Browse code

won't generate color matrix when type=='none'

Zuguang Gu authored on 15/12/2020 12:01:39
Showing139 changed files

... ...
@@ -1,8 +1,8 @@
1 1
 Package: ComplexHeatmap
2 2
 Type: Package
3 3
 Title: Make Complex Heatmaps
4
-Version: 2.7.1.1012
5
-Date: 2020-12-14
4
+Version: 2.7.1.1013
5
+Date: 2020-12-15
6 6
 Author: Zuguang Gu
7 7
 Maintainer: Zuguang Gu <z.gu@dkfz.de>
8 8
 Depends: R (>= 3.1.2), methods, grid, graphics, stats, grDevices
... ...
@@ -44,7 +44,10 @@ setMethod(f = "draw_heatmap_body",
44 44
     pushViewport(viewport(name = paste(object@name, "heatmap_body", kr, kc, sep = "_"), ...))
45 45
 
46 46
     mat = object@matrix[row_order, column_order, drop = FALSE]
47
-    col_matrix = map_to_colors(object@matrix_color_mapping, mat)
47
+    oe = try(col_matrix <- map_to_colors(object@matrix_color_mapping, mat), silent = TRUE)
48
+    if(inherits(oe, "try-error")) {
49
+        col_matrix = matrix(NA, nrow = nrow(mat), ncol = ncol(mat))
50
+    }
48 51
 
49 52
     nc = ncol(mat)
50 53
     nr = nrow(mat)
... ...
@@ -8,6 +8,7 @@
8 8
 #      value representing whether the alteration is present or absent. 
9 9
 #      When the value is a list, the names of the list represent alteration types.
10 10
 #      You can use `unify_mat_list` to make all matrix having same row names and column names.
11
+# -name Name of the oncoPrint. Not necessary to specify.
11 12
 # -get_type If different alterations are encoded in the matrix as complex strings, this self-defined function
12 13
 #           determines how to extract them. It only works when ``mat`` is a matrix. The default value is `default_get_type`.
13 14
 # -alter_fun A single function or a list of functions which defines how to add graphics for different alterations.
... ...
@@ -53,7 +54,7 @@
53 54
 # == author
54 55
 # Zuguang Gu <z.gu@dkfz.de>
55 56
 #
56
-oncoPrint = function(mat, 
57
+oncoPrint = function(mat, name,
57 58
 	get_type = default_get_type,
58 59
 	alter_fun, 
59 60
 	alter_fun_is_vectorized = NULL,
... ...
@@ -182,6 +183,14 @@ oncoPrint = function(mat,
182 183
 		arr[, , i] = mat_list[[i]]
183 184
 	}
184 185
 
186
+	if(missing(name)) {
187
+        name = paste0("matrix_", get_oncoprint_index() + 1)
188
+        increase_oncoprint_index()
189
+    } else if(is.null(name)) {
190
+        name = paste0("matrix_", get_oncoprint_index() + 1)
191
+        increase_oncoprint_index()
192
+    }
193
+
185 194
 	oncoprint_row_order = function() {
186 195
 		order(rowSums(count_matrix), n_mut, decreasing = TRUE)
187 196
 	}
... ...
@@ -468,13 +477,17 @@ oncoPrint = function(mat,
468 477
 	
469 478
 	#####################################################################
470 479
 	# the main matrix
471
-	if(length(col)) {
472
-		pheudo = c(names(col), rep(NA, nrow(arr)*ncol(arr) - length(col)))
473
-	} else {
474
-		pheudo = c("mutation", rep(NA, nrow(arr)*ncol(arr) - 1))
480
+	if(length(col) == 0) {
475 481
 		col = c("mutation" = "black")
476 482
 	}
477 483
 
484
+	pheudo = apply(arr, 1:2, function(x) {
485
+		if(all(!x)) {
486
+			return("")
487
+		} else {
488
+			paste(all_type[x], collapse = ";")
489
+		}
490
+	})
478 491
 	dim(pheudo) = dim(arr)[1:2]
479 492
 	dimnames(pheudo) = dimnames(arr)[1:2]
480 493
 	
... ...
@@ -558,7 +571,7 @@ oncoPrint = function(mat,
558 571
 		}
559 572
 	}
560 573
 
561
-	ht = Heatmap(pheudo, col = col, 
574
+	ht = Heatmap(pheudo, name = name, col = col, 
562 575
 		rect_gp = gpar(type = "none"), 
563 576
 		cluster_rows = cluster_rows, cluster_columns = cluster_columns, 
564 577
 		row_order = row_order, column_order = column_order,
... ...
@@ -54,8 +54,8 @@ heatmap = function(x,
54 54
     margins = c(5, 5), 
55 55
     ColSideColors, 
56 56
     RowSideColors,
57
-    cexRow = 0.2 + 1/log10(nr), 
58
-    cexCol = 0.2 + 1/log10(nc),
57
+    cexRow = 0.6, 
58
+    cexCol = 0.6,
59 59
     labRow = NULL, 
60 60
     labCol = NULL, 
61 61
     main = NULL,
... ...
@@ -368,7 +368,7 @@ heatmap.2 = function(x,
368 368
 
369 369
     # data scaling
370 370
     scale = c("none","row", "column"),
371
-    na.rm=TRUE,
371
+    na.rm = TRUE,
372 372
 
373 373
     # image plot
374 374
     revC = identical(Colv, "Rowv"),
... ...
@@ -376,36 +376,36 @@ heatmap.2 = function(x,
376 376
 
377 377
     # mapping data to colors
378 378
     breaks,
379
-    symbreaks=any(x < 0, na.rm=TRUE) || scale!="none",
379
+    symbreaks = any(x < 0, na.rm = TRUE) || scale != "none",
380 380
 
381 381
     # colors
382
-    col="heat.colors",
382
+    col = "heat.colors",
383 383
 
384 384
     # block sepration
385 385
     colsep,
386 386
     rowsep,
387
-    sepcolor="white",
388
-    sepwidth=c(0.05,0.05),
387
+    sepcolor = "white",
388
+    sepwidth = c(0.05, 0.05),
389 389
 
390 390
     # cell labeling
391 391
     cellnote,
392
-    notecex=1.0,
393
-    notecol="cyan",
394
-    na.color=par("bg"),
392
+    notecex = 0.6,
393
+    notecol = "cyan",
394
+    na.color = par("bg"),
395 395
 
396 396
     # level trace
397
-    trace=c("column","row","both","none"),
398
-    tracecol="cyan",
399
-    hline=median(breaks),
400
-    vline=median(breaks),
401
-    linecol=tracecol,
397
+    trace = c("column", "row", "both", "none"),
398
+    tracecol = "cyan",
399
+    hline = median(breaks),
400
+    vline = median(breaks),
401
+    linecol = tracecol,
402 402
 
403 403
     # Row/Column Labeling
404 404
     margins = c(5, 5),
405 405
     ColSideColors,
406 406
     RowSideColors,
407
-    cexRow = 0.2 + 1/log10(nr),
408
-    cexCol = 0.2 + 1/log10(nc),
407
+    cexRow = 0.6,
408
+    cexCol = 0.6,
409 409
     labRow = NULL,
410 410
     labCol = NULL,
411 411
     srtRow = NULL,
... ...
@@ -420,16 +420,16 @@ heatmap.2 = function(x,
420 420
     # color key + density info
421 421
     key = TRUE,
422 422
     keysize = 1.5,
423
-    density.info=c("histogram","density","none"),
424
-    denscol=tracecol,
425
-    symkey = any(x < 0, na.rm=TRUE) || symbreaks,
423
+    density.info = c("histogram", "density", "none"),
424
+    denscol = tracecol,
425
+    symkey = any(x < 0, na.rm = TRUE) || symbreaks,
426 426
     densadj = 0.25,
427 427
     key.title = NULL,
428 428
     key.xlab = NULL,
429 429
     key.ylab = NULL,
430 430
     key.xtickfun = NULL,
431 431
     key.ytickfun = NULL,
432
-    key.par=list(),
432
+    key.par = list(),
433 433
 
434 434
     # plot labels
435 435
     main = NULL,
... ...
@@ -442,7 +442,7 @@ heatmap.2 = function(x,
442 442
     lwid = NULL,
443 443
 
444 444
     # extras
445
-    extrafun=NULL,
445
+    extrafun = NULL,
446 446
     ...
447 447
     ) {
448 448
 
... ...
@@ -458,6 +458,10 @@ heatmap.2 = function(x,
458 458
 
459 459
     ht_param = list()
460 460
 
461
+    if(identical(Rowv, FALSE) && identical(symm, TRUE)) {
462
+        Colv = FALSE
463
+    }
464
+
461 465
     # Rowv can be 1. NA, 2. a dendrogram object, 3. a vector, 4. a logical value, 5. NULL
462 466
     if(identical(Rowv, NA) || identical(Rowv, NULL) || identical(Rowv, FALSE)) {
463 467
         ht_param$cluster_rows = FALSE
... ...
@@ -571,7 +575,7 @@ heatmap.2 = function(x,
571 575
     
572 576
     n_col = ncol
573 577
 
574
-    if(identical(scale, "row") || identical(scale, "column")) {
578
+    if(exists("extreme")) {
575 579
         lim = max(abs(mat), na.rm = TRUE)
576 580
         ht_param$col = colorRamp2(seq(-lim, lim, length = n_col), col)
577 581
     } else {
... ...
@@ -604,7 +608,7 @@ heatmap.2 = function(x,
604 608
             show_legend = FALSE, show_annotation_name = FALSE)
605 609
     }
606 610
 
607
-    if(identical(ht_param$cluster_rows, FALSE)) {
611
+    if(identical(ht_param$cluster_rows, FALSE) || dendrogram %in% c("none", "column")) {
608 612
         if(is.null(ht_param$left_annotation)) {
609 613
             ht_param$left_annotation = rowAnnotation(foo1 = anno_empty(width = unit(4, "cm"), border = FALSE))
610 614
         } else {
... ...
@@ -612,7 +616,7 @@ heatmap.2 = function(x,
612 616
         }
613 617
     }
614 618
 
615
-    if(identical(ht_param$cluster_columns, FALSE)) {
619
+    if(identical(ht_param$cluster_columns, FALSE) || dendrogram %in% c("none", "row")) {
616 620
         if(is.null(ht_param$top_annotation)) {
617 621
             ht_param$top_annotation = HeatmapAnnotation(foo2 = anno_empty(height = unit(3, "cm"), border = FALSE))
618 622
         } else {
... ...
@@ -643,9 +647,13 @@ heatmap.2 = function(x,
643 647
 
644 648
     if(!is.null(srtRow)) {
645 649
         ht_param$row_names_rot = srtRow
650
+    } else {
651
+        ht_param$row_names_rot = 0
646 652
     }
647 653
     if(!is.null(srtCol)) {
648 654
         ht_param$column_names_rot = srtCol
655
+    } else {
656
+        ht_param$column_names_rot = 90
649 657
     }
650 658
 
651 659
     if(!is.null(main)) {
... ...
@@ -656,7 +664,7 @@ heatmap.2 = function(x,
656 664
             ht_param$bottom_annotation = HeatmapAnnotation(xlab = anno_block(labels = xlab, gp = gpar(col = NA)))
657 665
         } else {
658 666
             ht_param$bottom_annotation = HeatmapAnnotation(
659
-                colnames = anno_text(ht_param$column_labels, gp = ht_param$column_names_gp),
667
+                colnames = anno_text(ht_param$column_labels, gp = ht_param$column_names_gp, rot = ht_param$column_names_rot),
660 668
                 xlab = anno_block(labels = xlab, gp = gpar(col = NA))
661 669
             )
662 670
             ht_param$show_column_names = FALSE
... ...
@@ -667,7 +675,7 @@ heatmap.2 = function(x,
667 675
             ht_param$right_annotation = rowAnnotation(ylab = anno_block(labels = ylab, gp = gpar(col = NA)))
668 676
         } else {
669 677
             ht_param$right_annotation = rowAnnotation(
670
-                rownames = anno_text(ht_param$row_labels, gp = ht_param$row_names_gp),
678
+                rownames = anno_text(ht_param$row_labels, gp = ht_param$row_names_gp, rot = ht_param$row_names_rot),
671 679
                 ylab = anno_block(labels = ylab, gp = gpar(col = NA))
672 680
             )
673 681
             ht_param$show_row_names = FALSE
... ...
@@ -717,7 +725,7 @@ heatmap.2 = function(x,
717 725
             }
718 726
         }
719 727
     }
720
-    if(!is.null(ht_param$layer_fun)) {
728
+    if(!is.null(ht_param$layer_fun) && trace %in% c("row", "column")) {
721 729
         fun1 = ht_param$layer_fun
722 730
         fun2 = layer_fun
723 731
         fun3 = function(j, i, x, y, w, h, fill) {
... ...
@@ -725,9 +733,10 @@ heatmap.2 = function(x,
725 733
             fun2(j, i, x, y, w, h, fill)
726 734
         }
727 735
         layer_fun = fun3
736
+        ht_param$layer_fun = layer_fun
737
+    } else if(is.null(ht_param$layer_fun) && trace %in% c("row", "column")) {
738
+        ht_param$layer_fun = layer_fun
728 739
     }
729
-    ht_param$layer_fun = layer_fun
730
-
731 740
 
732 741
     random_str = paste(sample(c(letters, LETTERS, 0:9), 8), collapse = "")
733 742
     ht_param$name = paste0("heatmap.2_", random_str)
... ...
@@ -24,6 +24,14 @@ increase_heatmap_index = function() {
24 24
 	INDEX_ENV$I_HEATMAP = INDEX_ENV$I_HEATMAP + 1
25 25
 }
26 26
 
27
+get_oncoprint_index = function() {
28
+    INDEX_ENV$I_ONCOPRINT
29
+}
30
+
31
+increase_oncoprint_index = function() {
32
+    INDEX_ENV$I_ONCOPRINT = INDEX_ENV$I_ONCOPRINT + 1
33
+}
34
+
27 35
 get_annotation_index = function() {
28 36
 	INDEX_ENV$I_ANNOTATION
29 37
 }
... ...
@@ -15,4 +15,5 @@ method and the \code{\%v\%v} method so that above three classes can be appended
15 15
 \examples{
16 16
 # There is no example
17 17
 NULL
18
+
18 19
 }
... ...
@@ -26,4 +26,5 @@ Zuguang Gu <z.gu@dkfz.de>
26 26
 \examples{
27 27
 # There is no example
28 28
 NULL
29
+
29 30
 }
... ...
@@ -22,4 +22,5 @@ See \code{\link{AnnotationFunction}} constructor for details.
22 22
 \examples{
23 23
 # There is no example
24 24
 NULL
25
+
25 26
 }
... ...
@@ -26,4 +26,5 @@ Zuguang Gu <z.gu@dkfz.de>
26 26
 \examples{
27 27
 # There is no example
28 28
 NULL
29
+
29 30
 }
... ...
@@ -40,4 +40,5 @@ The complete reference of ComplexHeatmap package is available at \url{http://jok
40 40
 \examples{
41 41
 # There is no example
42 42
 NULL
43
+
43 44
 }
... ...
@@ -22,4 +22,5 @@ Internally used.
22 22
 \examples{
23 23
 # There is no example
24 24
 NULL
25
+
25 26
 }
... ...
@@ -30,4 +30,5 @@ Zuguang Gu <z.gu@dkfz.de>
30 30
 \examples{
31 31
 # There is no example
32 32
 NULL
33
+
33 34
 }
... ...
@@ -212,4 +212,5 @@ Zuguang Gu <z.gu@dkfz.de>
212 212
 \examples{
213 213
 # There is no example
214 214
 NULL
215
+
215 216
 }
... ...
@@ -25,4 +25,5 @@ Zuguang Gu <z.gu@dkfz.de>
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -84,4 +84,5 @@ Zuguang Gu <z.gu@dkfz.de>
84 84
 \examples{
85 85
 # There is no example
86 86
 NULL
87
+
87 88
 }
... ...
@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
+
30 31
 }
... ...
@@ -26,4 +26,5 @@ Zuguang Gu <z.gu@dkfz.de>
26 26
 \examples{
27 27
 # There is no example
28 28
 NULL
29
+
29 30
 }
... ...
@@ -26,4 +26,5 @@ Zuguang Gu <z.gu@dkfz.de>
26 26
 \examples{
27 27
 # There is no example
28 28
 NULL
29
+
29 30
 }
... ...
@@ -28,4 +28,5 @@ Zuguang Gu <z.gu@dkfz.de>
28 28
 \examples{
29 29
 # There is no example
30 30
 NULL
31
+
31 32
 }
... ...
@@ -40,4 +40,5 @@ Zuguang Gu <z.gu@dkfz.de>
40 40
 \examples{
41 41
 # There is no example
42 42
 NULL
43
+
43 44
 }
... ...
@@ -28,4 +28,5 @@ Zuguang Gu <z.gu@dkfz.de>
28 28
 \examples{
29 29
 # There is no example
30 30
 NULL
31
+
31 32
 }
... ...
@@ -28,4 +28,5 @@ Zuguang Gu <z.gu@dkfz.de>
28 28
 \examples{
29 29
 # There is no example
30 30
 NULL
31
+
31 32
 }
... ...
@@ -28,4 +28,5 @@ Zuguang Gu <z.gu@dkfz.de>
28 28
 \examples{
29 29
 # There is no example
30 30
 NULL
31
+
31 32
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{adjust_heatmap_list-HeatmapList-method}
2 2
 \alias{adjust_heatmap_list,HeatmapList-method}
3
+\alias{adjust_heatmap_list}
3 4
 \title{
4 5
 Adjust Heatmap List
5 6
 }
... ...
@@ -23,8 +24,8 @@ This function is only for internal use.
23 24
 \author{
24 25
 Zuguang Gu <z.gu@dkfz.de>
25 26
 }
26
-\alias{adjust_heatmap_list}
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
+
30 31
 }
... ...
@@ -20,4 +20,5 @@ This function is the same as \code{\link{anno_zoom}}. It links subsets of rows o
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
+
23 24
 }
... ...
@@ -35,4 +35,5 @@ Zuguang Gu <z.gu@dkfz.de>
35 35
 \examples{
36 36
 # There is no example
37 37
 NULL
38
+
38 39
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{annotation_legend_size-HeatmapList-method}
2 2
 \alias{annotation_legend_size,HeatmapList-method}
3
+\alias{annotation_legend_size}
3 4
 \title{
4 5
 Size of the Annotation Legends
5 6
 }
... ...
@@ -27,8 +28,8 @@ A \code{\link[grid]{unit}} object.
27 28
 \author{
28 29
 Zuguang Gu <z.gu@dkfz.de>
29 30
 }
30
-\alias{annotation_legend_size}
31 31
 \examples{
32 32
 # There is no example
33 33
 NULL
34
+
34 35
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{attach_annotation-Heatmap-method}
2 2
 \alias{attach_annotation,Heatmap-method}
3
+\alias{attach_annotation}
3 4
 \title{
4 5
 Attach heatmap annotations to the heatmap
5 6
 }
... ...
@@ -28,4 +29,3 @@ ha2 = HeatmapAnnotation(bar = letters[1:10])
28 29
 ht = attach_annotation(ht, ha2)
29 30
 ht
30 31
 }
31
-\alias{attach_annotation}
... ...
@@ -23,4 +23,5 @@ A \code{\link[GenomicRanges:GRanges-class]{GRanges}} object of the genomic bins.
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{color_mapping_legend-ColorMapping-method}
2 2
 \alias{color_mapping_legend,ColorMapping-method}
3
+\alias{color_mapping_legend}
3 4
 \title{
4 5
 Draw Legend Based on Color Mapping
5 6
 }
... ...
@@ -69,8 +70,8 @@ A \code{\link{Legends-class}} object.
69 70
 \author{
70 71
 Zuguang Gu <z.gu@dkfz.de>
71 72
 }
72
-\alias{color_mapping_legend}
73 73
 \examples{
74 74
 # There is no example
75 75
 NULL
76
+
76 77
 }
... ...
@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
+
32 33
 }
... ...
@@ -20,4 +20,5 @@ If there is no complement set, it returns zero.
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
+
23 24
 }
... ...
@@ -31,4 +31,5 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 \examples{
32 32
 # There is no example
33 33
 NULL
34
+
34 35
 }
... ...
@@ -24,4 +24,5 @@ Zuguang Gu <z.gu@dkfz.de>
24 24
 \examples{
25 25
 # There is no example
26 26
 NULL
27
+
27 28
 }
... ...
@@ -30,4 +30,5 @@ Zuguang Gu <z.gu@dkfz.de>
30 30
 \examples{
31 31
 # There is no example
32 32
 NULL
33
+
33 34
 }
... ...
@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
+
30 31
 }
... ...
@@ -26,4 +26,5 @@ The environment is at \code{object@var_env}.
26 26
 \examples{
27 27
 # There is no example
28 28
 NULL
29
+
29 30
 }
... ...
@@ -21,4 +21,5 @@ it calls \code{\link{copy_all,AnnotationFunction-method}} to hard copy the varia
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
+
24 25
 }
... ...
@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
+
30 31
 }
... ...
@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
+
30 31
 }
... ...
@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
+
30 31
 }
... ...
@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
+
30 31
 }
... ...
@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
+
30 31
 }
... ...
@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
+
30 31
 }
... ...
@@ -20,4 +20,5 @@ It recognizes following separators: \code{;:,|}.
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
+
23 24
 }
... ...
@@ -17,4 +17,5 @@ dend_heights(x)
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -28,4 +28,5 @@ A \code{\link{grob}} object which is contructed by \code{\link[grid:grid.segment
28 28
 \examples{
29 29
 # There is no example
30 30
 NULL
31
+
31 32
 }
... ...
@@ -17,4 +17,5 @@ Dimension of the Heatmap
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -28,4 +28,5 @@ which is generally for testing purpose.
28 28
 \examples{
29 29
 # There is no example
30 30
 NULL
31
+
31 32
 }
... ...
@@ -33,4 +33,5 @@ Zuguang Gu <z.gu@dkfz.de>
33 33
 \examples{
34 34
 # There is no example
35 35
 NULL
36
+
36 37
 }
... ...
@@ -30,4 +30,5 @@ Zuguang Gu <z.gu@dkfz.de>
30 30
 \examples{
31 31
 # There is no example
32 32
 NULL
33
+
33 34
 }
... ...
@@ -202,4 +202,5 @@ Zuguang Gu <z.gu@dkfz.de>
202 202
 \examples{
203 203
 # There is no example
204 204
 NULL
205
+
205 206
 }
... ...
@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
+
32 33
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{draw_annotation-Heatmap-method}
2 2
 \alias{draw_annotation,Heatmap-method}
3
+\alias{draw_annotation}
3 4
 \title{
4 5
 Draw Heatmap Annotations on the Heatmap
5 6
 }
... ...
@@ -30,8 +31,8 @@ This function returns no value.
30 31
 \author{
31 32
 Zuguang Gu <z.gu@dkfz.de>
32 33
 }
33
-\alias{draw_annotation}
34 34
 \examples{
35 35
 # There is no example
36 36
 NULL
37
+
37 38
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{draw_annotation_legend-HeatmapList-method}
2 2
 \alias{draw_annotation_legend,HeatmapList-method}
3
+\alias{draw_annotation_legend}
3 4
 \title{
4 5
 Draw legends for All Annotations
5 6
 }
... ...
@@ -31,8 +32,8 @@ This function returns no value.
31 32
 \author{
32 33
 Zuguang Gu <z.gu@dkfz.de>
33 34
 }
34
-\alias{draw_annotation_legend}
35 35
 \examples{
36 36
 # There is no example
37 37
 NULL
38
+
38 39
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{draw_dend-Heatmap-method}
2 2
 \alias{draw_dend,Heatmap-method}
3
+\alias{draw_dend}
3 4
 \title{
4 5
 Draw Heatmap Dendrograms
5 6
 }
... ...
@@ -33,8 +34,8 @@ This function returns no value.
33 34
 \author{
34 35
 Zuguang Gu <z.gu@dkfz.de>
35 36
 }
36
-\alias{draw_dend}
37 37
 \examples{
38 38
 # There is no example
39 39
 NULL
40
+
40 41
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{draw_dimnames-Heatmap-method}
2 2
 \alias{draw_dimnames,Heatmap-method}
3
+\alias{draw_dimnames}
3 4
 \title{
4 5
 Draw row names or column names
5 6
 }
... ...
@@ -29,8 +30,8 @@ This function returns no value.
29 30
 \author{
30 31
 Zuguang Gu <z.gu@dkfz.de>
31 32
 }
32
-\alias{draw_dimnames}
33 33
 \examples{
34 34
 # There is no example
35 35
 NULL
36
+
36 37
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{draw_heatmap_body-Heatmap-method}
2 2
 \alias{draw_heatmap_body,Heatmap-method}
3
+\alias{draw_heatmap_body}
3 4
 \title{
4 5
 Draw Heatmap Body
5 6
 }
... ...
@@ -28,8 +29,8 @@ This function returns no value.
28 29
 \author{
29 30
 Zuguang Gu <z.gu@dkfz.de>
30 31
 }
31
-\alias{draw_heatmap_body}
32 32
 \examples{
33 33
 # There is no example
34 34
 NULL
35
+
35 36
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{draw_heatmap_legend-HeatmapList-method}
2 2
 \alias{draw_heatmap_legend,HeatmapList-method}
3
+\alias{draw_heatmap_legend}
3 4
 \title{
4 5
 Draw legends for All Heatmaps
5 6
 }
... ...
@@ -32,8 +33,8 @@ This function returns no value.
32 33
 \author{
33 34
 Zuguang Gu <z.gu@dkfz.de>
34 35
 }
35
-\alias{draw_heatmap_legend}
36 36
 \examples{
37 37
 # There is no example
38 38
 NULL
39
+
39 40
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{draw_heatmap_list-HeatmapList-method}
2 2
 \alias{draw_heatmap_list,HeatmapList-method}
3
+\alias{draw_heatmap_list}
3 4
 \title{
4 5
 Draw the List of Heatmaps
5 6
 }
... ...
@@ -25,8 +26,8 @@ This function returns no value.
25 26
 \author{
26 27
 Zuguang Gu <z.gu@dkfz.de>
27 28
 }
28
-\alias{draw_heatmap_list}
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
+
32 33
 }
... ...
@@ -32,4 +32,5 @@ Zuguang Gu <z.gu@dkfz.de>
32 32
 \examples{
33 33
 # There is no example
34 34
 NULL
35
+
35 36
 }
... ...
@@ -30,4 +30,5 @@ Zuguang Gu <z.gu@dkfz.de>
30 30
 \examples{
31 31
 # There is no example
32 32
 NULL
33
+
33 34
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{get_color_mapping_list-HeatmapAnnotation-method}
2 2
 \alias{get_color_mapping_list,HeatmapAnnotation-method}
3
+\alias{get_color_mapping_list}
3 4
 \title{
4 5
 Get a List of ColorMapping objects
5 6
 }
... ...
@@ -25,8 +26,8 @@ A list of \code{\link{ColorMapping-class}} objects or an empty list.
25 26
 \author{
26 27
 Zuguang Gu <z.gu@dkfz.de>
27 28
 }
28
-\alias{get_color_mapping_list}
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
+
32 33
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{get_legend_param_list-HeatmapAnnotation-method}
2 2
 \alias{get_legend_param_list,HeatmapAnnotation-method}
3
+\alias{get_legend_param_list}
3 4
 \title{
4 5
 Get a List of Annotation Legend Parameters
5 6
 }
... ...
@@ -25,8 +26,8 @@ A list.
25 26
 \author{
26 27
 Zuguang Gu <z.gu@dkfz.de>
27 28
 }
28
-\alias{get_legend_param_list}
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
+
32 33
 }
... ...
@@ -20,7 +20,7 @@ heatmap.2(x,
20 20
     
21 21
     # data scaling
22 22
     scale = c("none","row", "column"),
23
-    na.rm=TRUE,
23
+    na.rm = TRUE,
24 24
     
25 25
     # image plot
26 26
     revC = identical(Colv, "Rowv"),
... ...
@@ -28,36 +28,36 @@ heatmap.2(x,
28 28
     
29 29
     # mapping data to colors
30 30
     breaks,
31
-    symbreaks=any(x < 0, na.rm=TRUE) || scale!="none",
31
+    symbreaks = any(x < 0, na.rm = TRUE) || scale != "none",
32 32
     
33 33
     # colors
34
-    col="heat.colors",
34
+    col = "heat.colors",
35 35
     
36 36
     # block sepration
37 37
     colsep,
38 38
     rowsep,
39
-    sepcolor="white",
40
-    sepwidth=c(0.05,0.05),
39
+    sepcolor = "white",
40
+    sepwidth = c(0.05, 0.05),
41 41
     
42 42
     # cell labeling
43 43
     cellnote,
44
-    notecex=1.0,
45
-    notecol="cyan",
46
-    na.color=par("bg"),
44
+    notecex = 0.6,
45
+    notecol = "cyan",
46
+    na.color = par("bg"),
47 47
     
48 48
     # level trace
49
-    trace=c("column","row","both","none"),
50
-    tracecol="cyan",
51
-    hline=median(breaks),
52
-    vline=median(breaks),
53
-    linecol=tracecol,
49
+    trace = c("column", "row", "both", "none"),
50
+    tracecol = "cyan",
51
+    hline = median(breaks),
52
+    vline = median(breaks),
53
+    linecol = tracecol,
54 54
     
55 55
     # Row/Column Labeling
56 56
     margins = c(5, 5),
57 57
     ColSideColors,
58 58
     RowSideColors,
59
-    cexRow = 0.2 + 1/log10(nr),
60
-    cexCol = 0.2 + 1/log10(nc),
59
+    cexRow = 0.6,
60
+    cexCol = 0.6,
61 61
     labRow = NULL,
62 62
     labCol = NULL,
63 63
     srtRow = NULL,
... ...
@@ -72,16 +72,16 @@ heatmap.2(x,
72 72
     # color key + density info
73 73
     key = TRUE,
74 74
     keysize = 1.5,
75
-    density.info=c("histogram","density","none"),
76
-    denscol=tracecol,
77
-    symkey = any(x < 0, na.rm=TRUE) || symbreaks,
75
+    density.info = c("histogram", "density", "none"),
76
+    denscol = tracecol,
77
+    symkey = any(x < 0, na.rm = TRUE) || symbreaks,
78 78
     densadj = 0.25,
79 79
     key.title = NULL,
80 80
     key.xlab = NULL,
81 81
     key.ylab = NULL,
82 82
     key.xtickfun = NULL,
83 83
     key.ytickfun = NULL,
84
-    key.par=list(),
84
+    key.par = list(),
85 85
     
86 86
     # plot labels
87 87
     main = NULL,
... ...
@@ -94,7 +94,7 @@ heatmap.2(x,
94 94
     lwid = NULL,
95 95
     
96 96
     # extras
97
-    extrafun=NULL,
97
+    extrafun = NULL,
98 98
     ...)
99 99
 }
100 100
 \arguments{
... ...
@@ -176,4 +176,5 @@ A \code{\link{Heatmap-class}} object.
176 176
 \examples{
177 177
 # There is no example
178 178
 NULL
179
+
179 180
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{heatmap_legend_size-HeatmapList-method}
2 2
 \alias{heatmap_legend_size,HeatmapList-method}
3
+\alias{heatmap_legend_size}
3 4
 \title{
4 5
 Size of the Heatmap Legends
5 6
 }
... ...
@@ -27,8 +28,8 @@ A \code{\link[grid]{unit}} object.
27 28
 \author{
28 29
 Zuguang Gu <z.gu@dkfz.de>
29 30
 }
30
-\alias{heatmap_legend_size}
31 31
 \examples{
32 32
 # There is no example
33 33
 NULL
34
+
34 35
 }
... ...
@@ -18,4 +18,5 @@ Height of the Heatmap
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -21,4 +21,5 @@ Internally used.
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
+
24 25
 }
... ...
@@ -18,4 +18,5 @@ Height of the Heatmap List
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -21,4 +21,5 @@ Internally used.
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
+
24 25
 }
... ...
@@ -23,4 +23,5 @@ Internally used.
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -23,4 +23,5 @@ Internally used.
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -23,4 +23,5 @@ Internally used.
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -20,4 +20,5 @@ The physical height of the grob can be get by \code{convertWidth(grobHeight(axis
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
+
23 24
 }
... ...
@@ -17,4 +17,5 @@ Grob height for packed_legends
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -17,4 +17,5 @@ Grob height for legend_body
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -17,4 +17,5 @@ Grob height for packed_legends
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -25,4 +25,5 @@ will also be sychronized in \code{\link{ht_opt}}.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -20,4 +20,5 @@ A list of two elements: width and height.
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
+
23 24
 }
... ...
@@ -17,4 +17,5 @@ Number of Annotations
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -17,4 +17,5 @@ Length of the HeatmapList object
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -20,4 +20,5 @@ A vector of viewport names.
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
+
23 24
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{make_column_cluster-Heatmap-method}
2 2
 \alias{make_column_cluster,Heatmap-method}
3
+\alias{make_column_cluster}
3 4
 \title{
4 5
 Make Cluster on Columns
5 6
 }
... ...
@@ -28,8 +29,8 @@ A \code{\link{Heatmap-class}} object.
28 29
 \author{
29 30
 Zuguang Gu <z.gu@dkfz.de>
30 31
 }
31
-\alias{make_column_cluster}
32 32
 \examples{
33 33
 # There is no example
34 34
 NULL
35
+
35 36
 }
... ...
@@ -32,4 +32,5 @@ Zuguang Gu <z.gu@dkfz.de>
32 32
 \examples{
33 33
 # There is no example
34 34
 NULL
35
+
35 36
 }
... ...
@@ -155,4 +155,5 @@ Zuguang Gu <z.gu@dkfz.de>
155 155
 \examples{
156 156
 # There is no example
157 157
 NULL
158
+
158 159
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{make_row_cluster-Heatmap-method}
2 2
 \alias{make_row_cluster,Heatmap-method}
3
+\alias{make_row_cluster}
3 4
 \title{
4 5
 Make Cluster on Rows
5 6
 }
... ...
@@ -27,8 +28,8 @@ A \code{\link{Heatmap-class}} object.
27 28
 \author{
28 29
 Zuguang Gu <z.gu@dkfz.de>
29 30
 }
30
-\alias{make_row_cluster}
31 31
 \examples{
32 32
 # There is no example
33 33
 NULL
34
+
34 35
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{map_to_colors-ColorMapping-method}
2 2
 \alias{map_to_colors,ColorMapping-method}
3
+\alias{map_to_colors}
3 4
 \title{
4 5
 Map Values to Colors
5 6
 }
... ...
@@ -34,4 +35,3 @@ col_fun = colorRamp2(c(0, 1), c("white", "red"))
34 35
 cm = ColorMapping(col_fun = col_fun)
35 36
 map_to_colors(cm, runif(10))
36 37
 }
37
-\alias{map_to_colors}
... ...
@@ -17,4 +17,5 @@ Names of the heatmaps/annotations
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -17,4 +17,5 @@ Number of Columns in the Heatmap
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -22,4 +22,5 @@ it returns \code{NA}.
22 22
 \examples{
23 23
 # There is no example
24 24
 NULL
25
+
25 26
 }
... ...
@@ -21,4 +21,5 @@ It returns the \code{n} slot of the annotaton function. If it does not exist, it
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
+
24 25
 }
... ...
@@ -24,4 +24,5 @@ The sets (by \code{\link{set_name}}) from all combination matrice should be the
24 24
 \examples{
25 25
 # There is no example
26 26
 NULL
27
+
27 28
 }
... ...
@@ -17,4 +17,5 @@ Number of Rows in the Heatmap
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -7,7 +7,7 @@ Make oncoPrint
7 7
 Make oncoPrint
8 8
 }
9 9
 \usage{
10
-oncoPrint(mat,
10
+oncoPrint(mat, name,
11 11
     get_type = default_get_type,
12 12
     alter_fun,
13 13
     alter_fun_is_vectorized = NULL,
... ...
@@ -47,6 +47,7 @@ oncoPrint(mat,
47 47
 \arguments{
48 48
 
49 49
   \item{mat}{The value should be a character matrix which encodes mulitple alterations  or a list of matrices for which every matrix contains binary value representing whether the alteration is present or absent.  When the value is a list, the names of the list represent alteration types. You can use \code{\link{unify_mat_list}} to make all matrix having same row names and column names.}
50
+  \item{name}{Name of the oncoPrint. Not necessary to specify.}
50 51
   \item{get_type}{If different alterations are encoded in the matrix as complex strings, this self-defined function determines how to extract them. It only works when \code{mat} is a matrix. The default value is \code{\link{default_get_type}}.}
51 52
   \item{alter_fun}{A single function or a list of functions which defines how to add graphics for different alterations. You can use \code{\link{alter_graphic}} to automatically generate for rectangles and points.}
52 53
   \item{alter_fun_is_vectorized}{Whether \code{alter_fun} is implemented vectorized. Internally the function will guess.}
... ...
@@ -94,4 +95,5 @@ Zuguang Gu <z.gu@dkfz.de>
94 95
 \examples{
95 96
 # There is no example
96 97
 NULL
98
+
97 99
 }
... ...
@@ -23,4 +23,5 @@ by the combination matrix.
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -39,4 +39,5 @@ Zuguang Gu <z.gu@dkfz.de>
39 39
 \examples{
40 40
 # There is no example
41 41
 NULL
42
+
42 43
 }
... ...
@@ -132,4 +132,5 @@ A \code{\link{Heatmap-class}} object.
132 132
 \examples{
133 133
 # There is no example
134 134
 NULL
135
+
135 136
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{prepare-Heatmap-method}
2 2
 \alias{prepare,Heatmap-method}
3
+\alias{prepare}
3 4
 \title{
4 5
 Prepare the Heatmap
5 6
 }
... ...
@@ -33,8 +34,8 @@ The \code{\link{Heatmap-class}} object.
33 34
 \author{
34 35
 Zuguang Gu <z.gu@dkfz.de>
35 36
 }
36
-\alias{prepare}
37 37
 \examples{
38 38
 # There is no example
39 39
 NULL
40
+
40 41
 }
... ...
@@ -18,4 +18,5 @@ Print the comb_mat Object
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{re_size-HeatmapAnnotation-method}
2 2
 \alias{re_size,HeatmapAnnotation-method}
3
+\alias{re_size}
3 4
 \title{
4 5
 Resize the Width or Height of Heatmap Annotations
5 6
 }
... ...
@@ -41,8 +42,8 @@ The basic rules are (take \code{height} and \code{annotation_height} for example
41 42
      and \code{simple_anno_size} is disabled.
42 43
 6. If \code{simple_anno_size_adjust} is \code{FALSE}, the size of the simple annotations will not change.
43 44
 }
44
-\alias{re_size}
45 45
 \examples{
46 46
 # There is no example
47 47
 NULL
48
+
48 49
 }
... ...
@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
+
32 33
 }
... ...
@@ -25,4 +25,5 @@ See help page of \code{\link{anno_barplot}}.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -25,4 +25,5 @@ See help page of \code{\link{anno_boxplot}}.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -25,4 +25,5 @@ See help page of \code{\link{anno_density}}.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -25,4 +25,5 @@ See help page of \code{\link{anno_histogram}}.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -25,4 +25,5 @@ See help page of \code{\link{anno_points}}.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -25,4 +25,5 @@ See help page of \code{\link{anno_text}}.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{set_component_height-Heatmap-method}
2 2
 \alias{set_component_height,Heatmap-method}
3
+\alias{set_component_height}
3 4
 \title{
4 5
 Set Height of Heatmap Component
5 6
 }
... ...
@@ -29,8 +30,8 @@ The \code{\link{Heatmap-class}} object.
29 30
 \author{
30 31
 Zuguang Gu <z.gu@dkfz.de>
31 32
 }
32
-\alias{set_component_height}
33 33
 \examples{
34 34
 # There is no example
35 35
 NULL
36
+
36 37
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{set_component_width-Heatmap-method}
2 2
 \alias{set_component_width,Heatmap-method}
3
+\alias{set_component_width}
3 4
 \title{
4 5
 Set Width of Heatmap Component
5 6
 }
... ...
@@ -28,8 +29,8 @@ The \code{\link{Heatmap-class}} object.
28 29
 \author{
29 30
 Zuguang Gu <z.gu@dkfz.de>
30 31
 }
31
-\alias{set_component_width}
32 32
 \examples{
33 33
 # There is no example
34 34
 NULL
35
+
35 36
 }
... ...
@@ -17,4 +17,5 @@ Print the AnnotationFunction Object
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -23,4 +23,5 @@ Zuguang Gu <z.gu@dkfz.de>
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
+
30 31
 }
... ...
@@ -23,4 +23,5 @@ Zuguang Gu <z.gu@dkfz.de>
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -24,4 +24,5 @@ This function returns no value.
24 24
 \examples{
25 25
 # There is no example
26 26
 NULL
27
+
27 28
 }
... ...
@@ -23,4 +23,5 @@ Zuguang Gu <z.gu@dkfz.de>
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -23,4 +23,5 @@ Internally used.
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -23,4 +23,5 @@ Internally used.
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -25,4 +25,5 @@ Internally used.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -25,4 +25,5 @@ Internally used.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -23,8 +23,8 @@ heatmap(x,
23 23
     margins = c(5, 5),
24 24
     ColSideColors,
25 25
     RowSideColors,
26
-    cexRow = 0.2 + 1/log10(nr),
27
-    cexCol = 0.2 + 1/log10(nc),
26
+    cexRow = 0.6,
27
+    cexCol = 0.6,
28 28
     labRow = NULL,
29 29
     labCol = NULL,
30 30
     main = NULL,
... ...
@@ -75,4 +75,5 @@ A \code{\link{Heatmap-class}} object.
75 75
 \examples{
76 76
 # There is no example
77 77
 NULL
78
+
78 79
 }
... ...
@@ -18,4 +18,5 @@ str method
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -21,4 +21,5 @@ Mainly used for constructing the \code{\link{AnnotationFunction-class}} object.
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
+
24 25
 }
... ...
@@ -21,4 +21,5 @@ Mainly used for constructing the \code{\link{AnnotationFunction-class}} object.
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
+
24 25
 }
... ...
@@ -18,4 +18,5 @@ Print the Summary of a Heatmap
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -18,4 +18,5 @@ Summary of a Heatmap List
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
+
30 31
 }
... ...
@@ -41,4 +41,5 @@ and if under the union mode, it is \code{union_size}.
41 41
 \examples{
42 42
 # There is no example
43 43
 NULL
44
+
44 45
 }
... ...
@@ -41,4 +41,5 @@ and if under the union mode, it is \code{union_size}.
41 41
 \examples{
42 42
 # There is no example
43 43
 NULL
44
+
44 45
 }
... ...
@@ -18,4 +18,5 @@ Width of the Heatmap
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -21,4 +21,5 @@ Internally used.
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
+
24 25
 }
... ...
@@ -18,4 +18,5 @@ Width of the Heatmap List
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -21,4 +21,5 @@ Internally used.
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
+
24 25
 }
... ...
@@ -23,4 +23,5 @@ Internally used.
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -23,4 +23,5 @@ Internally used.
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -23,4 +23,5 @@ Internally used.
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -20,4 +20,5 @@ The physical width of the grob can be get by \code{convertWidth(grobWidth(axis_g
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
+
23 24
 }
... ...
@@ -17,4 +17,5 @@ Grob width for packed_legends
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -17,4 +17,5 @@ Grob width for legend_body
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -17,4 +17,5 @@ Grob width for packed_legends
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }