Browse code

rename to anno_textbox()

Zuguang Gu authored on 15/06/2022 10:11:58
Showing1 changed files
... ...
@@ -48,8 +48,8 @@ S3method("heightDetails", "legend_body")
48 48
 export("heightDetails.legend_body")
49 49
 S3method("heightDetails", "packed_legends")
50 50
 export("heightDetails.packed_legends")
51
-S3method("heightDetails", "text_box")
52
-export("heightDetails.text_box")
51
+S3method("heightDetails", "textbox")
52
+export("heightDetails.textbox")
53 53
 S3method("length", "HeatmapAnnotation")
54 54
 export("length.HeatmapAnnotation")
55 55
 S3method("length", "HeatmapList")
... ...
@@ -124,8 +124,8 @@ S3method("widthDetails", "legend_body")
124 124
 export("widthDetails.legend_body")
125 125
 S3method("widthDetails", "packed_legends")
126 126
 export("widthDetails.packed_legends")
127
-S3method("widthDetails", "text_box")
128
-export("widthDetails.text_box")
127
+S3method("widthDetails", "textbox")
128
+export("widthDetails.textbox")
129 129
 export("%v%")
130 130
 export("AdditiveUnit")
131 131
 export("AnnotationFunction")
... ...
@@ -159,7 +159,7 @@ export("anno_points")
159 159
 export("anno_simple")
160 160
 export("anno_summary")
161 161
 export("anno_text")
162
-export("anno_text_box")
162
+export("anno_textbox")
163 163
 export("anno_zoom")
164 164
 export("annotation_axis_grob")
165 165
 export("bar3D")
... ...
@@ -199,7 +199,7 @@ export("getXY_in_parent_vp")
199 199
 export("grid.annotation_axis")
200 200
 export("grid.boxplot")
201 201
 export("grid.dendrogram")
202
-export("grid.text_box")
202
+export("grid.textbox")
203 203
 export("gt_render")
204 204
 export("ht_global_opt")
205 205
 export("ht_opt")
... ...
@@ -235,7 +235,7 @@ export("subset_matrix_by_row")
235 235
 export("subset_no")
236 236
 export("subset_vector")
237 237
 export("test_alter_fun")
238
-export("text_box_grob")
238
+export("textbox_grob")
239 239
 export("unify_mat_list")
240 240
 export("upset_left_annotation")
241 241
 export("upset_right_annotation")
... ...
@@ -290,7 +290,6 @@ exportMethods("set_component_height")
290 290
 exportMethods("set_component_width")
291 291
 
292 292
 import(digest)
293
-import(parallel)
294 293
 import(doParallel)
295 294
 import(foreach)
296 295
 import(grDevices)
... ...
@@ -298,6 +297,7 @@ import(graphics)
298 297
 import(grid)
299 298
 import(matrixStats)
300 299
 import(methods)
300
+import(parallel)
301 301
 import(png)
302 302
 import(stats)
303 303
 importFrom("GetoptLong", qq)
... ...
@@ -324,5 +324,4 @@ importFrom("utils", "combn")
324 324
 importFrom("utils", "getFromNamespace")
325 325
 importFrom("utils", "packageDescription")
326 326
 importFrom("utils", "str")
327
-importFrom("utils", "sessionInfo")
328 327
 
Browse code

use foreach

Zuguang Gu authored on 31/05/2022 13:27:23
Showing1 changed files
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@@ -324,4 +324,5 @@ importFrom("utils", "combn")
324 324
 importFrom("utils", "getFromNamespace")
325 325
 importFrom("utils", "packageDescription")
326 326
 importFrom("utils", "str")
327
+importFrom("utils", "sessionInfo")
327 328
 
Browse code

better .libPath env setup

trile965 authored on 24/05/2022 10:10:19
Showing1 changed files
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@@ -290,6 +290,7 @@ exportMethods("set_component_height")
290 290
 exportMethods("set_component_width")
291 291
 
292 292
 import(digest)
293
+import(parallel)
293 294
 import(doParallel)
294 295
 import(foreach)
295 296
 import(grDevices)
Browse code

fixed warnings

Zuguang Gu authored on 02/04/2022 19:28:24
Showing1 changed files
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@@ -313,6 +313,7 @@ importFrom("clue", as.cl_hard_partition)
313 313
 importFrom("clue", cl_class_ids)
314 314
 importFrom("clue", cl_consensus)
315 315
 importFrom("clue", cl_ensemble)
316
+importFrom("codetools", "findGlobals")
316 317
 importFrom("colorspace", RGB)
317 318
 importFrom("colorspace", coords)
318 319
 importFrom("colorspace", diverge_hcl)
Browse code

add show_name in anno_empty()

Zuguang Gu authored on 03/02/2022 09:53:48
Showing1 changed files
... ...
@@ -48,6 +48,8 @@ S3method("heightDetails", "legend_body")
48 48
 export("heightDetails.legend_body")
49 49
 S3method("heightDetails", "packed_legends")
50 50
 export("heightDetails.packed_legends")
51
+S3method("heightDetails", "text_box")
52
+export("heightDetails.text_box")
51 53
 S3method("length", "HeatmapAnnotation")
52 54
 export("length.HeatmapAnnotation")
53 55
 S3method("length", "HeatmapList")
... ...
@@ -122,6 +124,8 @@ S3method("widthDetails", "legend_body")
122 124
 export("widthDetails.legend_body")
123 125
 S3method("widthDetails", "packed_legends")
124 126
 export("widthDetails.packed_legends")
127
+S3method("widthDetails", "text_box")
128
+export("widthDetails.text_box")
125 129
 export("%v%")
126 130
 export("AdditiveUnit")
127 131
 export("AnnotationFunction")
... ...
@@ -149,11 +153,13 @@ export("anno_joyplot")
149 153
 export("anno_lines")
150 154
 export("anno_link")
151 155
 export("anno_mark")
156
+export("anno_numeric")
152 157
 export("anno_oncoprint_barplot")
153 158
 export("anno_points")
154 159
 export("anno_simple")
155 160
 export("anno_summary")
156 161
 export("anno_text")
162
+export("anno_text_box")
157 163
 export("anno_zoom")
158 164
 export("annotation_axis_grob")
159 165
 export("bar3D")
... ...
@@ -193,6 +199,7 @@ export("getXY_in_parent_vp")
193 199
 export("grid.annotation_axis")
194 200
 export("grid.boxplot")
195 201
 export("grid.dendrogram")
202
+export("grid.text_box")
196 203
 export("gt_render")
197 204
 export("ht_global_opt")
198 205
 export("ht_opt")
... ...
@@ -228,6 +235,7 @@ export("subset_matrix_by_row")
228 235
 export("subset_no")
229 236
 export("subset_vector")
230 237
 export("test_alter_fun")
238
+export("text_box_grob")
231 239
 export("unify_mat_list")
232 240
 export("upset_left_annotation")
233 241
 export("upset_right_annotation")
Browse code

update

Zuguang Gu authored on 25/10/2021 10:18:45
Showing1 changed files
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@@ -139,6 +139,7 @@ export("alter_graphic")
139 139
 export("anno_barplot")
140 140
 export("anno_block")
141 141
 export("anno_boxplot")
142
+export("anno_customize")
142 143
 export("anno_density")
143 144
 export("anno_empty")
144 145
 export("anno_histogram")
... ...
@@ -224,6 +225,7 @@ export("set_size")
224 225
 export("smartAlign2")
225 226
 export("subset_gp")
226 227
 export("subset_matrix_by_row")
228
+export("subset_no")
227 229
 export("subset_vector")
228 230
 export("test_alter_fun")
229 231
 export("unify_mat_list")
Browse code

add plot() method

Zuguang Gu authored on 29/09/2021 08:38:35
Showing1 changed files
... ...
@@ -68,6 +68,12 @@ S3method("nobs", "SingleAnnotation")
68 68
 export("nobs.SingleAnnotation")
69 69
 S3method("nrow", "Heatmap")
70 70
 export("nrow.Heatmap")
71
+S3method("plot", "Heatmap")
72
+export("plot.Heatmap")
73
+S3method("plot", "HeatmapAnnotation")
74
+export("plot.HeatmapAnnotation")
75
+S3method("plot", "HeatmapList")
76
+export("plot.HeatmapList")
71 77
 S3method("print", "comb_mat")
72 78
 export("print.comb_mat")
73 79
 S3method("size", "AnnotationFunction")
Browse code

add numbers to the barplot annotations

Zuguang Gu authored on 03/08/2021 12:22:45
Showing1 changed files
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@@ -221,6 +221,7 @@ export("subset_matrix_by_row")
221 221
 export("subset_vector")
222 222
 export("test_alter_fun")
223 223
 export("unify_mat_list")
224
+export("upset_left_annotation")
224 225
 export("upset_right_annotation")
225 226
 export("upset_top_annotation")
226 227
 exportClasses("AdditiveUnit")
Browse code

support GRangesList objects in make_comb_mat

Zuguang Gu authored on 02/08/2021 10:26:51
Showing1 changed files
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@@ -282,7 +282,6 @@ import(matrixStats)
282 282
 import(methods)
283 283
 import(png)
284 284
 import(stats)
285
-importFrom("Cairo", "CairoPNG")
286 285
 importFrom("GetoptLong", qq)
287 286
 importFrom("GetoptLong", qq.options)
288 287
 importFrom("GetoptLong", qqcat)
Browse code

rename rect3D to bar3D

Zuguang authored on 24/03/2021 20:15:32
Showing1 changed files
... ...
@@ -149,6 +149,7 @@ export("anno_summary")
149 149
 export("anno_text")
150 150
 export("anno_zoom")
151 151
 export("annotation_axis_grob")
152
+export("bar3D")
152 153
 export("bin_genome")
153 154
 export("cluster_between_groups")
154 155
 export("cluster_within_group")
... ...
@@ -203,7 +204,6 @@ export("order.comb_mat")
203 204
 export("packLegend")
204 205
 export("pheatmap")
205 206
 export("pindex")
206
-export("rect3D")
207 207
 export("restore_matrix")
208 208
 export("rowAnnotation")
209 209
 export("row_anno_barplot")
Browse code

add Heatmap3d()

Zuguang authored on 24/03/2021 09:05:20
Showing1 changed files
... ...
@@ -121,6 +121,7 @@ export("AdditiveUnit")
121 121
 export("AnnotationFunction")
122 122
 export("ColorMapping")
123 123
 export("Heatmap")
124
+export("Heatmap3D")
124 125
 export("HeatmapAnnotation")
125 126
 export("HeatmapList")
126 127
 export("Legend")
... ...
@@ -178,6 +179,7 @@ export("dendrogramGrob")
178 179
 export("densityHeatmap")
179 180
 export("dist2")
180 181
 export("extract_comb")
182
+export("frequencyHeatmap")
181 183
 export("full_comb_code")
182 184
 export("getXY_in_parent_vp")
183 185
 export("grid.annotation_axis")
... ...
@@ -201,6 +203,7 @@ export("order.comb_mat")
201 203
 export("packLegend")
202 204
 export("pheatmap")
203 205
 export("pindex")
206
+export("rect3D")
204 207
 export("restore_matrix")
205 208
 export("rowAnnotation")
206 209
 export("row_anno_barplot")
... ...
@@ -294,8 +297,11 @@ importFrom("clue", as.cl_hard_partition)
294 297
 importFrom("clue", cl_class_ids)
295 298
 importFrom("clue", cl_consensus)
296 299
 importFrom("clue", cl_ensemble)
300
+importFrom("colorspace", RGB)
301
+importFrom("colorspace", coords)
297 302
 importFrom("colorspace", diverge_hcl)
298 303
 importFrom("colorspace", rainbow_hcl)
304
+importFrom("colorspace", sequential_hcl)
299 305
 importFrom("utils", "combn")
300 306
 importFrom("utils", "getFromNamespace")
301 307
 importFrom("utils", "packageDescription")
Browse code

add cluster_between_groups()

Zuguang Gu authored on 04/03/2021 09:51:27
Showing1 changed files
... ...
@@ -149,6 +149,7 @@ export("anno_text")
149 149
 export("anno_zoom")
150 150
 export("annotation_axis_grob")
151 151
 export("bin_genome")
152
+export("cluster_between_groups")
152 153
 export("cluster_within_group")
153 154
 export("columnAnnotation")
154 155
 export("comb_degree")
Browse code

update docs

Zuguang Gu authored on 09/02/2021 20:31:08
Showing1 changed files
... ...
@@ -269,6 +269,8 @@ exportMethods("set_component_height")
269 269
 exportMethods("set_component_width")
270 270
 
271 271
 import(digest)
272
+import(doParallel)
273
+import(foreach)
272 274
 import(grDevices)
273 275
 import(graphics)
274 276
 import(grid)
... ...
@@ -297,6 +299,4 @@ importFrom("utils", "combn")
297 299
 importFrom("utils", "getFromNamespace")
298 300
 importFrom("utils", "packageDescription")
299 301
 importFrom("utils", "str")
300
-import(foreach)
301
-import(doParallel)
302 302
 
Browse code

expression is properly processed for discrete legends

Zuguang Gu authored on 09/02/2021 13:53:11
Showing1 changed files
... ...
@@ -293,9 +293,10 @@ importFrom("clue", cl_consensus)
293 293
 importFrom("clue", cl_ensemble)
294 294
 importFrom("colorspace", diverge_hcl)
295 295
 importFrom("colorspace", rainbow_hcl)
296
-importFrom("parallel", "mclapply")
297 296
 importFrom("utils", "combn")
298 297
 importFrom("utils", "getFromNamespace")
299 298
 importFrom("utils", "packageDescription")
300 299
 importFrom("utils", "str")
300
+import(foreach)
301
+import(doParallel)
301 302
 
Browse code

anno_mark(): indices are reordered

Zuguang Gu authored on 22/12/2020 09:48:09
Showing1 changed files
... ...
@@ -183,7 +183,6 @@ export("grid.annotation_axis")
183 183
 export("grid.boxplot")
184 184
 export("grid.dendrogram")
185 185
 export("gt_render")
186
-export("heatmap.2")
187 186
 export("ht_global_opt")
188 187
 export("ht_opt")
189 188
 export("ht_size")
Browse code

move heatmap() as a private function

Zuguang Gu authored on 21/12/2020 16:03:30
Showing1 changed files
... ...
@@ -183,7 +183,6 @@ export("grid.annotation_axis")
183 183
 export("grid.boxplot")
184 184
 export("grid.dendrogram")
185 185
 export("gt_render")
186
-export("heatmap")
187 186
 export("heatmap.2")
188 187
 export("ht_global_opt")
189 188
 export("ht_opt")
Browse code

move code for interactive heatmap to InteractiveComplexHeatmap package

Zuguang Gu authored on 14/12/2020 08:38:56
Showing1 changed files
... ...
@@ -187,8 +187,6 @@ export("heatmap")
187 187
 export("heatmap.2")
188 188
 export("ht_global_opt")
189 189
 export("ht_opt")
190
-export("ht_pos_on_device")
191
-export("ht_shiny")
192 190
 export("ht_size")
193 191
 export("is_abs_unit")
194 192
 export("list_components")
... ...
@@ -212,8 +210,6 @@ export("row_anno_density")
212 210
 export("row_anno_histogram")
213 211
 export("row_anno_points")
214 212
 export("row_anno_text")
215
-export("selectArea")
216
-export("selectPosition")
217 213
 export("set_name")
218 214
 export("set_name<-")
219 215
 export("set_size")
Browse code

translate stats::heatmap() and gplots::heatmap.2()

Zuguang Gu authored on 13/12/2020 20:54:51
Showing1 changed files
... ...
@@ -154,6 +154,8 @@ export("columnAnnotation")
154 154
 export("comb_degree")
155 155
 export("comb_name")
156 156
 export("comb_size")
157
+export("compare_heatmap")
158
+export("compare_heatmap.2")
157 159
 export("compare_pheatmap")
158 160
 export("complement_size")
159 161
 export("decorate_annotation")
... ...
@@ -181,6 +183,8 @@ export("grid.annotation_axis")
181 183
 export("grid.boxplot")
182 184
 export("grid.dendrogram")
183 185
 export("gt_render")
186
+export("heatmap")
187
+export("heatmap.2")
184 188
 export("ht_global_opt")
185 189
 export("ht_opt")
186 190
 export("ht_pos_on_device")
Browse code

move S4vector to suggests

Zuguang Gu authored on 25/11/2020 14:04:09
Showing1 changed files
... ...
@@ -285,7 +285,6 @@ importFrom("GetoptLong", qqcat)
285 285
 importFrom("GlobalOptions", setGlobalOptions)
286 286
 importFrom("IRanges", "IntegerList")
287 287
 importFrom("RColorBrewer", brewer.pal)
288
-importFrom("S4Vectors", "DataFrame")
289 288
 importFrom("circlize", add_transparency)
290 289
 importFrom("circlize", colorRamp2)
291 290
 importFrom("circlize", rand_color)
Browse code

add functions to deal with genome-scale heatmaps

Zuguang Gu authored on 22/11/2020 20:40:20
Showing1 changed files
... ...
@@ -148,6 +148,7 @@ export("anno_summary")
148 148
 export("anno_text")
149 149
 export("anno_zoom")
150 150
 export("annotation_axis_grob")
151
+export("bin_genome")
151 152
 export("cluster_within_group")
152 153
 export("columnAnnotation")
153 154
 export("comb_degree")
... ...
@@ -193,6 +194,7 @@ export("max_text_height")
193 194
 export("max_text_width")
194 195
 export("merge_dendrogram")
195 196
 export("normalize_comb_mat")
197
+export("normalize_genomic_signals_to_bins")
196 198
 export("oncoPrint")
197 199
 export("order.comb_mat")
198 200
 export("packLegend")
Browse code

various improvements

Zuguang Gu authored on 23/10/2020 16:02:23
Showing1 changed files
... ...
@@ -238,6 +238,7 @@ export("SingleAnnotation")
238 238
 exportMethods("add_heatmap")
239 239
 exportMethods("adjust_heatmap_list")
240 240
 exportMethods("annotation_legend_size")
241
+exportMethods("attach_annotation")
241 242
 exportMethods("color_mapping_legend")
242 243
 exportMethods("column_dend")
243 244
 exportMethods("column_order")
Browse code

col argument can be a super set of the elements in the character matrix

Zuguang Gu authored on 20/10/2020 19:30:27
Showing1 changed files
... ...
@@ -275,6 +275,7 @@ import(matrixStats)
275 275
 import(methods)
276 276
 import(png)
277 277
 import(stats)
278
+importFrom("Cairo", "CairoPNG")
278 279
 importFrom("GetoptLong", qq)
279 280
 importFrom("GetoptLong", qq.options)
280 281
 importFrom("GetoptLong", qqcat)
... ...
@@ -297,5 +298,4 @@ importFrom("utils", "combn")
297 298
 importFrom("utils", "getFromNamespace")
298 299
 importFrom("utils", "packageDescription")
299 300
 importFrom("utils", "str")
300
-importFrom("Cairo", "CairoPNG")
301 301
 
Browse code

add imported functions

Zuguang Gu authored on 20/10/2020 13:21:50
Showing1 changed files
... ...
@@ -297,4 +297,5 @@ importFrom("utils", "combn")
297 297
 importFrom("utils", "getFromNamespace")
298 298
 importFrom("utils", "packageDescription")
299 299
 importFrom("utils", "str")
300
+importFrom("Cairo", "CairoPNG")
300 301
 
Browse code

pheatmap(): adjust the setting of color and breaks

simplifyEnrichment authored on 06/10/2020 12:07:17
Showing1 changed files
... ...
@@ -271,10 +271,10 @@ import(digest)
271 271
 import(grDevices)
272 272
 import(graphics)
273 273
 import(grid)
274
+import(matrixStats)
274 275
 import(methods)
275 276
 import(png)
276 277
 import(stats)
277
-import(matrixStats)
278 278
 importFrom("GetoptLong", qq)
279 279
 importFrom("GetoptLong", qq.options)
280 280
 importFrom("GetoptLong", qqcat)
Browse code

check NA in pheatmap()

Zuguang Gu authored on 09/09/2020 06:54:18
Showing1 changed files
... ...
@@ -274,6 +274,7 @@ import(grid)
274 274
 import(methods)
275 275
 import(png)
276 276
 import(stats)
277
+import(matrixStats)
277 278
 importFrom("GetoptLong", qq)
278 279
 importFrom("GetoptLong", qq.options)
279 280
 importFrom("GetoptLong", qqcat)
Browse code

anno_density(): add xlim argument

Zuguang Gu authored on 08/06/2020 09:53:31
Showing1 changed files
... ...
@@ -278,6 +278,7 @@ importFrom("GetoptLong", qq)
278 278
 importFrom("GetoptLong", qq.options)
279 279
 importFrom("GetoptLong", qqcat)
280 280
 importFrom("GlobalOptions", setGlobalOptions)
281
+importFrom("IRanges", "IntegerList")
281 282
 importFrom("RColorBrewer", brewer.pal)
282 283
 importFrom("S4Vectors", "DataFrame")
283 284
 importFrom("circlize", add_transparency)
... ...
@@ -295,4 +296,4 @@ importFrom("utils", "combn")
295 296
 importFrom("utils", "getFromNamespace")
296 297
 importFrom("utils", "packageDescription")
297 298
 importFrom("utils", "str")
298
-importFrom("IRanges", "IntegerList")
299
+
Browse code

export heatmaps as a shiny app

Zuguang Gu authored on 17/05/2020 13:20:00
Showing1 changed files
... ...
@@ -183,6 +183,7 @@ export("gt_render")
183 183
 export("ht_global_opt")
184 184
 export("ht_opt")
185 185
 export("ht_pos_on_device")
186
+export("ht_shiny")
186 187
 export("ht_size")
187 188
 export("is_abs_unit")
188 189
 export("list_components")
... ...
@@ -206,7 +207,6 @@ export("row_anno_histogram")
206 207
 export("row_anno_points")
207 208
 export("row_anno_text")
208 209
 export("selectArea")
209
-export("selectArea_shiny_demo")
210 210
 export("selectPosition")
211 211
 export("set_name")
212 212
 export("set_name<-")
... ...
@@ -267,6 +267,7 @@ exportMethods("row_order")
267 267
 exportMethods("set_component_height")
268 268
 exportMethods("set_component_width")
269 269
 
270
+import(digest)
270 271
 import(grDevices)
271 272
 import(graphics)
272 273
 import(grid)
... ...
@@ -278,6 +279,7 @@ importFrom("GetoptLong", qq.options)
278 279
 importFrom("GetoptLong", qqcat)
279 280
 importFrom("GlobalOptions", setGlobalOptions)
280 281
 importFrom("RColorBrewer", brewer.pal)
282
+importFrom("S4Vectors", "DataFrame")
281 283
 importFrom("circlize", add_transparency)
282 284
 importFrom("circlize", colorRamp2)
283 285
 importFrom("circlize", rand_color)
... ...
@@ -293,4 +295,4 @@ importFrom("utils", "combn")
293 295
 importFrom("utils", "getFromNamespace")
294 296
 importFrom("utils", "packageDescription")
295 297
 importFrom("utils", "str")
296
-
298
+importFrom("IRanges", "IntegerList")
Browse code

ht_list is saved into an environment

Zuguang Gu authored on 14/05/2020 11:48:03
Showing1 changed files
... ...
@@ -207,6 +207,7 @@ export("row_anno_points")
207 207
 export("row_anno_text")
208 208
 export("selectArea")
209 209
 export("selectArea_shiny_demo")
210
+export("selectPosition")
210 211
 export("set_name")
211 212
 export("set_name<-")
212 213
 export("set_size")
Browse code

add selectArea()

Zuguang Gu authored on 14/05/2020 06:36:17
Showing1 changed files
... ...
@@ -182,6 +182,7 @@ export("grid.dendrogram")
182 182
 export("gt_render")
183 183
 export("ht_global_opt")
184 184
 export("ht_opt")
185
+export("ht_pos_on_device")
185 186
 export("ht_size")
186 187
 export("is_abs_unit")
187 188
 export("list_components")
... ...
@@ -204,6 +205,8 @@ export("row_anno_density")
204 205
 export("row_anno_histogram")
205 206
 export("row_anno_points")
206 207
 export("row_anno_text")
208
+export("selectArea")
209
+export("selectArea_shiny_demo")
207 210
 export("set_name")
208 211
 export("set_name<-")
209 212
 export("set_size")
Browse code

update docs

Zuguang Gu authored on 13/05/2020 08:47:06
Showing1 changed files
... ...
@@ -182,6 +182,7 @@ export("grid.dendrogram")
182 182
 export("gt_render")
183 183
 export("ht_global_opt")
184 184
 export("ht_opt")
185
+export("ht_size")
185 186
 export("is_abs_unit")
186 187
 export("list_components")
187 188
 export("list_to_matrix")
Browse code

translate pheatmap to Heatmap

Zuguang Gu authored on 06/05/2020 07:21:34
Showing1 changed files
... ...
@@ -153,6 +153,7 @@ export("columnAnnotation")
153 153
 export("comb_degree")
154 154
 export("comb_name")
155 155
 export("comb_size")
156
+export("compare_pheatmap")
156 157
 export("complement_size")
157 158
 export("decorate_annotation")
158 159
 export("decorate_column_dend")
... ...
@@ -192,6 +193,7 @@ export("normalize_comb_mat")
192 193
 export("oncoPrint")
193 194
 export("order.comb_mat")
194 195
 export("packLegend")
196
+export("pheatmap")
195 197
 export("pindex")
196 198
 export("restore_matrix")
197 199
 export("rowAnnotation")
Browse code

update docs

Zuguang Gu authored on 14/04/2020 06:30:50
Showing1 changed files
... ...
@@ -199,7 +199,6 @@ export("row_anno_barplot")
199 199
 export("row_anno_boxplot")
200 200
 export("row_anno_density")
201 201
 export("row_anno_histogram")
202
-export("row_anno_link")
203 202
 export("row_anno_points")
204 203
 export("row_anno_text")
205 204
 export("set_name")
Browse code

add set_name<- method

Zuguang Gu authored on 08/04/2020 09:49:59
Showing1 changed files
... ...
@@ -203,6 +203,7 @@ export("row_anno_link")
203 203
 export("row_anno_points")
204 204
 export("row_anno_text")
205 205
 export("set_name")
206
+export("set_name<-")
206 207
 export("set_size")
207 208
 export("smartAlign2")
208 209
 export("subset_gp")
Browse code

improved subset method for comb_mat class

Zuguang Gu authored on 06/04/2020 13:08:25
Showing1 changed files
... ...
@@ -153,6 +153,7 @@ export("columnAnnotation")
153 153
 export("comb_degree")
154 154
 export("comb_name")
155 155
 export("comb_size")
156
+export("complement_size")
156 157
 export("decorate_annotation")
157 158
 export("decorate_column_dend")
158 159
 export("decorate_column_names")
Browse code

add 'alter_graphic()' function to automatically generate alteration graphic functions

Zuguang Gu authored on 03/04/2020 19:56:52
Showing1 changed files
... ...
@@ -128,6 +128,7 @@ export("Legends")
128 128
 export("SingleAnnotation")
129 129
 export("UpSet")
130 130
 export("adjust_dend_by_x")
131
+export("alter_graphic")
131 132
 export("anno_barplot")
132 133
 export("anno_block")
133 134
 export("anno_boxplot")
Browse code

improved upset plots

Zuguang Gu authored on 26/03/2020 20:10:50
Showing1 changed files
... ...
@@ -171,6 +171,7 @@ export("dendrogramGrob")
171 171
 export("densityHeatmap")
172 172
 export("dist2")
173 173
 export("extract_comb")
174
+export("full_comb_code")
174 175
 export("getXY_in_parent_vp")
175 176
 export("grid.annotation_axis")
176 177
 export("grid.boxplot")
Browse code

support gridtext

Zuguang Gu authored on 21/03/2020 14:32:08
Showing1 changed files
... ...
@@ -12,6 +12,8 @@ S3method("[", "SingleAnnotation")
12 12
 export("[.SingleAnnotation")
13 13
 S3method("[", "comb_mat")
14 14
 export("[.comb_mat")
15
+S3method("[", "gridtext")
16
+export("[.gridtext")
15 17
 S3method("c", "ColorMapping")
16 18
 export("c.ColorMapping")
17 19
 S3method("c", "HeatmapAnnotation")
... ...
@@ -173,6 +175,7 @@ export("getXY_in_parent_vp")
173 175
 export("grid.annotation_axis")
174 176
 export("grid.boxplot")
175 177
 export("grid.dendrogram")
178
+export("gt_render")
176 179
 export("ht_global_opt")
177 180
 export("ht_opt")
178 181
 export("is_abs_unit")
Browse code

remove show generics

Zuguang Gu authored on 07/08/2019 07:51:05
Showing1 changed files
... ...
@@ -12,6 +12,8 @@ S3method("[", "SingleAnnotation")
12 12
 export("[.SingleAnnotation")
13 13
 S3method("[", "comb_mat")
14 14
 export("[.comb_mat")
15
+S3method("c", "ColorMapping")
16
+export("c.ColorMapping")
15 17
 S3method("c", "HeatmapAnnotation")
16 18
 export("c.HeatmapAnnotation")
17 19
 S3method("dim", "Heatmap")
Browse code

support reverse axes for annotations

Zuguang Gu authored on 18/04/2019 09:52:51
Showing1 changed files
... ...
@@ -256,8 +256,8 @@ import(grDevices)
256 256
 import(graphics)
257 257
 import(grid)
258 258
 import(methods)
259
-import(stats)
260 259
 import(png)
260
+import(stats)
261 261
 importFrom("GetoptLong", qq)
262 262
 importFrom("GetoptLong", qq.options)
263 263
 importFrom("GetoptLong", qqcat)
Browse code

move png to Imports field

Zuguang Gu authored on 29/03/2019 08:28:36
Showing1 changed files
... ...
@@ -257,6 +257,7 @@ import(graphics)
257 257
 import(grid)
258 258
 import(methods)
259 259
 import(stats)
260
+import(png)
260 261
 importFrom("GetoptLong", qq)
261 262
 importFrom("GetoptLong", qq.options)
262 263
 importFrom("GetoptLong", qqcat)
Browse code

gp in anno_text() supports fill and border

Zuguang Gu authored on 24/03/2019 22:20:59
Showing1 changed files
... ...
@@ -185,6 +185,7 @@ export("oncoPrint")
185 185
 export("order.comb_mat")
186 186
 export("packLegend")
187 187
 export("pindex")
188
+export("restore_matrix")
188 189
 export("rowAnnotation")
189 190
 export("row_anno_barplot")
190 191
 export("row_anno_boxplot")
Browse code

show_heatmap_legend is set to FALSE if rect_gp = gpar(type = 'none')

Zuguang Gu authored on 23/03/2019 16:18:16
Showing1 changed files
... ...
@@ -78,6 +78,8 @@ S3method("size<-", "HeatmapAnnotation")
78 78
 export("size<-.HeatmapAnnotation")
79 79
 S3method("size<-", "SingleAnnotation")
80 80
 export("size<-.SingleAnnotation")
81
+S3method("str", "comb_mat")
82
+export("str.comb_mat")
81 83
 S3method("summary", "Heatmap")
82 84
 export("summary.Heatmap")
83 85
 S3method("summary", "HeatmapList")
Browse code

add consensus k-means

jokergoo authored on 22/03/2019 15:02:46
Showing1 changed files
... ...
@@ -263,6 +263,10 @@ importFrom("circlize", add_transparency)
263 263
 importFrom("circlize", colorRamp2)
264 264
 importFrom("circlize", rand_color)
265 265
 importFrom("circlize", smartAlign)
266
+importFrom("clue", as.cl_hard_partition)
267
+importFrom("clue", cl_class_ids)
268
+importFrom("clue", cl_consensus)
269
+importFrom("clue", cl_ensemble)
266 270
 importFrom("colorspace", diverge_hcl)
267 271
 importFrom("colorspace", rainbow_hcl)
268 272
 importFrom("parallel", "mclapply")
... ...
@@ -270,7 +274,4 @@ importFrom("utils", "combn")
270 274
 importFrom("utils", "getFromNamespace")
271 275
 importFrom("utils", "packageDescription")
272 276
 importFrom("utils", "str")
273
-importFrom("clue", as.cl_hard_partition)
274
-importFrom("clue", cl_ensemble)
275
-importFrom("clue", cl_consensus)
276
-importFrom("clue", cl_class_ids)
277
+
Browse code

run multiple times k-means to get a consensus partition

jokergoo authored on 22/03/2019 10:40:01
Showing1 changed files
... ...
@@ -270,4 +270,7 @@ importFrom("utils", "combn")
270 270
 importFrom("utils", "getFromNamespace")
271 271
 importFrom("utils", "packageDescription")
272 272
 importFrom("utils", "str")
273
-
273
+importFrom("clue", as.cl_hard_partition)
274
+importFrom("clue", cl_ensemble)
275
+importFrom("clue", cl_consensus)
276
+importFrom("clue", cl_class_ids)
Browse code

add test script for the heatmap annotation size

jokergoo authored on 15/03/2019 13:47:43
Showing1 changed files
... ...
@@ -265,8 +265,9 @@ importFrom("circlize", rand_color)
265 265
 importFrom("circlize", smartAlign)
266 266
 importFrom("colorspace", diverge_hcl)
267 267
 importFrom("colorspace", rainbow_hcl)
268
+importFrom("parallel", "mclapply")
268 269
 importFrom("utils", "combn")
269 270
 importFrom("utils", "getFromNamespace")
270 271
 importFrom("utils", "packageDescription")
271 272
 importFrom("utils", "str")
272
-importFrom("parallel", "mclapply")
273
+
Browse code

add mc.cores in densityHeatmap()

Zuguang Gu authored on 13/03/2019 17:39:11
Showing1 changed files
... ...
@@ -269,4 +269,4 @@ importFrom("utils", "combn")
269 269
 importFrom("utils", "getFromNamespace")
270 270
 importFrom("utils", "packageDescription")
271 271
 importFrom("utils", "str")
272
-
272
+importFrom("parallel", "mclapply")
Browse code

add test_alter_fun()

Zuguang Gu authored on 31/01/2019 10:36:07
Showing1 changed files
... ...
@@ -197,6 +197,7 @@ export("smartAlign2")
197 197
 export("subset_gp")
198 198
 export("subset_matrix_by_row")
199 199
 export("subset_vector")
200
+export("test_alter_fun")
200 201
 export("unify_mat_list")
201 202
 export("upset_right_annotation")
202 203
 export("upset_top_annotation")
Browse code

minor fix

Zuguang Gu authored on 29/12/2018 15:24:39
Showing1 changed files
... ...
@@ -159,8 +159,6 @@ export("decorate_row_title")
159 159
 export("decorate_title")
160 160
 export("default_axis_param")
161 161
 export("default_get_type")
162
-export("default_upset_right_annotation")
163
-export("default_upset_top_annotation")
164 162
 export("dend_heights")
165 163
 export("dend_xy")
166 164
 export("dendrogramGrob")
... ...
@@ -180,7 +178,9 @@ export("make_comb_mat")
180 178
 export("max_text_height")
181 179
 export("max_text_width")
182 180
 export("merge_dendrogram")
181
+export("normalize_comb_mat")
183 182
 export("oncoPrint")
183
+export("order.comb_mat")
184 184
 export("packLegend")
185 185
 export("pindex")
186 186
 export("rowAnnotation")
... ...
@@ -198,6 +198,8 @@ export("subset_gp")
198 198
 export("subset_matrix_by_row")
199 199
 export("subset_vector")
200 200
 export("unify_mat_list")
201
+export("upset_right_annotation")
202
+export("upset_top_annotation")
201 203
 exportClasses("AdditiveUnit")
202 204
 export("AdditiveUnit")
203 205
 exportClasses("AnnotationFunction")
Browse code

documentation for UpSet() finished

Zuguang Gu authored on 27/12/2018 12:09:22
Showing1 changed files
... ...
@@ -159,6 +159,8 @@ export("decorate_row_title")
159 159
 export("decorate_title")
160 160
 export("default_axis_param")
161 161
 export("default_get_type")
162
+export("default_upset_right_annotation")
163
+export("default_upset_top_annotation")
162 164
 export("dend_heights")
163 165
 export("dend_xy")
164 166
 export("dendrogramGrob")
Browse code

add documentations

Zuguang Gu authored on 26/12/2018 15:16:45
Showing1 changed files
... ...
@@ -10,6 +10,8 @@ S3method("[", "HeatmapList")
10 10
 export("[.HeatmapList")
11 11
 S3method("[", "SingleAnnotation")
12 12
 export("[.SingleAnnotation")
13
+S3method("[", "comb_mat")
14
+export("[.comb_mat")
13 15
 S3method("c", "HeatmapAnnotation")
14 16
 export("c.HeatmapAnnotation")
15 17
 S3method("dim", "Heatmap")
... ...
@@ -62,6 +64,8 @@ S3method("nobs", "SingleAnnotation")
62 64
 export("nobs.SingleAnnotation")
63 65
 S3method("nrow", "Heatmap")
64 66
 export("nrow.Heatmap")
67
+S3method("print", "comb_mat")
68
+export("print.comb_mat")
65 69
 S3method("size", "AnnotationFunction")
66 70
 export("size.AnnotationFunction")
67 71
 S3method("size", "HeatmapAnnotation")
... ...
@@ -78,6 +82,8 @@ S3method("summary", "Heatmap")
78 82
 export("summary.Heatmap")
79 83
 S3method("summary", "HeatmapList")
80 84
 export("summary.HeatmapList")
85
+S3method("t", "comb_mat")
86
+export("t.comb_mat")
81 87
 S3method("width", "AnnotationFunction")
82 88
 export("width.AnnotationFunction")
83 89
 S3method("width", "Heatmap")
... ...
@@ -114,6 +120,7 @@ export("HeatmapList")
114 120
 export("Legend")
115 121
 export("Legends")
116 122
 export("SingleAnnotation")
123
+export("UpSet")
117 124
 export("adjust_dend_by_x")
118 125
 export("anno_barplot")
119 126
 export("anno_block")
... ...
@@ -136,6 +143,9 @@ export("anno_zoom")
136 143
 export("annotation_axis_grob")
137 144
 export("cluster_within_group")
138 145
 export("columnAnnotation")
146
+export("comb_degree")
147
+export("comb_name")
148
+export("comb_size")
139 149
 export("decorate_annotation")
140 150
 export("decorate_column_dend")
141 151
 export("decorate_column_names")
... ...
@@ -154,6 +164,7 @@ export("dend_xy")
154 164
 export("dendrogramGrob")
155 165
 export("densityHeatmap")
156 166
 export("dist2")
167
+export("extract_comb")
157 168
 export("getXY_in_parent_vp")
158 169
 export("grid.annotation_axis")
159 170
 export("grid.boxplot")
... ...
@@ -162,6 +173,8 @@ export("ht_global_opt")
162 173
 export("ht_opt")
163 174
 export("is_abs_unit")
164 175
 export("list_components")
176
+export("list_to_matrix")
177
+export("make_comb_mat")
165 178
 export("max_text_height")
166 179
 export("max_text_width")
167 180
 export("merge_dendrogram")
... ...
@@ -176,6 +189,8 @@ export("row_anno_histogram")
176 189
 export("row_anno_link")
177 190
 export("row_anno_points")
178 191
 export("row_anno_text")
192
+export("set_name")
193
+export("set_size")
179 194
 export("smartAlign2")
180 195
 export("subset_gp")
181 196
 export("subset_matrix_by_row")
... ...
@@ -245,6 +260,7 @@ importFrom("circlize", rand_color)
245 260
 importFrom("circlize", smartAlign)
246 261
 importFrom("colorspace", diverge_hcl)
247 262
 importFrom("colorspace", rainbow_hcl)
263
+importFrom("utils", "combn")
248 264
 importFrom("utils", "getFromNamespace")
249 265
 importFrom("utils", "packageDescription")
250 266
 importFrom("utils", "str")
Browse code

add smartAlign2()

Zuguang Gu authored on 13/12/2018 11:37:32
Showing1 changed files
... ...
@@ -176,6 +176,7 @@ export("row_anno_histogram")
176 176
 export("row_anno_link")
177 177
 export("row_anno_points")
178 178
 export("row_anno_text")
179
+export("smartAlign2")
179 180
 export("subset_gp")
180 181
 export("subset_matrix_by_row")
181 182
 export("subset_vector")
Browse code

add anno_zoom()

Zuguang Gu authored on 12/12/2018 21:54:43
Showing1 changed files
... ...
@@ -132,6 +132,7 @@ export("anno_points")
132 132
 export("anno_simple")
133 133
 export("anno_summary")
134 134
 export("anno_text")
135
+export("anno_zoom")
135 136
 export("annotation_axis_grob")
136 137
 export("cluster_within_group")
137 138
 export("columnAnnotation")
... ...
@@ -147,6 +148,7 @@ export("decorate_row_names")
147 148
 export("decorate_row_title")
148 149
 export("decorate_title")
149 150
 export("default_axis_param")
151
+export("default_get_type")
150 152
 export("dend_heights")
151 153
 export("dend_xy")
152 154
 export("dendrogramGrob")
Browse code

vignettes added

Zuguang Gu authored on 30/10/2018 22:32:01
Showing1 changed files
... ...
@@ -153,6 +153,7 @@ export("dendrogramGrob")
153 153
 export("densityHeatmap")
154 154
 export("dist2")
155 155
 export("getXY_in_parent_vp")
156
+export("grid.annotation_axis")
156 157
 export("grid.boxplot")
157 158
 export("grid.dendrogram")
158 159
 export("ht_global_opt")
Browse code

documentation checked

Zuguang Gu authored on 23/10/2018 19:59:12
Showing1 changed files
... ...
@@ -18,8 +18,12 @@ S3method("grid.draw", "Legends")
18 18
 export("grid.draw.Legends")
19 19
 S3method("height", "AnnotationFunction")
20 20
 export("height.AnnotationFunction")
21
+S3method("height", "Heatmap")
22
+export("height.Heatmap")
21 23
 S3method("height", "HeatmapAnnotation")
22 24
 export("height.HeatmapAnnotation")
25
+S3method("height", "HeatmapList")
26
+export("height.HeatmapList")
23 27
 S3method("height", "Legends")
24 28
 export("height.Legends")
25 29
 S3method("height", "SingleAnnotation")
... ...
@@ -72,10 +76,16 @@ S3method("size<-", "SingleAnnotation")
72 76
 export("size<-.SingleAnnotation")
73 77
 S3method("summary", "Heatmap")
74 78
 export("summary.Heatmap")
79
+S3method("summary", "HeatmapList")
80
+export("summary.HeatmapList")
75 81
 S3method("width", "AnnotationFunction")
76 82
 export("width.AnnotationFunction")
83
+S3method("width", "Heatmap")
84
+export("width.Heatmap")
77 85
 S3method("width", "HeatmapAnnotation")
78 86
 export("width.HeatmapAnnotation")
87
+S3method("width", "HeatmapList")
88
+export("width.HeatmapList")
79 89
 S3method("width", "Legends")
80 90
 export("width.Legends")
81 91
 S3method("width", "SingleAnnotation")
... ...
@@ -125,7 +135,6 @@ export("anno_text")
125 135
 export("annotation_axis_grob")
126 136
 export("cluster_within_group")
127 137
 export("columnAnnotation")
128
-export("convertXY_in_vp")
129 138
 export("decorate_annotation")
130 139
 export("decorate_column_dend")
131 140
 export("decorate_column_names")
... ...
@@ -143,6 +152,7 @@ export("dend_xy")
143 152
 export("dendrogramGrob")
144 153
 export("densityHeatmap")
145 154
 export("dist2")
155
+export("getXY_in_parent_vp")
146 156
 export("grid.boxplot")
147 157
 export("grid.dendrogram")
148 158
 export("ht_global_opt")
Browse code

update

Zuguang Gu authored on 22/10/2018 05:57:29
Showing1 changed files
... ...
@@ -145,8 +145,6 @@ export("densityHeatmap")
145 145
 export("dist2")
146 146
 export("grid.boxplot")
147 147
 export("grid.dendrogram")
148
-export("height")
149
-export("height<-")
150 148
 export("ht_global_opt")
151 149
 export("ht_opt")
152 150
 export("is_abs_unit")
... ...
@@ -165,14 +163,10 @@ export("row_anno_histogram")
165 163
 export("row_anno_link")
166 164
 export("row_anno_points")
167 165
 export("row_anno_text")
168
-export("size")
169
-export("size<-")
170 166
 export("subset_gp")
171 167
 export("subset_matrix_by_row")
172 168
 export("subset_vector")
173 169
 export("unify_mat_list")
174
-export("width")
175
-export("width<-")
176 170
 exportClasses("AdditiveUnit")
177 171
 export("AdditiveUnit")
178 172
 exportClasses("AnnotationFunction")
... ...
@@ -215,7 +209,7 @@ exportMethods("make_layout")
215 209
 exportMethods("make_row_cluster")
216 210
 exportMethods("map_to_colors")
217 211
 exportMethods("prepare")
218
-exportMethods("resize")
212
+exportMethods("re_size")
219 213
 exportMethods("row_dend")
220 214
 exportMethods("row_order")
221 215
 exportMethods("set_component_height")
Browse code

fix some bugs

Zuguang Gu authored on 19/10/2018 19:08:59
Showing1 changed files
... ...
@@ -106,6 +106,7 @@ export("Legends")
106 106
 export("SingleAnnotation")
107 107
 export("adjust_dend_by_x")
108 108
 export("anno_barplot")
109
+export("anno_block")
109 110
 export("anno_boxplot")
110 111
 export("anno_density")
111 112
 export("anno_empty")
Browse code

update

Zuguang Gu authored on 17/10/2018 06:09:36
Showing1 changed files
... ...
@@ -149,7 +149,7 @@ export("height<-")
149 149
 export("ht_global_opt")
150 150
 export("ht_opt")
151 151
 export("is_abs_unit")
152
-export("list_component")
152
+export("list_components")
153 153
 export("max_text_height")
154 154
 export("max_text_width")
155 155
 export("merge_dendrogram")
Browse code

update

Zuguang Gu authored on 16/10/2018 05:54:05
Showing1 changed files
... ...
@@ -42,8 +42,6 @@ S3method("length", "HeatmapAnnotation")
42 42
 export("length.HeatmapAnnotation")
43 43
 S3method("length", "HeatmapList")
44 44
 export("length.HeatmapList")
45
-S3method("merge", "dendrogram")
46
-export("merge.dendrogram")
47 45
 S3method("names", "HeatmapAnnotation")
48 46
 export("names.HeatmapAnnotation")
49 47
 S3method("names", "HeatmapList")
... ...
@@ -154,6 +152,7 @@ export("is_abs_unit")
154 152
 export("list_component")
155 153
 export("max_text_height")
156 154
 export("max_text_width")
155
+export("merge_dendrogram")
157 156
 export("oncoPrint")
158 157
 export("packLegend")
159 158
 export("pindex")
Browse code

update

jokergoo authored on 12/10/2018 15:28:37
Showing1 changed files
... ...
@@ -6,6 +6,8 @@ S3method("[", "Heatmap")
6 6
 export("[.Heatmap")
7 7
 S3method("[", "HeatmapAnnotation")
8 8
 export("[.HeatmapAnnotation")
9
+S3method("[", "HeatmapList")
10
+export("[.HeatmapList")
9 11
 S3method("[", "SingleAnnotation")
10 12
 export("[.SingleAnnotation")
11 13
 S3method("c", "HeatmapAnnotation")
... ...
@@ -38,10 +40,14 @@ S3method("heightDetails", "packed_legends")
38 40
 export("heightDetails.packed_legends")
39 41
 S3method("length", "HeatmapAnnotation")
40 42
 export("length.HeatmapAnnotation")
43
+S3method("length", "HeatmapList")
44
+export("length.HeatmapList")
41 45
 S3method("merge", "dendrogram")
42 46
 export("merge.dendrogram")
43 47
 S3method("names", "HeatmapAnnotation")
44 48
 export("names.HeatmapAnnotation")
49
+S3method("names", "HeatmapList")
50
+export("names.HeatmapList")
45 51
 S3method("names<-", "HeatmapAnnotation")
46 52
 export("names<-.HeatmapAnnotation")
47 53
 S3method("ncol", "Heatmap")
... ...
@@ -115,7 +121,9 @@ export("anno_mark")
115 121
 export("anno_oncoprint_barplot")
116 122
 export("anno_points")
117 123
 export("anno_simple")
124
+export("anno_summary")
118 125
 export("anno_text")
126
+export("annotation_axis_grob")
119 127
 export("cluster_within_group")
120 128
 export("columnAnnotation")
121 129
 export("convertXY_in_vp")
... ...
@@ -136,12 +144,14 @@ export("dend_xy")
136 144
 export("dendrogramGrob")
137 145
 export("densityHeatmap")
138 146
 export("dist2")
147
+export("grid.boxplot")
139 148
 export("grid.dendrogram")
140 149
 export("height")
141 150
 export("height<-")
142 151
 export("ht_global_opt")
143 152
 export("ht_opt")
144 153
 export("is_abs_unit")
154
+export("list_component")
145 155
 export("max_text_height")
146 156
 export("max_text_width")
147 157
 export("oncoPrint")
Browse code

oncoPrint is vectorized

Zuguang Gu authored on 25/09/2018 07:59:43
Showing1 changed files
... ...
@@ -118,6 +118,7 @@ export("anno_simple")
118 118
 export("anno_text")
119 119
 export("cluster_within_group")
120 120
 export("columnAnnotation")
121
+export("convertXY_in_vp")
121 122
 export("decorate_annotation")
122 123
 export("decorate_column_dend")
123 124
 export("decorate_column_names")
... ...
@@ -145,6 +146,7 @@ export("max_text_height")
145 146
 export("max_text_width")
146 147
 export("oncoPrint")
147 148
 export("packLegend")
149
+export("pindex")
148 150
 export("rowAnnotation")
149 151
 export("row_anno_barplot")
150 152
 export("row_anno_boxplot")
Browse code

vignette check passed

Zuguang Gu authored on 20/09/2018 22:09:48
Showing1 changed files
... ...
@@ -28,6 +28,14 @@ S3method("height<-", "HeatmapAnnotation")
28 28
 export("height<-.HeatmapAnnotation")
29 29
 S3method("height<-", "SingleAnnotation")
30 30
 export("height<-.SingleAnnotation")
31
+S3method("heightDetails", "annotation_axis")
32
+export("heightDetails.annotation_axis")
33
+S3method("heightDetails", "legend")
34
+export("heightDetails.legend")
35
+S3method("heightDetails", "legend_body")
36
+export("heightDetails.legend_body")
37
+S3method("heightDetails", "packed_legends")
38
+export("heightDetails.packed_legends")
31 39
 S3method("length", "HeatmapAnnotation")
32 40
 export("length.HeatmapAnnotation")
33 41
 S3method("merge", "dendrogram")
... ...
@@ -74,6 +82,14 @@ S3method("width<-", "HeatmapAnnotation")
74 82
 export("width<-.HeatmapAnnotation")
75 83
 S3method("width<-", "SingleAnnotation")
76 84
 export("width<-.SingleAnnotation")
85
+S3method("widthDetails", "annotation_axis")
86
+export("widthDetails.annotation_axis")
87
+S3method("widthDetails", "legend")
88
+export("widthDetails.legend")
89
+S3method("widthDetails", "legend_body")
90
+export("widthDetails.legend_body")
91
+S3method("widthDetails", "packed_legends")
92
+export("widthDetails.packed_legends")
77 93
 export("%v%")
78 94
 export("AdditiveUnit")
79 95
 export("AnnotationFunction")
Browse code

R CMD check passed

Zuguang Gu authored on 20/09/2018 12:48:08
Showing1 changed files
... ...
@@ -1,100 +1,197 @@
1
-export('+.AdditiveUnit')
2
-export('grid.dendrogram')
3
-export('grid.dendrogram2')
4
-export(AdditiveUnit)
5
-export(ColorMapping)
6
-export(Heatmap)
7
-export(HeatmapAnnotation)
8
-export(HeatmapList)
9
-export(Legend)
10
-export(SingleAnnotation)
11
-export(adjust_dend_by_leaf_width)
12
-export(anno_barplot)
13
-export(anno_boxplot)
14
-export(anno_density)
15
-export(anno_histogram)
16
-export(anno_link)
17
-export(anno_oncoprint_barplot)
18
-export(anno_points)
19
-export(anno_text)
20
-export(columnAnnotation)
21
-export(column_anno_barplot)
22
-export(column_anno_boxplot)
23
-export(column_anno_density)
24
-export(column_anno_histogram)
25
-export(column_anno_link)
26
-export(column_anno_points)
27
-export(column_anno_text)
28
-export(decorate_annotation)
29
-export(decorate_column_dend)
30
-export(decorate_column_names)
31
-export(decorate_column_title)
32
-export(decorate_dend)
33
-export(decorate_dimnames)
34
-export(decorate_heatmap_body)
35
-export(decorate_row_dend)
36
-export(decorate_row_names)
37
-export(decorate_row_title)
38
-export(decorate_title)
39
-export(densityHeatmap)
40
-export(dist2)
41
-export(enhanced_basicplot)
42
-export(ht_global_opt)
43
-export(is_abs_unit)
44
-export(max_text_height)
45
-export(max_text_width)
46
-export(oncoPrint)
47
-export(packLegend)
48
-export(plotDataFrame)
49
-export(rowAnnotation)
50
-export(row_anno_barplot)
51
-export(row_anno_boxplot)
52
-export(row_anno_density)
53
-export(row_anno_histogram)
54
-export(row_anno_link)
55
-export(row_anno_points)
56
-export(row_anno_text)
57
-export(selectArea)
58
-export(unify_mat_list)
59
-exportClasses(AdditiveUnit)
60
-export(AdditiveUnit)
61
-exportClasses(ColorMapping)
62
-export(ColorMapping)
63
-exportClasses(Heatmap)
64
-export(Heatmap)
65
-exportClasses(HeatmapAnnotation)
66
-export(HeatmapAnnotation)
67
-exportClasses(HeatmapList)
68
-export(HeatmapList)
69
-exportClasses(SingleAnnotation)
70
-export(SingleAnnotation)
71
-exportMethods(add_heatmap)
72
-exportMethods(annotation_legend_size)
73
-exportMethods(color_mapping_legend)
74
-exportMethods(column_dend)
75
-exportMethods(column_order)
76
-exportMethods(component_height)
77
-exportMethods(component_width)
78
-exportMethods(draw)
79
-exportMethods(draw_annotation)
80
-exportMethods(draw_annotation_legend)
81
-exportMethods(draw_dend)
82
-exportMethods(draw_dimnames)
83
-exportMethods(draw_heatmap_body)
84
-exportMethods(draw_heatmap_legend)
85
-exportMethods(draw_heatmap_list)
86
-exportMethods(draw_title)
87
-exportMethods(get_color_mapping_list)
88
-exportMethods(get_color_mapping_param_list)
89
-exportMethods(heatmap_legend_size)
90
-exportMethods(make_column_cluster)
91
-exportMethods(make_layout)
92
-exportMethods(make_row_cluster)
93
-exportMethods(map_to_colors)
94
-exportMethods(prepare)
95
-exportMethods(row_dend)
96
-exportMethods(row_order)
97
-exportMethods(set_component_height)
1
+S3method("+", "AdditiveUnit")
2
+export("+.AdditiveUnit")
3
+S3method("[", "AnnotationFunction")
4
+export("[.AnnotationFunction")
5
+S3method("[", "Heatmap")
6
+export("[.Heatmap")
7
+S3method("[", "HeatmapAnnotation")
8
+export("[.HeatmapAnnotation")
9
+S3method("[", "SingleAnnotation")
10
+export("[.SingleAnnotation")
11
+S3method("c", "HeatmapAnnotation")
12
+export("c.HeatmapAnnotation")
13
+S3method("dim", "Heatmap")
14
+export("dim.Heatmap")
15
+S3method("grid.draw", "Legends")
16
+export("grid.draw.Legends")
17
+S3method("height", "AnnotationFunction")
18
+export("height.AnnotationFunction")
19
+S3method("height", "HeatmapAnnotation")
20
+export("height.HeatmapAnnotation")
21
+S3method("height", "Legends")
22
+export("height.Legends")
23
+S3method("height", "SingleAnnotation")
24
+export("height.SingleAnnotation")
25
+S3method("height<-", "AnnotationFunction")
26
+export("height<-.AnnotationFunction")
27
+S3method("height<-", "HeatmapAnnotation")
28
+export("height<-.HeatmapAnnotation")
29
+S3method("height<-", "SingleAnnotation")
30
+export("height<-.SingleAnnotation")
31
+S3method("length", "HeatmapAnnotation")
32
+export("length.HeatmapAnnotation")
33
+S3method("merge", "dendrogram")
34
+export("merge.dendrogram")
35
+S3method("names", "HeatmapAnnotation")
36
+export("names.HeatmapAnnotation")
37
+S3method("names<-", "HeatmapAnnotation")
38
+export("names<-.HeatmapAnnotation")
39
+S3method("ncol", "Heatmap")
40
+export("ncol.Heatmap")
41
+S3method("nobs", "AnnotationFunction")
42
+export("nobs.AnnotationFunction")
43
+S3method("nobs", "HeatmapAnnotation")
44
+export("nobs.HeatmapAnnotation")
45
+S3method("nobs", "SingleAnnotation")
46
+export("nobs.SingleAnnotation")
47
+S3method("nrow", "Heatmap")
48
+export("nrow.Heatmap")
49
+S3method("size", "AnnotationFunction")
50
+export("size.AnnotationFunction")
51
+S3method("size", "HeatmapAnnotation")
52
+export("size.HeatmapAnnotation")
53
+S3method("size", "SingleAnnotation")
54
+export("size.SingleAnnotation")
55
+S3method("size<-", "AnnotationFunction")
56
+export("size<-.AnnotationFunction")
57
+S3method("size<-", "HeatmapAnnotation")
58
+export("size<-.HeatmapAnnotation")
59
+S3method("size<-", "SingleAnnotation")
60
+export("size<-.SingleAnnotation")
61
+S3method("summary", "Heatmap")
62
+export("summary.Heatmap")
63
+S3method("width", "AnnotationFunction")
64
+export("width.AnnotationFunction")
65
+S3method("width", "HeatmapAnnotation")
66
+export("width.HeatmapAnnotation")
67
+S3method("width", "Legends")
68
+export("width.Legends")
69
+S3method("width", "SingleAnnotation")
70
+export("width.SingleAnnotation")
71
+S3method("width<-", "AnnotationFunction")
72
+export("width<-.AnnotationFunction")
73
+S3method("width<-", "HeatmapAnnotation")
74
+export("width<-.HeatmapAnnotation")
75
+S3method("width<-", "SingleAnnotation")
76
+export("width<-.SingleAnnotation")
77
+export("%v%")
78
+export("AdditiveUnit")
79
+export("AnnotationFunction")
80
+export("ColorMapping")
81
+export("Heatmap")
82
+export("HeatmapAnnotation")
83
+export("HeatmapList")
84
+export("Legend")
85
+export("Legends")
86
+export("SingleAnnotation")
87
+export("adjust_dend_by_x")
88
+export("anno_barplot")
89
+export("anno_boxplot")
90
+export("anno_density")
91
+export("anno_empty")
92
+export("anno_histogram")
93
+export("anno_horizon")
94
+export("anno_image")
95
+export("anno_joyplot")
96
+export("anno_lines")
97
+export("anno_link")
98
+export("anno_mark")
99
+export("anno_oncoprint_barplot")
100
+export("anno_points")
101
+export("anno_simple")
102
+export("anno_text")
103
+export("cluster_within_group")
104
+export("columnAnnotation")
105
+export("decorate_annotation")
106
+export("decorate_column_dend")
107
+export("decorate_column_names")
108
+export("decorate_column_title")
109
+export("decorate_dend")
110
+export("decorate_dimnames")
111
+export("decorate_heatmap_body")
112
+export("decorate_row_dend")
113
+export("decorate_row_names")
114
+export("decorate_row_title")
115
+export("decorate_title")
116
+export("default_axis_param")
117
+export("dend_heights")
118
+export("dend_xy")
119
+export("dendrogramGrob")
120
+export("densityHeatmap")
121
+export("dist2")
122
+export("grid.dendrogram")
123
+export("height")
124
+export("height<-")
125
+export("ht_global_opt")
126
+export("ht_opt")
127
+export("is_abs_unit")
128
+export("max_text_height")
129
+export("max_text_width")
130
+export("oncoPrint")
131
+export("packLegend")
132
+export("rowAnnotation")
133
+export("row_anno_barplot")
134
+export("row_anno_boxplot")
135
+export("row_anno_density")
136
+export("row_anno_histogram")
137
+export("row_anno_link")
138
+export("row_anno_points")
139
+export("row_anno_text")
140
+export("size")
141
+export("size<-")
142
+export("subset_gp")
143
+export("subset_matrix_by_row")
144
+export("subset_vector")
145
+export("unify_mat_list")
146
+export("width")
147
+export("width<-")
148
+exportClasses("AdditiveUnit")
149
+export("AdditiveUnit")
150
+exportClasses("AnnotationFunction")
151
+export("AnnotationFunction")
152
+exportClasses("ColorMapping")
153
+export("ColorMapping")
154
+exportClasses("Heatmap")
155
+export("Heatmap")
156
+exportClasses("HeatmapAnnotation")
157
+export("HeatmapAnnotation")
158
+exportClasses("HeatmapList")
159
+export("HeatmapList")
160
+exportClasses("Legends")
161
+export("Legends")
162
+exportClasses("SingleAnnotation")
163
+export("SingleAnnotation")
164
+exportMethods("add_heatmap")
165
+exportMethods("adjust_heatmap_list")
166
+exportMethods("annotation_legend_size")
167
+exportMethods("color_mapping_legend")
168
+exportMethods("column_dend")
169
+exportMethods("column_order")
170
+exportMethods("component_height")
171
+exportMethods("component_width")
172
+exportMethods("copy_all")
173
+exportMethods("draw")
174
+exportMethods("draw_annotation")
175
+exportMethods("draw_annotation_legend")
176
+exportMethods("draw_dend")
177
+exportMethods("draw_dimnames")
178
+exportMethods("draw_heatmap_body")
179
+exportMethods("draw_heatmap_legend")
180
+exportMethods("draw_heatmap_list")
181
+exportMethods("draw_title")
182
+exportMethods("get_color_mapping_list")
183
+exportMethods("get_legend_param_list")
184
+exportMethods("heatmap_legend_size")
185
+exportMethods("make_column_cluster")
186
+exportMethods("make_layout")
187
+exportMethods("make_row_cluster")
188
+exportMethods("map_to_colors")
189
+exportMethods("prepare")
190
+exportMethods("resize")
191
+exportMethods("row_dend")
192
+exportMethods("row_order")
193
+exportMethods("set_component_height")
194
+exportMethods("set_component_width")
98 195
 
99 196
 import(grDevices)
100 197
 import(graphics)
... ...
@@ -106,6 +203,7 @@ importFrom("GetoptLong", qq.options)
106 203
 importFrom("GetoptLong", qqcat)
107 204
 importFrom("GlobalOptions", setGlobalOptions)
108 205
 importFrom("RColorBrewer", brewer.pal)
206
+importFrom("circlize", add_transparency)
109 207
 importFrom("circlize", colorRamp2)
110 208
 importFrom("circlize", rand_color)
111 209
 importFrom("circlize", smartAlign)
... ...
@@ -113,4 +211,5 @@ importFrom("colorspace", diverge_hcl)
113 211
 importFrom("colorspace", rainbow_hcl)
114 212
 importFrom("utils", "getFromNamespace")
115 213
 importFrom("utils", "packageDescription")
214
+importFrom("utils", "str")
116 215
 
Browse code

import packageDescription()

Zuguang Gu authored on 31/10/2017 12:36:42
Showing1 changed files
... ...
@@ -112,4 +112,5 @@ importFrom("circlize", smartAlign)
112 112
 importFrom("colorspace", diverge_hcl)