ggtree:::get.offspring.df(df, nodes[i])] == i))
32 
+    }
33 
+
34 
+})
35 
+