1. ComplexHeatmap
  2. NAMESPACE
Browse code

rename to anno_textbox()

Zuguang Gu authored on 15/06/2022 10:11:58
Showing 1 changed files
NAMESPACE
History View file @ 5cefa67
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 2bb14c9
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 8564ce7
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 31cf716
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 8ed806b
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ c1b9be2
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 5fd49ed
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 00490f9
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ b836d24
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 7caac70
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 613c44f
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 3898acc
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ c7865b7
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 06550f3
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 3612bf5
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 46b5212
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 4c1a4a3
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 2f64420
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 8963bcc
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 6849854
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 8b0c851
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ b4addaf
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 4ce4721
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ b912615
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 4caa99d
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 97eef73
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 049449b
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ d5bb303
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ b62323e
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ ea8dcf7
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 17a402b
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 9357313
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ d360df3
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 73277ab
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ cce3c25
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 4acbc10
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 784c44e
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ bb2b2e5
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 5ffb507
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 02ad1d0
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 9c4d56c
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ e392c69
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ edfce52
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ de656d4
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 0c139e2
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 2756d2e
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 79f1915
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ a8d8d9d
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 8e31894
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ e7a974a
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 1f0f3de
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ fda8e6f
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 03d6a86
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 3c40a7c
... ... 
@@ -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
Showing 1 changed files
NAMESPACE
History View file @ 64d651f
... ... 
@@ -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