Browse code

merge by copy paste

Zuguang Gu authored on 17/10/2017 20:55:32
Showing31 changed files

... ...
@@ -99,6 +99,7 @@ exportMethods(set_component_height)
99 99
 import(grDevices)
100 100
 import(graphics)
101 101
 import(grid)
102
+import(methods)
102 103
 import(stats)
103 104
 importFrom("GetoptLong", qq)
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 importFrom("GetoptLong", qq.options)
... ...
@@ -110,12 +111,5 @@ importFrom("circlize", rand_color)
110 111
 importFrom("circlize", smartAlign)
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 importFrom("colorspace", diverge_hcl)
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 importFrom("colorspace", rainbow_hcl)
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-importFrom("dendextend", "labels<-")
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-importFrom("dendextend", get_branches_heights)
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-importFrom("dendextend", nnodes)
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-importFrom("methods", "new", "show")
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-importFrom("methods", setClass)
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-importFrom("methods", setGeneric)
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-importFrom("methods", setMethod)
120 114
 importFrom("utils", "getFromNamespace")
121 115
 
... ...
@@ -1,4 +1,3 @@
1
-<<<<<<< HEAD
2 1
 CHANGES in VERSION 1.15.1
3 2
 
4 3
 * random colors are generated by new `rand_color()` function in circlize package.
... ...
@@ -23,12 +22,6 @@ CHANGES in VERSION 1.15.1
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 CHANGES in VERSION 1.13.2
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25 24
 * add `packLegend()`
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-=======
27
-CHANGES in VERSION 1.13.2
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-
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-* add `packLegend()`
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-* Legend() supports to add txt labels on grids
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->>>>>>> bioc/master
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33 26
 ========================
34 27
 
35 28
deleted file mode 100755
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@@ -1,3 +0,0 @@
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-[Dolphin]
2
-Timestamp=2015,6,15,11,33,52
3
-ViewMode=2
... ...
@@ -1,5 +1,4 @@
1 1
 
2
-<<<<<<< HEAD
3 2
 setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
4 3
 
5 4
 setGeneric('get_color_mapping_param_list', function(object, ...) standardGeneric('get_color_mapping_param_list'))
... ...
@@ -42,49 +41,10 @@ setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_he
42 41
 
43 42
 setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
44 43
 
45
-=======
46
-setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
47
-
48
-setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
49
-
50
-setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
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-
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-setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
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-
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-setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
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-
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-setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
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-
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-setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
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-
60
-setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
61
-
62
-setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
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-
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-setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
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-
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-setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
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-
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-setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
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-
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-setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
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-
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-setGeneric('get_color_mapping_param_list', function(object, ...) standardGeneric('get_color_mapping_param_list'))
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-
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-setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
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-
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-setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
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-
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-setGeneric('draw', function(object, ...) standardGeneric('draw'))
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-
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-setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
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-
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->>>>>>> bioc/master
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 setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))
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85 46
 setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
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-<<<<<<< HEAD
88 48
 setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
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90 50
 setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
... ...
@@ -92,18 +52,3 @@ setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
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 setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
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94 54
 setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
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-=======
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-setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
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-
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-setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
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-
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-setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
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-
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-setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
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-
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-setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
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-
106
-setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
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-
108
-setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
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->>>>>>> bioc/master
... ...
@@ -180,10 +180,7 @@ setMethod(f = "map_to_colors",
180 180
 	x2 = vector(length = length(x))
181 181
 
182 182
 	if(object@type == "discrete") {
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-<<<<<<< HEAD
184 183
 		x[grepl("^\\s*$", x)] = NA
185
-=======
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->>>>>>> bioc/master
187 184
 		lna = is.na(x)
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189 186
 		if(is.numeric(x)) x = as.character(x)
... ...
@@ -215,17 +212,10 @@ setMethod(f = "map_to_colors",
215 212
 # -title title of the legend, by default it is the name of the legend
216 213
 # -title_gp graphical parameters for legend title
217 214
 # -title_position position of the title
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-<<<<<<< HEAD
219 215
 # -color_bar a string of "continous" or "discrete". If the mapping is continuous, whether show the legend as discrete color bar or continuous color bar
220 216
 # -grid_height height of each legend grid.
221 217
 # -grid_width width of each legend grid.
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 # -border color for legend grid borders.
223
-=======
224
-# -color_bar if the mapping is continuous, whether show the legend as discrete color bar or continuous color bar
225
-# -grid_height height of each legend grid.
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-# -grid_width width of each legend grid.
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-# -grid_border color for legend grid borders.
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->>>>>>> bioc/master
229 219
 # -at break values of the legend
230 220
 # -labels labels corresponding to break values
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 # -labels_gp graphcial parameters for legend labels
... ...
@@ -255,17 +245,10 @@ setMethod(f = "color_mapping_legend",
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 	title = object@name,
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 	title_gp = gpar(fontsize = 10, fontface = "bold"),
257 247
 	title_position = c("topleft", "topcenter", "leftcenter", "lefttop"),
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-<<<<<<< HEAD
259 248
 	color_bar = object@type,
260 249
 	grid_height = unit(4, "mm"),
261 250
 	grid_width = unit(4, "mm"),
262 251
 	border = NULL,
263
-=======
264
-	color_bar = c("discrete", "continuous"),
265
-	grid_height = unit(4, "mm"),
266
-	grid_width = unit(4, "mm"),
267
-	grid_border = NULL,
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->>>>>>> bioc/master
269 252
 	at = object@levels,
270 253
 	labels = at,
271 254
 	labels_gp = gpar(fontsize = 10),
... ...
@@ -285,17 +268,10 @@ setMethod(f = "color_mapping_legend",
285 268
 	title_gp = check_gp(title_gp)
286 269
 	labels_gp = check_gp(labels_gp)
287 270
 
288
-<<<<<<< HEAD
289 271
 	# color_bar = match.arg(color_bar)
290 272
 
291 273
 	if(object@type == "discrete" && color_bar == "continuous") {
292 274
 		stop("'color_bar' can only be set to 'discrete' only if the color mapping is discrete")
293
-=======
294
-	color_bar = match.arg(color_bar)
295
-
296
-	if(object@type == "discrete" && color_bar == "continuous") {
297
-		stop("'color_bar' can only be set to 'continuous' only if the color mapping is continuous")
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->>>>>>> bioc/master
299 275
 	}
300 276
 
301 277
 	# get labels
... ...
@@ -315,21 +291,13 @@ setMethod(f = "color_mapping_legend",
315 291
 			labels = rev(labels)
316 292
 		}
317 293
 		gf = Legend(at = at, labels = labels, title = title, title_gp = title_gp, grid_height = grid_height,
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-<<<<<<< HEAD
319 294
 			grid_width = grid_width, border = border, labels_gp = labels_gp, nrow = nrow, ncol = ncol,
320
-=======
321
-			grid_width = grid_width, border = grid_border, labels_gp = labels_gp, nrow = nrow, ncol = ncol,
322
->>>>>>> bioc/master
323 295
 			legend_gp = gpar(fill = map_to_colors(object, at)), title_position = title_position)
324 296
 
325 297
 	} else {
326 298
 
327 299
 		gf = Legend(at = at, labels = labels, col_fun = object@col_fun, title = title, title_gp = title_gp, grid_height = grid_height,
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-<<<<<<< HEAD
329 300
 			grid_width = grid_width, border = border, labels_gp = labels_gp, direction = legend_direction,
330
-=======
331
-			grid_width = grid_width, border = grid_border, labels_gp = labels_gp, direction = legend_direction,
332
->>>>>>> bioc/master
333 301
 			legend_width = legend_width, legend_height = legend_height, title_position = title_position)
334 302
 
335 303
 	}
... ...
@@ -191,11 +191,7 @@ Heatmap = setClass("Heatmap",
191 191
 # -bottom_annotation_height total height of the column annotations on the bottom.
192 192
 # -km do k-means clustering on rows. If the value is larger than 1, the heatmap will be split by rows according to the k-means clustering.
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 #     For each row-clusters, hierarchical clustering is still applied with parameters above.
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-<<<<<<< HEAD
195 194
 # -km_title row title for each cluster when ``km`` is set. It must a text with format of ".*\%i.*" where "\%i" is replaced by the index of the cluster.
196
-=======
197
-# -km_title row title for each cluster when ``km`` is set. It must a text with format of "*\%i*" where "\%i" is replaced by the index of the cluster.
198
->>>>>>> bioc/master
199 195
 # -split a vector or a data frame by which the rows are split. But if ``cluster_rows`` is a clustering object, ``split`` can be a single number
200 196
 #        indicating rows are to be split according to the split on the tree.
201 197
 # -gap gap between row-slices if the heatmap is split by rows, should be `grid::unit` object. If it is a vector, the order corresponds
... ...
@@ -206,12 +202,8 @@ Heatmap = setClass("Heatmap",
206 202
 #        is appended to a list of heatmaps.
207 203
 # -show_heatmap_legend whether show heatmap legend?
208 204
 # -heatmap_legend_param a list contains parameters for the heatmap legend. See `color_mapping_legend,ColorMapping-method` for all available parameters.
209
-<<<<<<< HEAD
210 205
 # -use_raster whether render the heatmap body as a raster image. It helps to reduce file size when the matrix is huge. Note if ``cell_fun``
211 206
 #       is set, ``use_raster`` is enforced to be ``FALSE``.
212
-=======
213
-# -use_raster whether render the heatmap body as a raster image. It helps to reduce file size when the matrix is huge.
214
->>>>>>> bioc/master
215 207
 # -raster_device graphic device which is used to generate the raster image
216 208
 # -raster_quality a value set to larger than 1 will improve the quality of the raster image.
217 209
 # -raster_device_param a list of further parameters for the selected graphic device
... ...
@@ -239,11 +231,7 @@ Heatmap = function(matrix, col, name,
239 231
     na_col = "grey", 
240 232
     color_space = "LAB",
241 233
     rect_gp = gpar(col = NA), 
242
-<<<<<<< HEAD
243 234
     cell_fun = NULL,
244
-=======
245
-    cell_fun = function(j, i, x, y, width, height, fill) NULL,
246
->>>>>>> bioc/master
247 235
     row_title = character(0), 
248 236
     row_title_side = c("left", "right"), 
249 237
     row_title_gp = gpar(fontsize = 14), 
... ...
@@ -282,19 +270,11 @@ Heatmap = function(matrix, col, name,
282 270
     column_order = NULL,
283 271
     row_names_side = c("right", "left"), 
284 272
     show_row_names = TRUE, 
285
-<<<<<<< HEAD
286 273
     row_names_max_width = default_row_names_max_width(), 
287 274
     row_names_gp = gpar(fontsize = 12), 
288 275
     column_names_side = c("bottom", "top"), 
289 276
     show_column_names = TRUE, 
290 277
     column_names_max_height = default_column_names_max_height(), 
291
-=======
292
-    row_names_max_width = unit(4, "cm"), 
293
-    row_names_gp = gpar(fontsize = 12), 
294
-    column_names_side = c("bottom", "top"), 
295
-    show_column_names = TRUE, 
296
-    column_names_max_height = unit(4, "cm"), 
297
->>>>>>> bioc/master
298 278
     column_names_gp = gpar(fontsize = 12),
299 279
     top_annotation = new("HeatmapAnnotation"),
300 280
     top_annotation_height = top_annotation@size,
... ...
@@ -307,17 +287,10 @@ Heatmap = function(matrix, col, name,
307 287
     combined_name_fun = function(x) paste(x, collapse = "/"),
308 288
     width = NULL, 
309 289
     show_heatmap_legend = TRUE,
310
-<<<<<<< HEAD
311 290
     heatmap_legend_param = list(title = name),
312 291
     use_raster = FALSE, 
313 292
     raster_device = c("png", "jpeg", "tiff", "CairoPNG", "CairoJPEG", "CairoTIFF"),
314 293
     raster_quality = 2,
315
-=======
316
-    heatmap_legend_param = list(title = name, color_bar = "discrete"),
317
-    use_raster = FALSE, 
318
-    raster_device = c("png", "jpeg", "tiff", "CairoPNG", "CairoJPEG", "CairoTIFF"),
319
-    raster_quality = 1,
320
->>>>>>> bioc/master
321 294
     raster_device_param = list()) {
322 295
 
323 296
     # re-define some of the argument values according to global settings
... ...
@@ -528,12 +501,9 @@ Heatmap = function(matrix, col, name,
528 501
     .Object@row_names_param$side = match.arg(row_names_side)[1]
529 502
     .Object@row_names_param$show = show_row_names
530 503
     .Object@row_names_param$gp = check_gp(row_names_gp)
531
-<<<<<<< HEAD
532 504
     default_row_names_max_width = function() {
533 505
         min(unit.c(unit(6, "cm")), max_text_width(rownames(matrix), gp = .Object@row_names_param$gp))
534 506
     }
535
-=======
536
->>>>>>> bioc/master
537 507
     .Object@row_names_param$max_width = row_names_max_width + unit(2, "mm")
538 508
 
539 509
     if(is.null(colnames(matrix))) {
... ...
@@ -542,12 +512,9 @@ Heatmap = function(matrix, col, name,
542 512
     .Object@column_names_param$side = match.arg(column_names_side)[1]
543 513
     .Object@column_names_param$show = show_column_names
544 514
     .Object@column_names_param$gp = check_gp(column_names_gp)
545
-<<<<<<< HEAD
546 515
     default_column_names_max_height = function() {
547 516
         min(unit.c(unit(6, "cm")), max_text_width(colnames(matrix), gp = .Object@column_names_param$gp))
548 517
     }
549
-=======
550
->>>>>>> bioc/master
551 518
     .Object@column_names_param$max_height = column_names_max_height + unit(2, "mm")
552 519
 
553 520
     if(inherits(cluster_rows, "dendrogram") || inherits(cluster_rows, "hclust")) {
... ...
@@ -1329,14 +1296,11 @@ setMethod(f = "draw_heatmap_body",
1329 1296
     y = (rev(seq_len(nr)) - 0.5) / nr
1330 1297
     expand_index = expand.grid(seq_len(nr), seq_len(nc))
1331 1298
     
1332
-<<<<<<< HEAD
1333 1299
     cell_fun = object@matrix_param$cell_fun
1334 1300
     if(!is.null(cell_fun)) {
1335 1301
         use_raster = FALSE
1336 1302
     }
1337 1303
         
1338
-=======
1339
->>>>>>> bioc/master
1340 1304
     if(use_raster) {
1341 1305
         # write the image into a temporary file and read it back
1342 1306
         device_info = switch(raster_device,
... ...
@@ -1359,7 +1323,6 @@ setMethod(f = "draw_heatmap_body",
1359 1323
         if(heatmap_width <= 0 || heatmap_height <= 0) {
1360 1324
             stop("The width or height of the raster image is zero, maybe you forget to turn off the previous graphic device or it was corrupted. Run `dev.off()` to close it.")
1361 1325
         }
1362
-<<<<<<< HEAD
1363 1326
         tmp_dir = "."
1364 1327
         # dir.create(tmp_dir, showWarnings = FALSE)
1365 1328
         temp_image = tempfile(pattern = paste0(".heatmap_body_", object@name, "_", k, "_"), tmpdir = tmp_dir, fileext = paste0(".", device_info[2]))
... ...
@@ -1415,43 +1378,10 @@ setMethod(f = "draw_heatmap_body",
1415 1378
         }
1416 1379
     }
1417 1380
 
1418
-=======
1419
-        temp_image = tempfile(pattern = paste0(".heatmap_body_", object@name, "_", k, "_"), tmpdir = ".", fileext = paste0(".", device_info[2]))
1420
-        #getFromNamespace(raster_device, ns = device_info[1])(temp_image, width = heatmap_width*raster_quality, height = heatmap_height*raster_quality)
1421
-        device_fun = getFromNamespace(raster_device, ns = device_info[1])
1422
-        do.call("device_fun", c(list(filename = temp_image, width = heatmap_width*raster_quality, height = heatmap_height*raster_quality), raster_device_param))
1423
-    }
1424
-
1425
-    if(any(names(gp) %in% c("type"))) {
1426
-        if(gp$type == "none") {
1427
-        } else {
1428
-            grid.rect(x[expand_index[[2]]], y[expand_index[[1]]], width = unit(1/nc, "npc"), height = unit(1/nr, "npc"), gp = do.call("gpar", c(list(fill = col_matrix), gp)))
1429
-        }
1430
-    } else {
1431
-        grid.rect(x[expand_index[[2]]], y[expand_index[[1]]], width = unit(1/nc, "npc"), height = unit(1/nr, "npc"), gp = do.call("gpar", c(list(fill = col_matrix), gp)))
1432
-    }
1433
-
1434
-    cell_fun = object@matrix_param$cell_fun
1435
-    for(i in row_order) {
1436
-        for(j in column_order) {
1437
-            cell_fun(j, i, unit(x[which(column_order == j)], "npc"), unit(y[which(row_order == i)], "npc"), unit(1/nc, "npc"), unit(1/nr, "npc"), col_matrix[which(row_order == i), which(column_order == j)])
1438
-        }
1439
-    }
1440
-
1441
-    if(use_raster) {
1442
-        dev.off()
1443
-        image = getFromNamespace(device_info[3], ns = device_info[2])(temp_image)
1444
-        image = as.raster(image)
1445
-        grid.raster(image, width = unit(1, "npc"), height = unit(1, "npc"))
1446
-        file.remove(temp_image)
1447
-    }
1448
-
1449
->>>>>>> bioc/master
1450 1381
     upViewport()
1451 1382
 
1452 1383
 })
1453 1384
 
1454
-<<<<<<< HEAD
1455 1385
 is_windows = function() {
1456 1386
     tolower(.Platform$OS.type) == "windows"
1457 1387
 }
... ...
@@ -1461,8 +1391,6 @@ R_binary = function() {
1461 1391
     return(file.path(R.home("bin"), R_exe))
1462 1392
 }
1463 1393
 
1464
-=======
1465
->>>>>>> bioc/master
1466 1394
 # == title
1467 1395
 # Draw dendrogram on row or column
1468 1396
 #
... ...
@@ -1517,11 +1445,7 @@ setMethod(f = "draw_dend",
1517 1445
 
1518 1446
     dend = as.dendrogram(hc)
1519 1447
     n = length(labels(dend))
1520
-<<<<<<< HEAD
1521 1448
     if(nobs(dend) <= 1) {
1522
-=======
1523
-    if(nnodes(dend) <= 1) {
1524
->>>>>>> bioc/master
1525 1449
         return(invisible(NULL))
1526 1450
     }
1527 1451
 
... ...
@@ -245,7 +245,6 @@ HeatmapAnnotation = function(df, name, col, na_col = "grey",
245 245
 			} else if(is.atomic(anno_arg_list[[ag]])) {
246 246
 
247 247
 			    if(is.null(simple_length)) {
248
-<<<<<<< HEAD
249 248
 			    	if(is.matrix(anno_arg_list[[ag]])) {
250 249
 			    		simple_length = nrow(anno_arg_list[[ag]])
251 250
 			    	} else {
... ...
@@ -261,11 +260,6 @@ HeatmapAnnotation = function(df, name, col, na_col = "grey",
261 260
 			    			stop("length of simple annotations differ.")
262 261
 			    		}
263 262
 			    	}
264
-=======
265
-			    	simple_length = length(anno_arg_list[[ag]])
266
-			    } else if(length(anno_arg_list[[ag]]) != simple_length) {
267
-			    	stop("length of simple annotations differ.")
268
->>>>>>> bioc/master
269 263
 			    }
270 264
 				if(missing(col)) {
271 265
 			        anno_list = c(anno_list, list(SingleAnnotation(name = ag, value = anno_arg_list[[ag]], na_col = na_col, which = which, 
... ...
@@ -322,7 +316,6 @@ HeatmapAnnotation = function(df, name, col, na_col = "grey",
322 316
 
323 317
 	if(length(anno_size) == 1) {
324 318
 		if(!is.unit(anno_size)) {
325
-<<<<<<< HEAD
326 319
 			anno_size = sapply(anno_list, function(x) {
327 320
 				if(is_simple_annotation(x)) {
328 321
 					return(1)
... ...
@@ -332,9 +325,6 @@ HeatmapAnnotation = function(df, name, col, na_col = "grey",
332 325
 					return(2)
333 326
 				}
334 327
 			})
335
-=======
336
-			anno_size = rep(anno_size, n_total_anno)
337
->>>>>>> bioc/master
338 328
 		}
339 329
 	}
340 330
 
... ...
@@ -154,22 +154,15 @@ setMethod(f = "add_heatmap",
154 154
     ht_name = names(object@ht_list)
155 155
     which_duplicated = duplicated(ht_name)
156 156
     if(any(which_duplicated)) {
157
-<<<<<<< HEAD
158 157
         warning(paste0("Heatmap/row annotation names are duplicated: ", paste(ht_name[which_duplicated], collapse = ", ")))
159
-=======
160
-        warning(paste0("Heatmap/row annotaiton names are duplicated: ", paste(ht_name[which_duplicated], collapse = ", ")))
161
->>>>>>> bioc/master
162 158
     }
163 159
 
164 160
     l = which(sapply(object@ht_list, inherits, "Heatmap"))
165 161
     nr = sapply(object@ht_list[l], function(ht) nrow(ht@matrix))
166 162
 
167 163
     if(length(unique(nr)) > 1) {
168
-<<<<<<< HEAD
169 164
         cat("`nrow` of all heatmaps:\n")
170 165
         print(nr)
171
-=======
172
->>>>>>> bioc/master
173 166
         stop("`nrow` of all heatmaps should be the same.")
174 167
         for(i in l) {
175 168
             cat(object@ht_list[[i]]@name, ":", nrow(object@ht_list[[i]]@matrix), "\n")
... ...
@@ -192,10 +185,7 @@ setMethod(f = "add_heatmap",
192 185
 # -column_title_side will the title be put on the top or bottom of the heatmap.
193 186
 # -column_title_gp graphic parameters for drawing text.
194 187
 # -heatmap_legend_side side of the heatmap legend.
195
-<<<<<<< HEAD
196 188
 # -merge_legends whether put heatmap legends and annotation legends in a same column
197
-=======
198
->>>>>>> bioc/master
199 189
 # -show_heatmap_legend whether show heatmap legend.
200 190
 # -heatmap_legend_list a list of self-defined legend, should be wrapped into `grid::grob` objects.
201 191
 # -annotation_legend_side side of annotation legend.
... ...
@@ -216,10 +206,7 @@ setMethod(f = "add_heatmap",
216 206
 # -row_order same setting as in `Heatmap`, if it is specified, ``row_order`` in main heatmap is ignored.
217 207
 # -km same setting as in `Heatmap`, if it is specified, ``km`` in main heatmap is ignored.
218 208
 # -split same setting as in `Heatmap`, if it is specified, ``split`` in main heatmap is ignored.
219
-<<<<<<< HEAD
220 209
 # -combined_name_fun same setting as in `Heatmap`, if it is specified, ``combined_name_fun`` in main heatmap is ignored.
221
-=======
222
->>>>>>> bioc/master
223 210
 #
224 211
 # == detail
225 212
 # It sets the size of each component of the heatmap list and adjusts graphic parameters for each heatmap if necessary.
... ...
@@ -243,10 +230,7 @@ setMethod(f = "make_layout",
243 230
     column_title_side = c("top", "bottom"), 
244 231
     column_title_gp = gpar(fontsize = 14), 
245 232
     heatmap_legend_side = c("right", "left", "bottom", "top"), 
246
-<<<<<<< HEAD
247 233
     merge_legends = FALSE,
248
-=======
249
->>>>>>> bioc/master
250 234
     show_heatmap_legend = TRUE, 
251 235
     heatmap_legend_list = list(),
252 236
     annotation_legend_side = c("right", "left", "bottom", "top"), 
... ...
@@ -266,12 +250,8 @@ setMethod(f = "make_layout",
266 250
     row_dend_gp = NULL,
267 251
     row_order = NULL,
268 252
     km = NULL,
269
-<<<<<<< HEAD
270 253
     split = NULL,
271 254
     combined_name_fun = NULL) {
272
-=======
273
-    split = NULL) {
274
->>>>>>> bioc/master
275 255
 
276 256
     if(object@layout$initialized) {
277 257
         return(object)
... ...
@@ -309,11 +289,8 @@ setMethod(f = "make_layout",
309 289
     }
310 290
     object@ht_list_param$gap = gap
311 291
 
312
-<<<<<<< HEAD
313 292
     object@ht_list_param$merge_legends = merge_legends
314 293
 
315
-=======
316
->>>>>>> bioc/master
317 294
     for(i in seq_len(n)) {
318 295
         # if the zero-column matrix is the first one
319 296
         if(inherits(object@ht_list[[i]], "Heatmap")) {
... ...
@@ -333,12 +310,9 @@ setMethod(f = "make_layout",
333 310
     if(!is.null(km)) {
334 311
         object@ht_list[[i_main]]@matrix_param$km = km
335 312
     }
336
-<<<<<<< HEAD
337 313
     if(!missing(combined_name_fun)) {
338 314
         object@ht_list[[i_main]]@matrix_param$combined_name_fun = combined_name_fun
339 315
     }
340
-=======
341
->>>>>>> bioc/master
342 316
 
343 317
     if(!is.null(cluster_rows)) {
344 318
 
... ...
@@ -482,12 +456,8 @@ setMethod(f = "make_layout",
482 456
     }
483 457
     object@ht_list_param$gap = gap
484 458
     object@ht_list_param$main_heatmap = i_main
485
-<<<<<<< HEAD
486 459
     object@ht_list_param$merge_legends = merge_legends
487 460
 
488
-=======
489
-    
490
->>>>>>> bioc/master
491 461
     n = length(object@ht_list)
492 462
 
493 463
     ## orders of other heatmaps should be changed
... ...
@@ -633,7 +603,6 @@ setMethod(f = "make_layout",
633 603
     for(i in seq_along(object@ht_list)) {
634 604
         ht = object@ht_list[[i]]
635 605
         if(inherits(ht, "Heatmap")) {
636
-<<<<<<< HEAD
637 606
             if(merge_legends && !is.null(ht@top_annotation)) {
638 607
                 ColorMappingList = c(ColorMappingList, get_color_mapping_list(ht@top_annotation))
639 608
             }
... ...
@@ -643,11 +612,6 @@ setMethod(f = "make_layout",
643 612
             if(merge_legends && !is.null(ht@bottom_annotation)) {
644 613
                 ColorMappingList = c(ColorMappingList, get_color_mapping_list(ht@bottom_annotation))
645 614
             }
646
-=======
647
-            if(ht@heatmap_param$show_heatmap_legend) {
648
-                ColorMappingList = c(ColorMappingList, ht@matrix_color_mapping)
649
-            }
650
->>>>>>> bioc/master
651 615
         }
652 616
         if(inherits(ht, "HeatmapAnnotation")) {
653 617
             ColorMappingList = c(ColorMappingList, get_color_mapping_list(ht))
... ...
@@ -695,7 +659,6 @@ setMethod(f = "make_layout",
695 659
     ## annotation legend to top, bottom, left and right
696 660
     # default values
697 661
     ColorMappingList = list()
698
-<<<<<<< HEAD
699 662
     if(!merge_legends) {
700 663
         for(i in seq_along(object@ht_list)) {
701 664
             ht = object@ht_list[[i]]
... ...
@@ -710,18 +673,6 @@ setMethod(f = "make_layout",
710 673
         }
711 674
     } else {
712 675
         annotation_legend_list = list()
713
-=======
714
-    for(i in seq_along(object@ht_list)) {
715
-        ht = object@ht_list[[i]]
716
-        if(inherits(ht, "Heatmap")) {
717
-            if(!is.null(ht@top_annotation)) {
718
-                ColorMappingList = c(ColorMappingList, get_color_mapping_list(ht@top_annotation))
719
-            }
720
-            if(!is.null(ht@bottom_annotation)) {
721
-                ColorMappingList = c(ColorMappingList, get_color_mapping_list(ht@bottom_annotation))
722
-            }
723
-        }
724
->>>>>>> bioc/master
725 676
     }
726 677
     if(length(ColorMappingList) == 0 && length(annotation_legend_list) == 0) {
727 678
         show_annotation_legend = FALSE
... ...
@@ -1244,27 +1195,20 @@ setMethod(f = "draw_heatmap_legend",
1244 1195
     ColorMappingList = list()
1245 1196
     ColorMappingParamList = list()
1246 1197
     for(i in seq_along(object@ht_list)) {
1247
-<<<<<<< HEAD
1248 1198
         ht = object@ht_list[[i]]
1249 1199
         if(inherits(object@ht_list[[i]], "Heatmap")) {
1250 1200
             if(object@ht_list_param$merge_legends && !is.null(ht@top_annotation)) {
1251 1201
                 ColorMappingList = c.list(ColorMappingList, list = get_color_mapping_list(ht@top_annotation))
1252 1202
                 ColorMappingParamList = c.list(ColorMappingParamList, list = get_color_mapping_param_list(ht@top_annotation))
1253 1203
             }
1254
-=======
1255
-        if(inherits(object@ht_list[[i]], "Heatmap")) {
1256
->>>>>>> bioc/master
1257 1204
             if(object@ht_list[[i]]@heatmap_param$show_heatmap_legend) {
1258 1205
                 ColorMappingList = c.list(ColorMappingList, object@ht_list[[i]]@matrix_color_mapping)
1259 1206
                 ColorMappingParamList = c.list(ColorMappingParamList, object@ht_list[[i]]@matrix_color_mapping_param)
1260 1207
             }
1261
-<<<<<<< HEAD
1262 1208
             if(object@ht_list_param$merge_legends && !is.null(ht@bottom_annotation)) {
1263 1209
                 ColorMappingList = c.list(ColorMappingList, list = get_color_mapping_list(ht@bottom_annotation))
1264 1210
                 ColorMappingParamList = c.list(ColorMappingParamList, list = get_color_mapping_param_list(ht@bottom_annotation))
1265 1211
             }
1266
-=======
1267
->>>>>>> bioc/master
1268 1212
         } else if(inherits(object@ht_list[[i]], "HeatmapAnnotation")) {
1269 1213
             ColorMappingList = c.list(ColorMappingList, list = get_color_mapping_list(object@ht_list[[i]]))
1270 1214
             ColorMappingParamList = c.list(ColorMappingParamList, list = get_color_mapping_param_list(object@ht_list[[i]]))
... ...
@@ -1385,28 +1329,21 @@ setMethod(f = "heatmap_legend_size",
1385 1329
     ColorMappingList = list()
1386 1330
     ColorMappingParamList = list()
1387 1331
     for(i in seq_along(object@ht_list)) {
1388
-<<<<<<< HEAD
1389 1332
         ht = object@ht_list[[i]]
1390 1333
         if(inherits(object@ht_list[[i]], "Heatmap")) {
1391 1334
             if(object@ht_list_param$merge_legends && !is.null(ht@top_annotation)) {
1392 1335
                 ColorMappingList = c.list(ColorMappingList, list = get_color_mapping_list(ht@top_annotation))
1393 1336
                 ColorMappingParamList = c.list(ColorMappingParamList, list = get_color_mapping_param_list(ht@top_annotation))
1394 1337
             }
1395
-=======
1396
-        if(inherits(object@ht_list[[i]], "Heatmap")) {
1397
->>>>>>> bioc/master
1398 1338
             if(object@ht_list[[i]]@heatmap_param$show_heatmap_legend) {
1399 1339
                 ColorMappingList = c.list(ColorMappingList, object@ht_list[[i]]@matrix_color_mapping)
1400 1340
                 ColorMappingParamList = c.list(ColorMappingParamList, object@ht_list[[i]]@matrix_color_mapping_param)
1401 1341
             }
1402
-<<<<<<< HEAD
1403 1342
             if(object@ht_list_param$merge_legends && !is.null(ht@bottom_annotation)) {
1404 1343
                 ColorMappingList = c.list(ColorMappingList, list = get_color_mapping_list(ht@bottom_annotation))
1405 1344
                 ColorMappingParamList = c.list(ColorMappingParamList, list = get_color_mapping_param_list(ht@bottom_annotation))
1406 1345
             }
1407 1346
             
1408
-=======
1409
->>>>>>> bioc/master
1410 1347
         } else if(inherits(object@ht_list[[i]], "HeatmapAnnotation")) {
1411 1348
             ColorMappingList = c.list(ColorMappingList, list = get_color_mapping_list(object@ht_list[[i]]))
1412 1349
             ColorMappingParamList = c.list(ColorMappingParamList, list = get_color_mapping_param_list(object@ht_list[[i]]))
... ...
@@ -1473,15 +1410,12 @@ draw_legend = function(ColorMappingList, ColorMappingParamList, side = c("right"
1473 1410
 
1474 1411
     side = match.arg(side)[1]
1475 1412
 
1476
-<<<<<<< HEAD
1477 1413
     # remove legends which are duplicated by testing the names
1478 1414
     legend_names = sapply(ColorMappingList, function(x) x@name)
1479 1415
     l = !duplicated(legend_names)
1480 1416
     ColorMappingList = ColorMappingList[l]
1481 1417
     ColorMappingParamList = ColorMappingParamList[l]
1482 1418
 
1483
-=======
1484
->>>>>>> bioc/master
1485 1419
     n = length(ColorMappingList)
1486 1420
     if(n == 0 && length(legend_list) == 0) {
1487 1421
         return(unit(c(0, 0), "null"))
... ...
@@ -135,17 +135,10 @@ Legend = function(at, labels = at, nrow = NULL, ncol = 1, col_fun,
135 135
 	# for(i in seq_len(length(odevlist) - length(dev.list()))) {
136 136
 	# 	dev.off()
137 137
 	# }
138
-<<<<<<< HEAD
139 138
 	return(gf)
140 139
 }
141 140
 
142 141
 # grids are arranged by rows
143
-=======
144
-
145
-	return(gf)
146
-}
147
-
148
->>>>>>> bioc/master
149 142
 discrete_legend_body = function(at, labels = at, nrow = NULL, ncol = 1,
150 143
 	grid_height = unit(4, "mm"), grid_width = unit(4, "mm"), gap = unit(2, "mm"),
151 144
 	labels_gp = gpar(fontsize = 10),
... ...
@@ -163,27 +156,18 @@ discrete_legend_body = function(at, labels = at, nrow = NULL, ncol = 1,
163 156
 		nrow = 1
164 157
 		ncol = 1
165 158
 	}
166
-<<<<<<< HEAD
167 159
 	ncol = ifelse(ncol > n_labels, n_labels, ncol)
168 160
 
169 161
 	labels_mat = matrix(c(labels, rep("", nrow*ncol - n_labels)), nrow = nrow, ncol = ncol, byrow = TRUE)
170 162
 	index_mat = matrix(1:(nrow*ncol), nrow = nrow, ncol = ncol, byrow = TRUE)
171 163
 
172
-=======
173
->>>>>>> bioc/master
174 164
 
175 165
 	labels_padding_left = unit(1, "mm")
176 166
 	
177 167
 	labels_max_width = NULL
178 168
 	for(i in 1:ncol) {
179
-<<<<<<< HEAD
180 169
 		if(i == 1) {
181 170
 			labels_max_width = max(do.call("unit.c", lapply(labels_mat[, i], function(x) {
182
-=======
183
-		index = seq(nrow*(i-1)+1, min(c(nrow*i, n_labels)))
184
-		if(i == 1) {
185
-			labels_max_width = max(do.call("unit.c", lapply(labels[index], function(x) {
186
->>>>>>> bioc/master
187 171
 					g = grobWidth(textGrob(x, gp = labels_gp))
188 172
 					if(i < ncol) {
189 173
 						g = g + gap
... ...
@@ -191,11 +175,7 @@ discrete_legend_body = function(at, labels = at, nrow = NULL, ncol = 1,
191 175
 					g
192 176
 				})))
193 177
 		} else {
194
-<<<<<<< HEAD
195 178
 			labels_max_width = unit.c(labels_max_width, max(do.call("unit.c", lapply(labels_mat[, i], function(x) {
196
-=======
197
-			labels_max_width = unit.c(labels_max_width, max(do.call("unit.c", lapply(labels[index], function(x) {
198
->>>>>>> bioc/master
199 179
 					g = grobWidth(textGrob(x, gp = labels_gp))
200 180
 					if(i < ncol) {
201 181
 						g = g + gap
... ...
@@ -215,11 +195,7 @@ discrete_legend_body = function(at, labels = at, nrow = NULL, ncol = 1,
215 195
 
216 196
 	# legend grid
217 197
 	for(i in 1:ncol) {
218
-<<<<<<< HEAD
219 198
 		index = index_mat[, i][labels_mat[, i] != ""]
220
-=======
221
-		index = seq(nrow*(i-1)+1, min(c(nrow*i, n_labels)))
222
->>>>>>> bioc/master
223 199
 		ni = length(index)
224 200
 		x = unit(rep(0, ni), "npc")
225 201
 		y = (0:(ni-1))*(grid_height)
... ...
@@ -245,15 +221,7 @@ discrete_legend_body = function(at, labels = at, nrow = NULL, ncol = 1,
245 221
 		if(any(c("points", "p") %in% type)) {
246 222
 			if(length(pch) == 1) pch = rep(pch, n_labels)
247 223
 			if(length(size) == 1) size = rep(size, n_labels)
248
-<<<<<<< HEAD
249 224
 			gf = placeGrob(gf, row = 1, col = 2*i-1, grob = pointsGrob(x+grid_width*0.5, y-grid_height*0.5, pch = pch[index], size = size[index], gp = subset_gp(legend_gp, index)))
250
-=======
251
-			if(inherits(pch, "character")) {
252
-				gf = placeGrob(gf, row = 1, col = 2*i-1, grob = textGrob(pch[index], x+grid_width*0.5, y-grid_height*0.5, gp = subset_gp(legend_gp, index)))
253
-			} else {
254
-				gf = placeGrob(gf, row = 1, col = 2*i-1, grob = pointsGrob(x+grid_width*0.5, y-grid_height*0.5, pch = pch[index], size = size[index], gp = subset_gp(legend_gp, index)))
255
-			}
256
->>>>>>> bioc/master
257 225
 		}
258 226
 		if(any(c("lines", "l") %in% type)) {
259 227
 			gf = placeGrob(gf, row = 1, col = 2*i-1, grob = segmentsGrob(x+unit(0.5, "mm"), y-grid_height*0.5, x+grid_width - unit(0.5, "mm"), y-grid_height*0.5, gp = subset_gp(legend_gp, index)))
... ...
@@ -35,12 +35,8 @@ SingleAnnotation = setClass("SingleAnnotation",
35 35
 		show_legend = "logical",
36 36
 		which = "character",
37 37
 		name_to_data_vp = "logical",
38
-<<<<<<< HEAD
39 38
 		name_param = "list",
40 39
         is_anno_matrix = "logical"
41
-=======
42
-		name_param = "list"
43
->>>>>>> bioc/master
44 40
 	),
45 41
 	prototype = list(
46 42
 		color_mapping = NULL,
... ...
@@ -142,7 +138,6 @@ SingleAnnotation = function(name, value, col, fun,
142 138
         stop("`name_rot` can only take values in c(0, 90, 180, 270)")
143 139
     }
144 140
 
145
-<<<<<<< HEAD
146 141
     .Object@is_anno_matrix = FALSE
147 142
     use_mat_column_names = FALSE
148 143
     if(!missing(value)) {
... ...
@@ -161,15 +156,11 @@ SingleAnnotation = function(name, value, col, fun,
161 156
         }
162 157
     }
163 158
 
164
-=======
165
-    
166
->>>>>>> bioc/master
167 159
     if(which == "column") {
168 160
     	if(!name_side %in% c("left", "right")) {
169 161
     		stop("`name_side` should be 'left' or 'right' when it is a column annotation.")
170 162
     	}
171 163
     	if(name_side == "left") {
172
-<<<<<<< HEAD
173 164
     		
174 165
             if(use_mat_column_names) {
175 166
                 name_x = unit(rep(0, use_mat_nc), "npc") - name_offset
... ...
@@ -178,10 +169,6 @@ SingleAnnotation = function(name, value, col, fun,
178 169
                 name_x = unit(0, "npc") - name_offset
179 170
                 name_y = unit(0.5, "npc")
180 171
             }
181
-=======
182
-    		name_x = unit(0, "npc") - name_offset
183
-    		name_y = unit(0.5, "npc")
184
->>>>>>> bioc/master
185 172
             if(name_rot == 0) {
186 173
                 name_just = "right"
187 174
             } else if(name_rot == 90) {
... ...
@@ -192,7 +179,6 @@ SingleAnnotation = function(name, value, col, fun,
192 179
                 name_just = "top"
193 180
             }
194 181
     	} else {
195
-<<<<<<< HEAD
196 182
             if(use_mat_column_names) {
197 183
                 name_x = unit(rep(1, use_mat_nc), "npc") + name_offset
198 184
                 name_y = unit((use_mat_nc - seq_len(use_mat_nc) + 0.5)/use_mat_nc, "npc")
... ...
@@ -200,10 +186,6 @@ SingleAnnotation = function(name, value, col, fun,
200 186
         		name_x = unit(1, "npc") + name_offset
201 187
         		name_y = unit(0.5, "npc")
202 188
             }
203
-=======
204
-    		name_x = unit(1, "npc") + name_offset
205
-    		name_y = unit(0.5, "npc")
206
->>>>>>> bioc/master
207 189
             if(name_rot == 0) {
208 190
                 name_just = "left"
209 191
             } else if(name_rot == 90) {
... ...
@@ -219,7 +201,6 @@ SingleAnnotation = function(name, value, col, fun,
219 201
     		stop("`name_side` should be 'left' or 'right' when it is a column annotation.")
220 202
     	}
221 203
     	if(name_side == "top") {
222
-<<<<<<< HEAD
223 204
             if(use_mat_column_names) {
224 205
                 name_x = unit((seq_len(use_mat_nc) - 0.5)/use_mat_nc, "npc")
225 206
                 name_y = unit(rep(1, use_mat_nc), "npc") + name_offset
... ...
@@ -227,10 +208,6 @@ SingleAnnotation = function(name, value, col, fun,
227 208
         		name_x = unit(0.5, "npc")
228 209
         		name_y = unit(1, "npc") + name_offset
229 210
             }
230
-=======
231
-    		name_x = unit(0.5, "npc")
232
-    		name_y = unit(1, "npc") + name_offset
233
->>>>>>> bioc/master
234 211
             if(name_rot == 0) {
235 212
                 name_just = "bottom"
236 213
             } else if(name_rot == 90) {
... ...
@@ -241,7 +218,6 @@ SingleAnnotation = function(name, value, col, fun,
241 218
                 name_just = "right"
242 219
             }
243 220
     	} else {
244
-<<<<<<< HEAD
245 221
             if(use_mat_column_names) {
246 222
                 name_x = unit((seq_len(use_mat_nc) - 0.5)/use_mat_nc, "npc")
247 223
                 name_y = unit(rep(0, use_mat_nc), "npc") - name_offset
... ...
@@ -249,10 +225,6 @@ SingleAnnotation = function(name, value, col, fun,
249 225
         		name_x = unit(0.5, "npc")
250 226
         		name_y = unit(0, "npc") - name_offset
251 227
             }
252
-=======
253
-    		name_x = unit(0.5, "npc")
254
-    		name_y = unit(0, "npc") - name_offset
255
->>>>>>> bioc/master
256 228
             if(name_rot == 0) {
257 229
                 name_just = "top"
258 230
             } else if(name_rot == 90) {
... ...
@@ -269,38 +241,18 @@ SingleAnnotation = function(name, value, col, fun,
269 241
     						  y = name_y,
270 242
     						  just = name_just,
271 243
     	                      gp = check_gp(name_gp),
272
-<<<<<<< HEAD
273 244
     	                      rot = name_rot,
274 245
                               side = name_side)
275
-=======
276
-    	                      rot = name_rot)
277
->>>>>>> bioc/master
278 246
 
279 247
     gp = check_gp(gp)
280 248
     if(!is.null(gp$fill)) {
281 249
     	stop("You should not set `fill`.")
282 250
     }
283 251
 
284
-<<<<<<< HEAD
285
-=======
286
-    if(!missing(value)) {
287
-	    if(is.logical(value)) {
288
-	    	value = as.character(value)
289
-	    }
290
-	    if(is.factor(value)) {
291
-            value = as.vector(value)
292
-        }
293
-	}
294
-
295
->>>>>>> bioc/master
296 252
     if(missing(fun)) {
297 253
     	if(missing(col)) {
298 254
     		col = default_col(value)
299 255
     	}
300
-<<<<<<< HEAD
301
-=======
302
-        
303
->>>>>>> bioc/master
304 256
     	if(is.atomic(col)) {
305 257
     	    if(is.null(names(col))) {
306 258
                 if(is.factor(value)) {
... ...
@@ -328,7 +280,6 @@ SingleAnnotation = function(name, value, col, fun,
328 280
 	        .Object@fun = function(index) {
329 281
 	        	n = length(index)
330 282
 				x = (seq_len(n) - 0.5) / n
331
-<<<<<<< HEAD
332 283
                 if(is.matrix(value)) {
333 284
                     nc = ncol(value)
334 285
                     for(i in seq_len(nc)) {
... ...
@@ -339,17 +290,11 @@ SingleAnnotation = function(name, value, col, fun,
339 290
     				fill = map_to_colors(color_mapping, value[index])
340 291
     				grid.rect(x, y = 0.5, width = 1/n, height = 1, gp = do.call("gpar", c(list(fill = fill), gp)))
341 292
                 }
342
-=======
343
-				fill = map_to_colors(color_mapping, value[index])
344
-				#l = which(!is.na(value[index]))
345
-				grid.rect(x, y = 0.5, width = 1/n, height = 1, gp = do.call("gpar", c(list(fill = fill), gp)))
346
->>>>>>> bioc/master
347 293
 			}
348 294
 		} else {
349 295
 			.Object@fun = function(index, k = NULL, N = NULL) {
350 296
 				n = length(index)
351 297
 				y = (n - seq_len(n) + 0.5) / n
352
-<<<<<<< HEAD
353 298
                 if(is.matrix(value)) {
354 299
                     nc = ncol(value)
355 300
                     for(i in seq_len(nc)) {
... ...
@@ -360,11 +305,6 @@ SingleAnnotation = function(name, value, col, fun,
360 305
     				fill = map_to_colors(color_mapping, value[index])
361 306
     				grid.rect(x = 0.5, y, height = 1/n, width = 1, gp = do.call("gpar", c(list(fill = fill), gp)))
362 307
                 }
363
-=======
364
-				fill = map_to_colors(color_mapping, value[index])
365
-				#l = which(!is.na(value[index]))
366
-				grid.rect(x = 0.5, y, height = 1/n, width = 1, gp = do.call("gpar", c(list(fill = fill), gp)))
367
->>>>>>> bioc/master
368 308
 			}
369 309
 		}
370 310
 
... ...
@@ -407,11 +347,7 @@ SingleAnnotation = function(name, value, col, fun,
407 347
 # == param
408 348
 # -object a `SingleAnnotation-class` object.
409 349
 # -index a vector of orders
410
-<<<<<<< HEAD
411 350
 # -k if row annotation is splitted, the value identifies which row slice. It is only used for the names of the viewport
412
-=======
413
-# -k if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewport
414
->>>>>>> bioc/master
415 351
 #    which contains the annotation graphics.
416 352
 # -n total number of row slices
417 353
 #
... ...
@@ -450,7 +386,6 @@ setMethod(f = "draw",
450 386
 	}
451 387
 	# add annotation name
452 388
 	if(object@name_param$show) {
453
-<<<<<<< HEAD
454 389
         draw_name = TRUE
455 390
         if(object@which == "row") {
456 391
             if(!is.null(k)) {
... ...
@@ -480,10 +415,6 @@ setMethod(f = "draw",
480 415
         			rot = object@name_param$rot, gp = object@name_param$gp)
481 416
             }
482 417
         }
483
-=======
484
-		grid.text(object@name, x = object@name_param$x, y = object@name_param$y, just = object@name_param$just, 
485
-			rot = object@name_param$rot, gp = object@name_param$gp)
486
->>>>>>> bioc/master
487 418
 	}
488 419
 	upViewport()
489 420
 
... ...
@@ -504,11 +435,7 @@ setMethod(f = "draw",
504 435
 setMethod(f = "show",
505 436
 	signature = "SingleAnnotation",
506 437
 	definition = function(object) {
507
-<<<<<<< HEAD
508 438
 	if(is_fun_annotation(object)) {
509
-=======
510
-	if(is.null(object@color_mapping)) {
511
->>>>>>> bioc/master
512 439
 		cat("An annotation with self-defined function\n")
513 440
 		cat("name:", object@name, "\n")
514 441
 		cat("position:", object@which, "\n")
... ...
@@ -517,7 +444,6 @@ setMethod(f = "show",
517 444
 		cat("name:", object@name, "\n")
518 445
 		cat("position:", object@which, "\n")
519 446
 		cat("show legend:", object@show_legend, "\n")
520
-<<<<<<< HEAD
521 447
         if(is_matrix_annotation(object)) {
522 448
             cat("a matrix with", attr(object@is_anno_matrix, "k"), "columns\n")
523 449
         }
... ...
@@ -536,7 +462,3 @@ is_matrix_annotation = function(single_anno) {
536 462
 is_fun_annotation = function(single_anno) {
537 463
     is.null(single_anno@color_mapping)
538 464
 }
539
-=======
540
-	}
541
-})
542
->>>>>>> bioc/master
... ...
@@ -1050,11 +1050,7 @@ column_anno_text = function(...) {
1050 1050
 # == param
1051 1051
 # -at numeric index in the original matrix
1052 1052
 # -labels corresponding labels
1053
-<<<<<<< HEAD
1054 1053
 # -which column annotation or row annotation
1055
-=======
1056
-# -which column annotaiton or row annotation
1057
->>>>>>> bioc/master
1058 1054
 # -side side of the labels. If it is a column annotation, permitted values are "top" and "bottom";
1059 1055
 #       If it is a row annotation, permitted values are "left" and "right".
1060 1056
 # -lines_gp graphic settings for the segments
... ...
@@ -1141,11 +1137,7 @@ anno_link = function(at, labels, which = c("column", "row"), side = ifelse(which
1141 1137
 					grid.segments(rep(link_width*(1/3), n2), n-i2+1, rep(link_width*(2/3), n2), h, default.units = "native", gp = lines_gp)
1142 1138
 					grid.segments(rep(link_width*(2/3), n2), h, rep(link_width, n2), h, default.units = "native", gp = lines_gp)
1143 1139
 				} else {
1144
-<<<<<<< HEAD
1145 1140
 					grid.text(labels, unit(1, "npc")-rep(link_width, n2), h, default.units = "native", gp = labels_gp, just = "right")
1146
-=======
1147
-					grid.text(labels, rep(link_width, n2), h, default.units = "native", gp = labels_gp, just = "right")
1148
->>>>>>> bioc/master
1149 1141
 					link_width = link_width - unit(1, "mm")
1150 1142
 					grid.segments(unit(rep(1, n2), "npc"), n-i2+1, unit(1, "npc")-rep(link_width*(1/3), n2), n-i2+1, default.units = "native", gp = lines_gp)
1151 1143
 					grid.segments(unit(1, "npc")-rep(link_width*(1/3), n2), n-i2+1, unit(1, "npc")-rep(link_width*(2/3), n2), h, default.units = "native", gp = lines_gp)
... ...
@@ -1237,7 +1229,6 @@ row_anno_link = function(...) {
1237 1229
 column_anno_link = function(...) {
1238 1230
 	anno_link(..., which = "column")
1239 1231
 }
1240
-<<<<<<< HEAD
1241 1232
 
1242 1233
 
1243 1234
 grid.xaxis = function(main = TRUE, at = NULL, label = NULL, gp = gpar()) {
... ...
@@ -1260,5 +1251,3 @@ grid.xaxis = function(main = TRUE, at = NULL, label = NULL, gp = gpar()) {
1260 1251
 		grid.text(label, at, unit(1, "npc") + unit(rep(1, n), "lines"), rot = 90, just = "left", gp = gp, default.units = "native")
1261 1252
 	}
1262 1253
 }
1263
-=======
1264
->>>>>>> bioc/master
... ...
@@ -44,14 +44,11 @@
44 44
 #
45 45
 decorate_heatmap_body = function(heatmap, code, slice = 1, envir = new.env(parent = parent.frame())) {
46 46
 
47
-<<<<<<< HEAD
48 47
 	current_vp = current.viewport()$name
49 48
 	if(current_vp == "ROOT") {
50 49
 		current_vp = "global"
51 50
 	}
52 51
 	
53
-=======
54
->>>>>>> bioc/master
55 52
 	if(is.null(slice)) {
56 53
 		vp_name = paste0(heatmap, "_heatmap_body_", 1)
57 54
 		seekViewport(vp_name)
... ...
@@ -63,11 +60,7 @@ decorate_heatmap_body = function(heatmap, code, slice = 1, envir = new.env(paren
63 60
 
64 61
 	eval(substitute(code), envir = envir)
65 62
 
66
-<<<<<<< HEAD
67 63
 	seekViewport(current_vp)
68
-=======
69
-	seekViewport("global")
70
->>>>>>> bioc/master
71 64
 }
72 65
 
73 66
 # == title
... ...
@@ -110,14 +103,11 @@ decorate_heatmap_body = function(heatmap, code, slice = 1, envir = new.env(paren
110 103
 decorate_dend = function(heatmap, code, slice = 1, which = c("column", "row"), 
111 104
 	envir = new.env(parent = parent.frame())) {
112 105
 	
113
-<<<<<<< HEAD
114 106
 	current_vp = current.viewport()$name
115 107
 	if(current_vp == "ROOT") {
116 108
 		current_vp = "global"
117 109
 	}
118 110
 
119
-=======
120
->>>>>>> bioc/master
121 111
 	which = match.arg(which)[1]
122 112
 	if(which == "column") {
123 113
 		vp_name = paste0(heatmap, "_dend_", which)
... ...
@@ -136,11 +126,7 @@ decorate_dend = function(heatmap, code, slice = 1, which = c("column", "row"),
136 126
 	e = new.env(parent = parent.frame())
137 127
 	eval(substitute(code), envir = e)
138 128
 
139
-<<<<<<< HEAD
140 129
 	seekViewport(current_vp)
141
-=======
142
-	seekViewport("global")
143
->>>>>>> bioc/master
144 130
 }
145 131
 
146 132
 # == title
... ...
@@ -236,14 +222,11 @@ decorate_row_dend = function(..., envir = new.env(parent = parent.frame())) {
236 222
 decorate_dimnames = function(heatmap, code, slice = 1, which = c("column", "row"), 
237 223
 	envir = new.env(parent = parent.frame())) {
238 224
 	
239
-<<<<<<< HEAD
240 225
 	current_vp = current.viewport()$name
241 226
 	if(current_vp == "ROOT") {
242 227
 		current_vp = "global"
243 228
 	}
244 229
 
245
-=======
246
->>>>>>> bioc/master
247 230
 	which = match.arg(which)[1]
248 231
 	if(which == "column") {
249 232
 		vp_name = paste0(heatmap, "_", which, "_names")
... ...
@@ -260,11 +243,7 @@ decorate_dimnames = function(heatmap, code, slice = 1, which = c("column", "row"
260 243
 
261 244
 	seekViewport(vp_name)
262 245
 	eval(substitute(code), envir = envir)
263
-<<<<<<< HEAD
264 246
 	seekViewport(current_vp)
265
-=======
266
-	seekViewport("global")
267
->>>>>>> bioc/master
268 247
 }
269 248
 
270 249
 # == title
... ...
@@ -348,14 +327,11 @@ decorate_column_names = function(..., envir = new.env(parent = parent.frame()))
348 327
 decorate_title = function(heatmap, code, slice = 1, which = c("column", "row"), 
349 328
 	envir = new.env(parent = parent.frame())) {
350 329
 	
351
-<<<<<<< HEAD
352 330
 	current_vp = current.viewport()$name
353 331
 	if(current_vp == "ROOT") {
354 332
 		current_vp = "global"
355 333
 	}
356 334
 
357
-=======
358
->>>>>>> bioc/master
359 335
 	which = match.arg(which)[1]
360 336
 	if(which == "column") {
361 337
 		vp_name = paste0(heatmap, "_", which, "_title")
... ...
@@ -372,11 +348,7 @@ decorate_title = function(heatmap, code, slice = 1, which = c("column", "row"),
372 348
 
373 349
 	seekViewport(vp_name)
374 350
 	eval(substitute(code), envir = envir)
375
-<<<<<<< HEAD
376 351
 	seekViewport(current_vp)
377
-=======
378
-	seekViewport("global")
379
->>>>>>> bioc/master
380 352
 }
381 353
 
382 354
 # == title
... ...
@@ -464,14 +436,11 @@ decorate_column_title = function(..., envir = new.env(parent = parent.frame()))
464 436
 #
465 437
 decorate_annotation = function(annotation, code, slice, envir = new.env(parent = parent.frame())) {
466 438
 
467
-<<<<<<< HEAD
468 439
 	current_vp = current.viewport()$name
469 440
 	if(current_vp == "ROOT") {
470 441
 		current_vp = "global"
471 442
 	}
472 443
 	
473
-=======
474
->>>>>>> bioc/master
475 444
 	if(missing(slice)) {
476 445
 		vp_name = paste0("annotation_", annotation)
477 446
 		o = try(seekViewport(vp_name), silent = TRUE)
... ...
@@ -496,10 +465,6 @@ decorate_annotation = function(annotation, code, slice, envir = new.env(parent =
496 465
 	}
497 466
 
498 467
 	eval(substitute(code), envir = envir)
499
-<<<<<<< HEAD
500 468
 	seekViewport(current_vp)
501
-=======
502
-	seekViewport("global")
503
->>>>>>> bioc/master
504 469
 }
505 470
 
... ...
@@ -5,10 +5,7 @@
5 5
 # == param
6 6
 # -data  a matrix or a list. If it is a matrix, density will be calculated by columns.
7 7
 # -col a list of colors that density values are mapped to.
8
-<<<<<<< HEAD
9 8
 # -density_param parameters send to `stats::density`, ``na.rm`` is enforced to ``TRUE``.
10
-=======
11
->>>>>>> bioc/master
12 9
 # -color_space the color space in which colors are interpolated. Pass to `circlize::colorRamp2`.
13 10
 # -anno annotation for the matrix columns or the list. The value should be a vector or a data frame 
14 11
 #       and colors for annotations are randomly assigned. If you want to customize the annotation colors,
... ...
@@ -37,12 +34,9 @@
37 34
 # in each column (or each vector in the list) through a heatmap. It is useful if you have huge number 
38 35
 # of columns in ``data`` to visualize.
39 36
 #
40
-<<<<<<< HEAD
41 37
 # The density matrix is generated with 500 rows ranging between the maximun and minimal values in all densities.
42 38
 # The density values in each row are linearly intepolated between the two density values at the two nearest bounds.
43 39
 #
44
-=======
45
->>>>>>> bioc/master
46 40
 # == value
47 41
 # No value is returned.
48 42
 #
... ...
@@ -64,10 +58,7 @@
64 58
 #
65 59
 densityHeatmap = function(data, 
66 60
 	col = rev(brewer.pal(11, "Spectral")),
67
-<<<<<<< HEAD
68 61
 	density_param = list(na.rm = TRUE),
69
-=======
70
->>>>>>> bioc/master
71 62
 	color_space = "LAB", 
72 63
 	anno = NULL, 
73 64
 	ylab = deparse(substitute(data)), 
... ...
@@ -88,7 +79,6 @@ densityHeatmap = function(data,
88 79
 	column_order = NULL,
89 80
 	...) {
90 81
 
91
-<<<<<<< HEAD
92 82
 	density_param$na.rm = TRUE
93 83
 
94 84
 	if(is.matrix(data)) {
... ...
@@ -97,14 +87,6 @@ densityHeatmap = function(data,
97 87
 		mean_value = apply(data, 2, mean, na.rm = TRUE)
98 88
 	} else if(is.data.frame(data) || is.list(data)) {
99 89
 		density_list = lapply(data, function(x) do.call(density, c(list(x = x), density_param)))
100
-=======
101
-	if(is.matrix(data)) {
102
-		density_list = apply(data, 2, density, na.rm = TRUE)
103
-		quantile_list = apply(data, 2, quantile, na.rm = TRUE)
104
-		mean_value = apply(data, 2, mean, na.rm = TRUE)
105
-	} else if(is.data.frame(data) || is.list(data)) {
106
-		density_list = lapply(data, density, na.rm = TRUE)
107
->>>>>>> bioc/master
108 90
 		quantile_list = sapply(data, quantile, na.rm = TRUE)
109 91
 		mean_value = sapply(data, mean, na.rm = TRUE)
110 92
 	} else {
... ...
@@ -16,10 +16,6 @@
16 16
 #                            Set it to ``NULL`` if you don't want to set the order
17 17
 # -column_order order of samples. By default the order is calculated by the 'memo sort' method which can visualize
18 18
 #                                 the mutual exclusivity across genes. Set it to ``NULL`` if you don't want to set the order
19
-<<<<<<< HEAD
20
-=======
21
-# -show_column_names whether show column names
22
->>>>>>> bioc/master
23 19
 # -show_pct whether show percent values on the left of the oncoprint
24 20
 # -pct_gp graphic paramters for percent row annotation
25 21
 # -pct_digits digits for percent values
... ...
@@ -29,7 +25,6 @@
29 25
 # -remove_empty_columns if there is no alteration in that sample, whether remove it on the heatmap
30 26
 # -heatmap_legend_param pass to `Heatmap`
31 27
 # -top_annotation by default the top annotation contains barplots representing frequency of mutations in every sample.
32
-<<<<<<< HEAD
33 28
 # -top_annotation_height total height of the column annotations on the top.
34 29
 # -bottom_annotation a `HeatmapAnnotation` object.
35 30
 # -bottom_annotation_height total height of the column annotations on the bottom.
... ...
@@ -55,10 +50,6 @@
55 50
 #                 The input parameter for this function is a vector which contains level names under each column in ``split``.
56 51
 # -width the width of the single heatmap, should be a fixed `grid::unit` object. It is used for the layout when the heatmap
57 52
 #        is appended to a list of heatmaps.
58
-=======
59
-# -barplot_ignore specific alterations that you don't want to put on the barplots. If you want to really suppress the top barplot
60
-#        set ``top_annotation`` to ``NULL``.
61
->>>>>>> bioc/master
62 53
 # -... pass to `Heatmap`, so can set ``bottom_annotation`` here.
63 54
 #
64 55
 # == details
... ...
@@ -82,12 +73,7 @@ oncoPrint = function(mat, get_type = function(x) x,
82 73
 	alter_fun = alter_fun_list, alter_fun_list = NULL, col, 
83 74
 	row_order = oncoprint_row_order(),
84 75
 	column_order = oncoprint_column_order(),
85
-<<<<<<< HEAD
86 76
 	show_pct = TRUE, pct_gp = row_names_gp, pct_digits = 0,
87
-=======
88
-	show_column_names = FALSE,
89
-	show_pct = TRUE, pct_gp = gpar(), pct_digits = 0,
90
->>>>>>> bioc/master
91 77
 	axis_gp = gpar(fontsize = 8), 
92 78
 	show_row_barplot = TRUE, 
93 79
 	row_barplot_width = unit(2, "cm"),
... ...
@@ -95,7 +81,6 @@ oncoPrint = function(mat, get_type = function(x) x,
95 81
 	heatmap_legend_param = list(title = "Alterations"),
96 82
 	top_annotation = HeatmapAnnotation(column_bar = anno_oncoprint_barplot(), 
97 83
 		annotation_height = unit(2, "cm")),
98
-<<<<<<< HEAD
99 84
 	top_annotation_height = top_annotation@size,
100 85
 	bottom_annotation = new("HeatmapAnnotation"),
101 86
     bottom_annotation_height = bottom_annotation@size,
... ...
@@ -116,9 +101,6 @@ oncoPrint = function(mat, get_type = function(x) x,
116 101
     gap = unit(1, "mm"),
117 102
     combined_name_fun = function(x) paste(x, collapse = "/"),
118 103
     width = NULL,
119
-=======
120
-	barplot_ignore = NULL,
121
->>>>>>> bioc/master
122 104
 	...) {
123 105
 
124 106
 	if(length(names(list(...))) > 0) {
... ...
@@ -340,7 +322,6 @@ oncoPrint = function(mat, get_type = function(x) x,
340 322
 			z = arr[i, j, ]
341 323
 			names(z) = dimnames(arr)[[3]]
342 324
 			af(x, y, width, height, z)
343
-<<<<<<< HEAD
344 325
 		},
345 326
 		top_annotation = top_annotation,
346 327
 		top_annotation_height = top_annotation_height,
... ...
@@ -364,11 +345,6 @@ oncoPrint = function(mat, get_type = function(x) x,
364 345
 		combined_name_fun = combined_name_fun,
365 346
 		width = width,
366 347
 		...)
367
-=======
368
-		}, show_column_names = show_column_names,
369
-		top_annotation = top_annotation,
370
-		heatmap_legend_param = heatmap_legend_param, ...)
371
->>>>>>> bioc/master
372 348
 
373 349
 	ht@matrix_param$oncoprint = list()
374 350
 	ht@matrix_param$oncoprint$arr = arr
... ...
@@ -424,11 +400,7 @@ unify_mat_list = function(mat_list, default = 0) {
424 400
 
425 401
 
426 402
 # == title
427
-<<<<<<< HEAD
428 403
 # Column barplot annotation for oncoPrint
429
-=======
430
-# Column barplot annotaiton for oncoPrint
431
->>>>>>> bioc/master
432 404
 #
433 405
 # == details
434 406
 # This function is only used for column annotation
... ...
@@ -2,16 +2,12 @@
2 2
 # environment that contains global variables
3 3
 INDEX_ENV = new.env()
4 4
 
5
-<<<<<<< HEAD
6 5
 INDEX_ENV$I_FIGURE = 0
7
-=======
8
->>>>>>> bioc/master
9 6
 INDEX_ENV$I_HEATMAP = 0
10 7
 INDEX_ENV$I_ANNOTATION = 0
11 8
 INDEX_ENV$I_ROW_ANNOTATION = 0
12 9
 INDEX_ENV$I_COLOR_MAPPING = 0
13 10
 
14
-<<<<<<< HEAD
15 11
 get_figure_index = function() {
16 12
     INDEX_ENV$I_FIGURE
17 13
 }
... ...
@@ -20,8 +16,6 @@ increase_figure_index = function() {
20 16
     INDEX_ENV$I_FIGURE = INDEX_ENV$I_FIGURE + 1
21 17
 }
22 18
 
23
-=======
24
->>>>>>> bioc/master
25 19
 get_heatmap_index = function() {
26 20
 	INDEX_ENV$I_HEATMAP
27 21
 }
... ...
@@ -72,12 +66,8 @@ default_col = function(x, main_matrix = FALSE) {
72 66
 
73 67
     if(is.character(x)) {  # discrete
74 68
         levels = unique(x)
75
-<<<<<<< HEAD
76 69
         #colors = hsv(runif(length(levels)), 1-runif(1)/2, 1-runif(1)/2)
77 70
         colors = rand_color(length(levels), luminosity = sample(c("bright", "light", "dark", "random"), 1))
78
-=======
79
-        colors = hsv(runif(length(levels)), 1-runif(1)/2, 1-runif(1)/2)
80
->>>>>>> bioc/master
81 71
         names(colors) = levels
82 72
         return(colors)
83 73
     } else if(is.numeric(x)) {
... ...
@@ -88,12 +78,8 @@ default_col = function(x, main_matrix = FALSE) {
88 78
                 col_fun = colorRamp2(seq(min(x), max(x), length = 3), c("blue", "#EEEEEE", "red"))
89 79
             }
90 80
         } else {
91
-<<<<<<< HEAD
92 81
             #col_fun = colorRamp2(range(min(x), max(x)), c("white", hsv(runif(1), 1, 1)))
93 82
             col_fun = colorRamp2(range(min(x), max(x)), c("white", rand_color(1, luminosity = sample(c("bright", "dark"), 1))))
94
-=======
95
-            col_fun = colorRamp2(range(min(x), max(x)), c("white", hsv(runif(1), 1, 1)))
96
->>>>>>> bioc/master
97 83
         }
98 84
         return(col_fun)
99 85
     }
... ...
@@ -147,11 +133,6 @@ grid.dendrogram = function(dend, facing = c("bottom", "top", "left", "right"),
147 133
             leaf
148 134
         }
149 135
     }
150
-<<<<<<< HEAD
151
-=======
152
-
153
-    labels(dend) = paste0("leaf_", seq_len(nnodes(dend)))
154
->>>>>>> bioc/master
155 136
     
156 137
     draw.d = function(dend, max_height, facing = "bottom", order = "normal", max_width = 0, env = NULL) {
157 138
         leaf = attr(dend, "leaf")
... ...
@@ -302,7 +283,6 @@ grid.dendrogram = function(dend, facing = c("bottom", "top", "left", "right"),
302 283
 }
303 284
 
304 285
 # == title
305
-<<<<<<< HEAD
306 286
 # Adjust dendrogram based on width of leaves
307 287
 #
308 288
 # == param
... ...
@@ -584,8 +564,6 @@ grid.dendrogram2 = function(dend, facing = c("bottom", "top", "left", "right"),
584 564
 }
585 565
 
586 566
 # == title
587
-=======
588
->>>>>>> bioc/master
589 567
 # Calculate pairwise distance from a matrix
590 568
 #
591 569
 # == param
... ...
@@ -676,17 +654,12 @@ get_dend_order = function(x) {
676 654
 
677 655
 # can only cut dendrogram for which branches at every node are two
678 656
 cut_dendrogram = function(dend, k) {
679
-<<<<<<< HEAD
680 657
     h = sort(dend_branches_heights(dend), decreasing = TRUE)
681
-=======
682
-    h = sort(get_branches_heights(dend), decreasing = TRUE)
683
->>>>>>> bioc/master
684 658
     height = (h[k-1] + h[k])/2
685 659
     trees = cut(dend, h = height)
686 660
     trees$lower
687 661
 }
688 662
 
689
-<<<<<<< HEAD
690 663
 dend_branches_heights = function(d, v = NULL) {
691 664
     if(!is.leaf(d)) {
692 665
         v = c(v, attr(d, "height"))
... ...
@@ -696,8 +669,6 @@ dend_branches_heights = function(d, v = NULL) {
696 669
     return(v)
697 670
 }
698 671
 
699
-=======
700
->>>>>>> bioc/master
701 672
 recycle_gp = function(gp, n = 1) {
702 673
     for(i in seq_along(gp)) {
703 674
         x = gp[[i]]
... ...
@@ -818,12 +789,9 @@ list_component = function() {
818 789
 # max_text_width(x, gp = gpar(fontsize = 10))
819 790
 #
820 791
 max_text_width = function(text, ...) {
821
-<<<<<<< HEAD
822 792
     if(is.null(text)) {
823 793
         return(unit(0, "mm"))
824 794
     }
825
-=======
826
->>>>>>> bioc/master
827 795
     max(do.call("unit.c", lapply(text, function(x) grobWidth(textGrob(x, ...)))))
828 796
 }
829 797
 
... ...
@@ -851,11 +819,8 @@ max_text_width = function(text, ...) {
851 819
 # max_text_height(x, gp = gpar(fontsize = 10))
852 820
 #
853 821
 max_text_height = function(text, ...) {
854
-<<<<<<< HEAD
855 822
     if(is.null(text)) {
856 823
         return(unit(0, "mm"))
857 824
     }
858
-=======
859
->>>>>>> bioc/master
860 825
     max(do.call("unit.c", lapply(text, function(x) grobHeight(textGrob(x, ...)))))
861 826
 }
... ...
@@ -11,11 +11,7 @@ Heatmap(matrix, col, name,
11 11
     na_col = "grey",
12 12
     color_space = "LAB",
13 13
     rect_gp = gpar(col = NA),
14
-<<<<<<< HEAD
15 14
     cell_fun = NULL,
16
-=======
17
-    cell_fun = function(j, i, x, y, width, height, fill) NULL,
18
->>>>>>> bioc/master
19 15
     row_title = character(0),
20 16
     row_title_side = c("left", "right"),
21 17
     row_title_gp = gpar(fontsize = 14),
... ...
@@ -54,19 +50,11 @@ Heatmap(matrix, col, name,
54 50
     column_order = NULL,
55 51
     row_names_side = c("right", "left"),
56 52
     show_row_names = TRUE,
57
-<<<<<<< HEAD
58 53
     row_names_max_width = default_row_names_max_width(),
59 54
     row_names_gp = gpar(fontsize = 12),
60 55
     column_names_side = c("bottom", "top"),
61 56
     show_column_names = TRUE,
62 57
     column_names_max_height = default_column_names_max_height(),
63
-=======
64
-    row_names_max_width = unit(4, "cm"),
65
-    row_names_gp = gpar(fontsize = 12),
66
-    column_names_side = c("bottom", "top"),
67
-    show_column_names = TRUE,
68
-    column_names_max_height = unit(4, "cm"),
69
->>>>>>> bioc/master
70 58
     column_names_gp = gpar(fontsize = 12),
71 59
     top_annotation = new("HeatmapAnnotation"),
72 60
     top_annotation_height = top_annotation@size,
... ...
@@ -79,11 +67,7 @@ Heatmap(matrix, col, name,
79 67
     combined_name_fun = function(x) paste(x, collapse = "/"),
80 68
     width = NULL,
81 69
     show_heatmap_legend = TRUE,
82
-<<<<<<< HEAD
83 70
     heatmap_legend_param = list(title = name),
84
-=======
85
-    heatmap_legend_param = list(title = name, color_bar = "discrete"),
86
->>>>>>> bioc/master
87 71
     use_raster = FALSE,
88 72
     raster_device = c("png", "jpeg", "tiff", "CairoPNG", "CairoJPEG", "CairoTIFF"),
89 73
     raster_quality = 1,
... ...
@@ -147,22 +131,14 @@ Heatmap(matrix, col, name,
147 131
   \item{bottom_annotation}{a \code{\link{HeatmapAnnotation}} object.}
148 132
   \item{bottom_annotation_height}{total height of the column annotations on the bottom.}
149 133
   \item{km}{do k-means clustering on rows. If the value is larger than 1, the heatmap will be split by rows according to the k-means clustering. For each row-clusters, hierarchical clustering is still applied with parameters above.}
150
-<<<<<<< HEAD
151 134
   \item{km_title}{row title for each cluster when \code{km} is set. It must a text with format of ".*\%i.*" where "\%i" is replaced by the index of the cluster.}
152
-=======
153
-  \item{km_title}{row title for each cluster when \code{km} is set. It must a text with format of "*\%i*" where "\%i" is replaced by the index of the cluster.}
154
->>>>>>> bioc/master
155 135
   \item{split}{a vector or a data frame by which the rows are split. But if \code{cluster_rows} is a clustering object, \code{split} can be a single number indicating rows are to be split according to the split on the tree.}
156 136
   \item{gap}{gap between row-slices if the heatmap is split by rows, should be \code{\link[grid]{unit}} object. If it is a vector, the order corresponds to top to bottom in the heatmap}
157 137
   \item{combined_name_fun}{if the heatmap is split by rows, how to make a combined row title for each slice? The input parameter for this function is a vector which contains level names under each column in \code{split}.}
158 138
   \item{width}{the width of the single heatmap, should be a fixed \code{\link[grid]{unit}} object. It is used for the layout when the heatmap is appended to a list of heatmaps.}
159 139
   \item{show_heatmap_legend}{whether show heatmap legend?}
160 140
   \item{heatmap_legend_param}{a list contains parameters for the heatmap legend. See \code{\link{color_mapping_legend,ColorMapping-method}} for all available parameters.}
161
-<<<<<<< HEAD
162 141
   \item{use_raster}{whether render the heatmap body as a raster image. It helps to reduce file size when the matrix is huge. Note if \code{cell_fun} is set, \code{use_raster} is enforced to be \code{FALSE}.}
163
-=======
164
-  \item{use_raster}{whether render the heatmap body as a raster image. It helps to reduce file size when the matrix is huge.}
165
->>>>>>> bioc/master
166 142
   \item{raster_device}{graphic device which is used to generate the raster image}
167 143
   \item{raster_quality}{a value set to larger than 1 will improve the quality of the raster image.}
168 144
   \item{raster_device_param}{a list of further parameters for the selected graphic device}
... ...
@@ -11,13 +11,8 @@ Method dispatch page for \code{add_heatmap}.
11 11
 
12 12
 \itemize{
13 13
 \item \code{\link{add_heatmap,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
14
-<<<<<<< HEAD
15 14
 \item \code{\link{add_heatmap,Heatmap-method}}, \code{\link{Heatmap-class}} class method
16 15
 \item \code{\link{add_heatmap,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
17
-=======
18
-\item \code{\link{add_heatmap,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
19
-\item \code{\link{add_heatmap,Heatmap-method}}, \code{\link{Heatmap-class}} class method
20
->>>>>>> bioc/master
21 16
 }
22 17
 }
23 18
 \examples{
... ...
@@ -14,11 +14,7 @@ anno_link(at, labels, which = c("column", "row"), side = ifelse(which == "column
14 14
 
15 15
   \item{at}{numeric index in the original matrix}
16 16
   \item{labels}{corresponding labels}
17
-<<<<<<< HEAD
18 17
   \item{which}{column annotation or row annotation}
19
-=======
20
-  \item{which}{column annotaiton or row annotation}
21
->>>>>>> bioc/master
22 18
   \item{side}{side of the labels. If it is a column annotation, permitted values are "top" and "bottom"; If it is a row annotation, permitted values are "left" and "right".}
23 19
   \item{lines_gp}{graphic settings for the segments}
24 20
   \item{labels_gp}{graphic settings for the labels}
... ...
@@ -1,17 +1,10 @@
1 1
 \name{anno_oncoprint_barplot}
2 2
 \alias{anno_oncoprint_barplot}
3 3
 \title{
4
-<<<<<<< HEAD
5 4
 Column barplot annotation for oncoPrint
6 5
 }
7 6
 \description{
8 7
 Column barplot annotation for oncoPrint
9
-=======
10
-Column barplot annotaiton for oncoPrint
11
-}
12
-\description{
13
-Column barplot annotaiton for oncoPrint
14
->>>>>>> bioc/master
15 8
 }
16 9
 \usage{
17 10
 anno_oncoprint_barplot()
... ...
@@ -13,17 +13,10 @@ Draw legend based on color mapping
13 13
     title = object@name,
14 14
     title_gp = gpar(fontsize = 10, fontface = "bold"),
15 15
     title_position = c("topleft", "topcenter", "leftcenter", "lefttop"),
16
-<<<<<<< HEAD
17 16
     color_bar = object@type,
18 17
     grid_height = unit(4, "mm"),
19 18
     grid_width = unit(4, "mm"),
20 19
     border = NULL,
21
-=======
22
-    color_bar = c("discrete", "continuous"),
23
-    grid_height = unit(4, "mm"),
24
-    grid_width = unit(4, "mm"),
25
-    grid_border = NULL,
26
->>>>>>> bioc/master
27 20
     at = object@levels,
28 21
     labels = at,
29 22
     labels_gp = gpar(fontsize = 10),
... ...
@@ -40,17 +33,10 @@ Draw legend based on color mapping
40 33
   \item{title}{title of the legend, by default it is the name of the legend}
41 34
   \item{title_gp}{graphical parameters for legend title}
42 35
   \item{title_position}{position of the title}
43
-<<<<<<< HEAD
44 36
   \item{color_bar}{a string of "continous" or "discrete". If the mapping is continuous, whether show the legend as discrete color bar or continuous color bar}
45 37
   \item{grid_height}{height of each legend grid.}
46 38
   \item{grid_width}{width of each legend grid.}
47 39
   \item{border}{color for legend grid borders.}
48
-=======
49
-  \item{color_bar}{if the mapping is continuous, whether show the legend as discrete color bar or continuous color bar}
50
-  \item{grid_height}{height of each legend grid.}
51
-  \item{grid_width}{width of each legend grid.}
52
-  \item{grid_border}{color for legend grid borders.}
53
->>>>>>> bioc/master
54 40
   \item{at}{break values of the legend}
55 41
   \item{labels}{labels corresponding to break values}
56 42
   \item{labels_gp}{graphcial parameters for legend labels}
... ...
@@ -10,13 +10,8 @@ Method dispatch page for \code{component_height}.
10 10
 \code{component_height} can be dispatched on following classes:
11 11
 
12 12
 \itemize{
13
-<<<<<<< HEAD
14 13
 \item \code{\link{component_height,Heatmap-method}}, \code{\link{Heatmap-class}} class method
15 14
 \item \code{\link{component_height,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
16
-=======
17
-\item \code{\link{component_height,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
18
-\item \code{\link{component_height,Heatmap-method}}, \code{\link{Heatmap-class}} class method
19
->>>>>>> bioc/master
20 15
 }
21 16
 }
22 17
 \examples{
... ...
@@ -10,13 +10,8 @@ Method dispatch page for \code{component_width}.
10 10
 \code{component_width} can be dispatched on following classes:
11 11
 
12 12
 \itemize{
13
-<<<<<<< HEAD
14 13
 \item \code{\link{component_width,Heatmap-method}}, \code{\link{Heatmap-class}} class method
15 14
 \item \code{\link{component_width,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
16
-=======
17
-\item \code{\link{component_width,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
18
-\item \code{\link{component_width,Heatmap-method}}, \code{\link{Heatmap-class}} class method
19
->>>>>>> bioc/master
20 15
 }
21 16
 }
22 17
 \examples{
... ...
@@ -9,10 +9,7 @@ Use colors to represent density distribution
9 9
 \usage{
10 10
 densityHeatmap(data,
11 11
     col = rev(brewer.pal(11, "Spectral")),
12
-<<<<<<< HEAD
13 12
     density_param = list(na.rm = TRUE),
14
-=======
15
->>>>>>> bioc/master
16 13
     color_space = "LAB",
17 14
     anno = NULL,
18 15
     ylab = deparse(substitute(data)),
... ...
@@ -37,10 +34,7 @@ densityHeatmap(data,
37 34
 
38 35
   \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns.}
39 36
   \item{col}{a list of colors that density values are mapped to.}
40
-<<<<<<< HEAD
41 37
   \item{density_param}{parameters send to \code{\link[stats]{density}}, \code{na.rm} is enforced to \code{TRUE}.}
42
-=======
43
->>>>>>> bioc/master
44 38
   \item{color_space}{the color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}
45 39
   \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame  and colors for annotations are randomly assigned. If you want to customize the annotation colors, use a \code{\link{HeatmapAnnotation-class}} object directly.}
46 40
   \item{ylab}{label on y-axis in the plot}
... ...
@@ -67,12 +61,9 @@ To visualize data distribution in a matrix or in a list, sometimes we use boxplo
67 61
 Here we use colors to map the density values and visualize distribution of values
68 62
 in each column (or each vector in the list) through a heatmap. It is useful if you have huge number 
69 63
 of columns in \code{data} to visualize.
70
-<<<<<<< HEAD
71 64
 
72 65
 The density matrix is generated with 500 rows ranging between the maximun and minimal values in all densities.
73 66
 The density values in each row are linearly intepolated between the two density values at the two nearest bounds.
74
-=======
75
->>>>>>> bioc/master
76 67
 }
77 68
 \value{
78 69
 No value is returned.
... ...
@@ -13,11 +13,7 @@ Draw the single annotation
13 13
 
14 14
   \item{object}{a \code{\link{SingleAnnotation-class}} object.}
15 15
   \item{index}{a vector of orders}
16
-<<<<<<< HEAD
17 16
   \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the names of the viewport which contains the annotation graphics.}
18
-=======
19
-  \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewport which contains the annotation graphics.}
20
->>>>>>> bioc/master
21 17
   \item{n}{total number of row slices}
22 18
 
23 19
 }
... ...
@@ -10,15 +10,9 @@ Method dispatch page for \code{draw}.
10 10
 \code{draw} can be dispatched on following classes:
11 11
 
12 12
 \itemize{
13
-<<<<<<< HEAD
14 13
 \item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
15 14
 \item \code{\link{draw,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
16 15
 \item \code{\link{draw,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
17
-=======
18
-\item \code{\link{draw,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
19
-\item \code{\link{draw,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
20
-\item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
21
->>>>>>> bioc/master
22 16
 \item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method
23 17
 }
24 18
 }
... ...
@@ -14,10 +14,7 @@ Make layout for the complete plot
14 14
     column_title_side = c("top", "bottom"),
15 15
     column_title_gp = gpar(fontsize = 14),
16 16
     heatmap_legend_side = c("right", "left", "bottom", "top"),
17
-<<<<<<< HEAD
18 17
     merge_legends = FALSE,
19
-=======
20
->>>>>>> bioc/master
21 18
     show_heatmap_legend = TRUE,
22 19
     heatmap_legend_list = list(),
23 20
     annotation_legend_side = c("right", "left", "bottom", "top"),
... ...
@@ -37,12 +34,8 @@ Make layout for the complete plot
37 34
     row_dend_gp = NULL,
38 35
     row_order = NULL,
39 36
     km = NULL,
40
-<<<<<<< HEAD
41 37
     split = NULL,
42 38
     combined_name_fun = NULL)
43
-=======
44
-    split = NULL)
45
->>>>>>> bioc/master
46 39
 }
47 40
 \arguments{
48 41
 
... ...
@@ -54,10 +47,7 @@ Make layout for the complete plot
54 47
   \item{column_title_side}{will the title be put on the top or bottom of the heatmap.}
55 48
   \item{column_title_gp}{graphic parameters for drawing text.}
56 49
   \item{heatmap_legend_side}{side of the heatmap legend.}
57
-<<<<<<< HEAD
58 50
   \item{merge_legends}{whether put heatmap legends and annotation legends in a same column}
59
-=======
60
->>>>>>> bioc/master
61 51
   \item{show_heatmap_legend}{whether show heatmap legend.}
62 52
   \item{heatmap_legend_list}{a list of self-defined legend, should be wrapped into \code{\link[grid]{grob}} objects.}
63 53
   \item{annotation_legend_side}{side of annotation legend.}
... ...
@@ -78,10 +68,7 @@ Make layout for the complete plot
78 68
   \item{row_order}{same setting as in \code{\link{Heatmap}}, if it is specified, \code{row_order} in main heatmap is ignored.}
79 69
   \item{km}{same setting as in \code{\link{Heatmap}}, if it is specified, \code{km} in main heatmap is ignored.}
80 70
   \item{split}{same setting as in \code{\link{Heatmap}}, if it is specified, \code{split} in main heatmap is ignored.}
81
-<<<<<<< HEAD
82 71
   \item{combined_name_fun}{same setting as in \code{\link{Heatmap}}, if it is specified, \code{combined_name_fun} in main heatmap is ignored.}
83
-=======
84
->>>>>>> bioc/master
85 72
 
86 73
 }
87 74
 \details{
... ...
@@ -11,12 +11,7 @@ oncoPrint(mat, get_type = function(x) x,
11 11
     alter_fun = alter_fun_list, alter_fun_list = NULL, col,
12 12
     row_order = oncoprint_row_order(),
13 13
     column_order = oncoprint_column_order(),
14
-<<<<<<< HEAD
15 14
     show_pct = TRUE, pct_gp = row_names_gp, pct_digits = 0,
16
-=======
17
-    show_column_names = FALSE,
18
-    show_pct = TRUE, pct_gp = gpar(), pct_digits = 0,
19
->>>>>>> bioc/master
20 15
     axis_gp = gpar(fontsize = 8),
21 16
     show_row_barplot = TRUE,
22 17
     row_barplot_width = unit(2, "cm"),
... ...
@@ -24,7 +19,6 @@ oncoPrint(mat, get_type = function(x) x,
24 19
     heatmap_legend_param = list(title = "Alterations"),
25 20
     top_annotation = HeatmapAnnotation(column_bar = anno_oncoprint_barplot(),
26 21
     annotation_height = unit(2, "cm")),
27
-<<<<<<< HEAD
28 22
     top_annotation_height = top_annotation@size,
29 23
     bottom_annotation = new("HeatmapAnnotation"),
30 24
     bottom_annotation_height = bottom_annotation@size,
... ...
@@ -45,9 +39,6 @@ oncoPrint(mat, get_type = function(x) x,
45 39
     gap = unit(1, "mm"),
46 40
     combined_name_fun = function(x) paste(x, collapse = "/"),
47 41
     width = NULL,
48
-=======
49
-    barplot_ignore = NULL,
50
->>>>>>> bioc/master
51 42
     ...)
52 43
 }
53 44
 \arguments{
... ...
@@ -59,10 +50,6 @@ oncoPrint(mat, get_type = function(x) x,
59 50
   \item{col}{a vector of color for which names correspond to alteration types.}
60 51
   \item{row_order}{order of genes. By default it is sorted by frequency of alterations decreasingly. Set it to \code{NULL} if you don't want to set the order}
61 52
   \item{column_order}{order of samples. By default the order is calculated by the 'memo sort' method which can visualize the mutual exclusivity across genes. Set it to \code{NULL} if you don't want to set the order}
62
-<<<<<<< HEAD
63
-=======
64
-  \item{show_column_names}{whether show column names}
65
->>>>>>> bioc/master
66 53
   \item{show_pct}{whether show percent values on the left of the oncoprint}
67 54
   \item{pct_gp}{graphic paramters for percent row annotation}
68 55
   \item{pct_digits}{digits for percent values}
... ...
@@ -72,7 +59,6 @@ oncoPrint(mat, get_type = function(x) x,
72 59
   \item{remove_empty_columns}{if there is no alteration in that sample, whether remove it on the heatmap}
73 60
   \item{heatmap_legend_param}{pass to \code{\link{Heatmap}}}
74 61
   \item{top_annotation}{by default the top annotation contains barplots representing frequency of mutations in every sample.}
75
-<<<<<<< HEAD
76 62
   \item{top_annotation_height}{total height of the column annotations on the top.}
77 63
   \item{bottom_annotation}{a \code{\link{HeatmapAnnotation}} object.}
78 64
   \item{bottom_annotation_height}{total height of the column annotations on the bottom.}
... ...
@@ -93,9 +79,6 @@ oncoPrint(mat, get_type = function(x) x,
93 79
   \item{gap}{gap between row-slices if the heatmap is split by rows, should be \code{\link[grid]{unit}} object. If it is a vector, the order corresponds to top to bottom in the heatmap}
94 80
   \item{combined_name_fun}{if the heatmap is split by rows, how to make a combined row title for each slice? The input parameter for this function is a vector which contains level names under each column in \code{split}.}
95 81
   \item{width}{the width of the single heatmap, should be a fixed \code{\link[grid]{unit}} object. It is used for the layout when the heatmap is appended to a list of heatmaps.}
96
-=======
97
-  \item{barplot_ignore}{specific alterations that you don't want to put on the barplots. If you want to really suppress the top barplot set \code{top_annotation} to \code{NULL}.}
98
->>>>>>> bioc/master
99 82
   \item{...}{pass to \code{\link{Heatmap}}, so can set \code{bottom_annotation} here.}
100 83
 
101 84
 }
... ...
@@ -10,17 +10,10 @@ Method dispatch page for \code{show}.
10 10
 \code{show} can be dispatched on following classes:
11 11
 
12 12
 \itemize{
13
-<<<<<<< HEAD
14 13
 \item \code{\link{show,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
15 14
 \item \code{\link{show,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method
16 15
 \item \code{\link{show,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
17 16
 \item \code{\link{show,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
18
-=======
19
-\item \code{\link{show,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method
20
-\item \code{\link{show,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
21
-\item \code{\link{show,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
22
-\item \code{\link{show,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
23
->>>>>>> bioc/master
24 17
 \item \code{\link{show,Heatmap-method}}, \code{\link{Heatmap-class}} class method
25 18
 }
26 19
 }
... ...
@@ -6,11 +6,7 @@ draw(anno, c(1, 4, 3, 5, 2))
6 6
 dev.off()
7 7
 
8 8
 test_that("discrete color mapping", {
9
-<<<<<<< HEAD
10 9
 	expect_that(show(anno), prints_text("An annotation with discrete color mapping"))
11
-=======
12
-	expect_that(show(anno), prints_text("An annotaiton with discrete color mapping"))
13
->>>>>>> bioc/master
14 10
 })
15 11
 
16 12
 pdf(NULL)
... ...
@@ -23,11 +19,7 @@ draw(anno, 1:10)
23 19
 dev.off()
24 20
 
25 21
 test_that("continuous color mapping", {
26
-<<<<<<< HEAD
27 22
 	expect_that(show(anno), prints_text("An annotation with continuous color mapping"))
28
-=======
29
-	expect_that(show(anno), prints_text("An annotaiton with continuous color mapping"))
30
->>>>>>> bioc/master
31 23
 })
32 24
 
33 25
 pdf(NULL)
... ...
@@ -194,11 +194,7 @@ ha = HeatmapAnnotation(boxplot = anno_boxplot(mat))
194 194
 draw(ha, 1:10)
195 195
 ```
196 196
 
197
-<<<<<<< HEAD
198 197
 You can mix simple annotations and complex annotations:
199
-=======
200
-You can mix simple annotaitons and complex annotations:
201
->>>>>>> bioc/master
202 198
 
203 199
 ```{r heatmap_annotation_mixed_with_complex, fig.width = 7, fig.height = 2}
204 200
 ha = HeatmapAnnotation(df = df, 
... ...
@@ -157,59 +157,36 @@ ht1 = Heatmap(mat, name = "ht1", show_heatmap_legend = FALSE)
157 157
 draw(ht1 + ha_chr, heatmap_legend_side = "bottom")
158 158
 ```
159 159
 
160
-<<<<<<< HEAD
161 160
 Discrete color bar for can be used for continuous values, if you specify `color_bar` to `discrete`.
162 161
 For the simple annotation which contains continuous values, `color_bar` can also be set to `discrete`.
163
-=======
164
-If you don't like the default discrete color bar for continuous values, you can specify `color_bar` to `continuous`.
165
-For the simple annotation which contains continuous values, `color_bar` can also be set to `continuous`.
166
->>>>>>> bioc/master
167 162
 
168 163
 ```{r}
169 164
 ha = HeatmapAnnotation(df = data.frame(value = runif(10)), 
170 165
     col = list(value = colorRamp2(c(0, 1), c("white", "blue"))), 
171
-<<<<<<< HEAD
172 166
     annotation_legend_param = list(color_bar = "discrete", at = c(0, 0.5, 1)))
173 167
 Heatmap(mat, name = "ht1", top_annotation = ha, heatmap_legend_param = list(color_bar = "discrete"))
174
-=======
175
-    annotation_legend_param = list(color_bar = "continuous", at = c(0, 0.5, 1), 
176
-        labels = c("low", "median", "high"), legend_height = unit(4, "cm")))
177
-Heatmap(mat, name = "ht1", top_annotation = ha, heatmap_legend_param = list(color_bar = "continuous"))
178
->>>>>>> bioc/master
179 168
 ```
180 169
 
181 170
 Some users prefer to put the legend at the bottom of heatmaps.
182 171
 
183 172
 ```{r}
184
-<<<<<<< HEAD
185 173
 ht = Heatmap(mat, name = "ht1", heatmap_legend_param = list(legend_direction = "horizontal",
186
-=======
187
-ht = Heatmap(mat, name = "ht1", heatmap_legend_param = list(color_bar = "continuous", legend_direction = "horizontal",
188
->>>>>>> bioc/master
189 174
     legend_width = unit(5, "cm"), title_position = "lefttop"))
190 175
 draw(ht, heatmap_legend_side = "bottom")
191 176
 ```
192 177
 
193
-<<<<<<< HEAD
194 178
 Similarly, the height of the legend can be adjusted by `legend_height` if the legend is vertical.
195 179
 
196 180
 ```{r}
197 181
 Heatmap(mat, name = "ht1", heatmap_legend_param = list(legend_height = unit(5, "cm")))
198 182
 ```
199 183
 
200
-=======
201
->>>>>>> bioc/master
202 184
 If you want to change default settings for all heatmaps/annotations, you can set it globally by `ht_global_opt()`.
203 185
 
204 186
 ```{r, fig.width = 10}
205 187
 ht_global_opt(heatmap_legend_title_gp = gpar(fontsize = 16), annotation_legend_labels_gp = gpar(fontface = "italic"))
206 188
 ha = HeatmapAnnotation(df = data.frame(value = runif(10)), 
207
-<<<<<<< HEAD
208 189
     col = list(value = colorRamp2(c(0, 1), c("white", "blue"))))
209
-=======
210
-    col = list(value = colorRamp2(c(0, 1), c("white", "blue"))), 
211
-    annotation_legend_param = list(color_bar = "continuous"))
212
->>>>>>> bioc/master
213 190
 ht1 = Heatmap(mat, name = "ht1", column_title = "Heatmap 1", top_annotation = ha)
214 191
 ht2 = Heatmap(mat, name = "ht2", column_title = "Heatmap 2", heatmap_legend_param = list(title_gp = gpar(fontsize = 8)))
215 192
 ht1 + ht2