Browse code

generate documentations by pkgdown

Zuguang Gu authored on 18/10/2019 11:34:02
Showing1 changed files
1 1
deleted file mode 100644
... ...
@@ -1,99 +0,0 @@
1
-\name{densityHeatmap}
2
-\alias{densityHeatmap}
3
-\title{
4
-Visualize Density Distribution by Heatmap
5
-}
6
-\description{
7
-Visualize Density Distribution by Heatmap
8
-}
9
-\usage{
10
-densityHeatmap(data,
11
-    density_param = list(na.rm = TRUE),
12
-    
13
-    col = rev(brewer.pal(11, "Spectral")),
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-    color_space = "LAB",
15
-    ylab = deparse(substitute(data)),
16
-    column_title = paste0("Density heatmap of ", deparse(substitute(data))),
17
-    title = column_title,
18
-    ylim = NULL,
19
-    range = ylim,
20
-    
21
-    title_gp = gpar(fontsize = 14),
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-    ylab_gp = gpar(fontsize = 12),
23
-    tick_label_gp = gpar(fontsize = 10),
24
-    quantile_gp = gpar(fontsize = 10),
25
-    show_quantiles = TRUE,
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-    
27
-    column_order = NULL,
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-    column_names_side = "bottom",
29
-    show_column_names = TRUE,
30
-    column_names_max_height = unit(6, "cm"),
31
-    column_names_gp = gpar(fontsize = 12),
32
-    column_names_rot = 90,
33
-    
34
-    cluster_columns = FALSE,
35
-    clustering_distance_columns = "ks",
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-    clustering_method_columns = "complete",
37
-    mc.cores = 1,
38
-    
39
-    ...)
40
-}
41
-\arguments{
42
-
43
-  \item{data}{A matrix or a list. If it is a matrix, density is calculated by columns.}
44
-  \item{density_param}{Parameters send to \code{\link[stats]{density}}, \code{na.rm} is enforced to be \code{TRUE}.}
45
-  \item{col}{A vector of colors that density values are mapped to.}
46
-  \item{color_space}{The color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}
47
-  \item{ylab}{Label on y-axis.}
48
-  \item{column_title}{Title of the heatmap.}
49
-  \item{title}{Same as \code{column_title}.}
50
-  \item{ylim}{Ranges on the y-axis.}
51
-  \item{range}{Same as \code{ylim}.}
52
-  \item{title_gp}{Graphic parameters for title.}
53
-  \item{ylab_gp}{Graphic parameters for y-labels.}
54
-  \item{tick_label_gp}{Graphic parameters for y-ticks.}
55
-  \item{quantile_gp}{Graphic parameters for the quantiles.}
56
-  \item{show_quantiles}{Whether show quantile lines.}
57
-  \item{column_order}{Order of columns.}
58
-  \item{column_names_side}{Pass to \code{\link{Heatmap}}.}
59
-  \item{show_column_names}{Pass to \code{\link{Heatmap}}.}
60
-  \item{column_names_max_height}{Pass to \code{\link{Heatmap}}.}
61
-  \item{column_names_gp}{Pass to \code{\link{Heatmap}}.}
62
-  \item{column_names_rot}{Pass to \code{\link{Heatmap}}.}
63
-  \item{cluster_columns}{Whether cluster columns?}
64
-  \item{clustering_distance_columns}{There is a specific distance method \code{ks} which is the Kolmogorov-Smirnov statistic between two distributions. For other methods, the distance is calculated on the density matrix.}
65
-  \item{clustering_method_columns}{Pass to \code{\link{Heatmap}}.}
66
-  \item{mc.cores}{Multiple cores for calculating ks distance.}
67
-  \item{...}{Pass to \code{\link{Heatmap}}.}
68
-
69
-}
70
-\details{
71
-To visualize data distribution in a matrix or in a list, we normally use
72
-boxplot or violinplot. We can also use colors to map the density values and
73
-visualize distribution of values through a heatmap. It is useful if you have
74
-huge number of columns in \code{data} to visualize.
75
-
76
-The density matrix is generated with 500 rows ranging between the maximun
77
-and minimal values in all densities.
78
-}
79
-\value{
80
-A \code{\link{Heatmap-class}} object. It can oly add other heatmaps/annotations vertically.
81
-}
82
-\seealso{
83
-\url{https://jokergoo.github.io/ComplexHeatmap-reference/book/other-high-level-plots.html#density-heatmap}
84
-}
85
-\author{
86
-Zuguang Gu <z.gu@dkfz.de>
87
-}
88
-\examples{
89
-matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10]
90
-densityHeatmap(matrix)
91
-
92
-lt = list(rnorm(10), rnorm(10))
93
-densityHeatmap(lt)
94
-
95
-ha = HeatmapAnnotation(points = anno_points(runif(10)),
96
-    anno = rep(c("A", "B"), each = 5), col = list(anno = c("A" = "red", "B" = "blue")))
97
-densityHeatmap(matrix, top_annotation = ha)
98
-densityHeatmap(matrix, top_annotation = ha) \%v\% Heatmap(matrix, height = unit(6, "cm"))
99
-}
Browse code

densityHeatmap() supports to self-define ylim

Zuguang Gu authored on 02/09/2019 20:19:02
Showing1 changed files
... ...
@@ -15,7 +15,7 @@ densityHeatmap(data,
15 15
     ylab = deparse(substitute(data)),
16 16
     column_title = paste0("Density heatmap of ", deparse(substitute(data))),
17 17
     title = column_title,
18
-    ylim = c(-Inf, Inf),
18
+    ylim = NULL,
19 19
     range = ylim,
20 20
     
21 21
     title_gp = gpar(fontsize = 14),
Browse code

add show_quantiles argument

Zuguang Gu authored on 08/05/2019 11:24:33
Showing1 changed files
... ...
@@ -22,6 +22,7 @@ densityHeatmap(data,
22 22
     ylab_gp = gpar(fontsize = 12),
23 23
     tick_label_gp = gpar(fontsize = 10),
24 24
     quantile_gp = gpar(fontsize = 10),
25
+    show_quantiles = TRUE,
25 26
     
26 27
     column_order = NULL,
27 28
     column_names_side = "bottom",
... ...
@@ -52,6 +53,7 @@ densityHeatmap(data,
52 53
   \item{ylab_gp}{Graphic parameters for y-labels.}
53 54
   \item{tick_label_gp}{Graphic parameters for y-ticks.}
54 55
   \item{quantile_gp}{Graphic parameters for the quantiles.}
56
+  \item{show_quantiles}{Whether show quantile lines.}
55 57
   \item{column_order}{Order of columns.}
56 58
   \item{column_names_side}{Pass to \code{\link{Heatmap}}.}
57 59
   \item{show_column_names}{Pass to \code{\link{Heatmap}}.}
Browse code

add mc.cores in densityHeatmap()

Zuguang Gu authored on 13/03/2019 17:39:11
Showing1 changed files
... ...
@@ -33,6 +33,7 @@ densityHeatmap(data,
33 33
     cluster_columns = FALSE,
34 34
     clustering_distance_columns = "ks",
35 35
     clustering_method_columns = "complete",
36
+    mc.cores = 1,
36 37
     
37 38
     ...)
38 39
 }
... ...
@@ -60,6 +61,7 @@ densityHeatmap(data,
60 61
   \item{cluster_columns}{Whether cluster columns?}
61 62
   \item{clustering_distance_columns}{There is a specific distance method \code{ks} which is the Kolmogorov-Smirnov statistic between two distributions. For other methods, the distance is calculated on the density matrix.}
62 63
   \item{clustering_method_columns}{Pass to \code{\link{Heatmap}}.}
64
+  \item{mc.cores}{Multiple cores for calculating ks distance.}
63 65
   \item{...}{Pass to \code{\link{Heatmap}}.}
64 66
 
65 67
 }
Browse code

documentation checked

Zuguang Gu authored on 23/10/2018 19:59:12
Showing1 changed files
... ...
@@ -45,22 +45,22 @@ densityHeatmap(data,
45 45
   \item{ylab}{Label on y-axis.}
46 46
   \item{column_title}{Title of the heatmap.}
47 47
   \item{title}{Same as \code{column_title}.}
48
-  \item{ylim}{Ranges on the y-axis. By default the range is between 1th quantile and 99th quantile of the data.}
48
+  \item{ylim}{Ranges on the y-axis.}
49 49
   \item{range}{Same as \code{ylim}.}
50
-  \item{title_gp}{= gpar(fontsize = 14),}
51
-  \item{ylab_gp}{= gpar(fontsize = 12),}
52
-  \item{tick_label_gp}{= gpar(fontsize = 10),}
53
-  \item{quantile_gp}{= gpar(fontsize = 10),}
54
-  \item{column_order}{column_order}
50
+  \item{title_gp}{Graphic parameters for title.}
51
+  \item{ylab_gp}{Graphic parameters for y-labels.}
52
+  \item{tick_label_gp}{Graphic parameters for y-ticks.}
53
+  \item{quantile_gp}{Graphic parameters for the quantiles.}
54
+  \item{column_order}{Order of columns.}
55 55
   \item{column_names_side}{Pass to \code{\link{Heatmap}}.}
56 56
   \item{show_column_names}{Pass to \code{\link{Heatmap}}.}
57 57
   \item{column_names_max_height}{Pass to \code{\link{Heatmap}}.}
58 58
   \item{column_names_gp}{Pass to \code{\link{Heatmap}}.}
59 59
   \item{column_names_rot}{Pass to \code{\link{Heatmap}}.}
60
-  \item{cluster_columns}{Whether cluster columns (here clustered by density values)? Normally we don't cluster columns.}
61
-  \item{clustering_distance_columns}{-clustering_distance_columns}
62
-  \item{clustering_method_columns}{-clustering_method_columns}
63
-  \item{...}{pass to \code{\link{Heatmap}}.}
60
+  \item{cluster_columns}{Whether cluster columns?}
61
+  \item{clustering_distance_columns}{There is a specific distance method \code{ks} which is the Kolmogorov-Smirnov statistic between two distributions. For other methods, the distance is calculated on the density matrix.}
62
+  \item{clustering_method_columns}{Pass to \code{\link{Heatmap}}.}
63
+  \item{...}{Pass to \code{\link{Heatmap}}.}
64 64
 
65 65
 }
66 66
 \details{
... ...
@@ -70,12 +70,13 @@ visualize distribution of values through a heatmap. It is useful if you have
70 70
 huge number of columns in \code{data} to visualize.
71 71
 
72 72
 The density matrix is generated with 500 rows ranging between the maximun
73
-and minimal values in all densities. The density values in each row are
74
-linearly intepolated between the two density values at the two nearest
75
-bounds.
73
+and minimal values in all densities.
76 74
 }
77 75
 \value{
78
-A \code{\link{HeatmapList-class}} object with only one heatmap, but it can only add other heatmaps/annotations vertically.
76
+A \code{\link{Heatmap-class}} object. It can oly add other heatmaps/annotations vertically.
77
+}
78
+\seealso{
79
+\url{https://jokergoo.github.io/ComplexHeatmap-reference/book/other-high-level-plots.html#density-heatmap}
79 80
 }
80 81
 \author{
81 82
 Zuguang Gu <z.gu@dkfz.de>
... ...
@@ -90,5 +91,5 @@ densityHeatmap(lt)
90 91
 ha = HeatmapAnnotation(points = anno_points(runif(10)),
91 92
     anno = rep(c("A", "B"), each = 5), col = list(anno = c("A" = "red", "B" = "blue")))
92 93
 densityHeatmap(matrix, top_annotation = ha)
93
-densityHeatmap(matrix, top_annotation = ha) %v% Heatmap(matrix, height = unit(6, "cm"))
94
+densityHeatmap(matrix, top_annotation = ha) \%v\% Heatmap(matrix, height = unit(6, "cm"))
94 95
 }
Browse code

update

Zuguang Gu authored on 22/10/2018 05:57:29
Showing1 changed files
... ...
@@ -57,7 +57,8 @@ densityHeatmap(data,
57 57
   \item{column_names_max_height}{Pass to \code{\link{Heatmap}}.}
58 58
   \item{column_names_gp}{Pass to \code{\link{Heatmap}}.}
59 59
   \item{column_names_rot}{Pass to \code{\link{Heatmap}}.}
60
-  \item{cluster_columns}{Whether cluster columns (here clustered by density values)? Normally we don't cluster columns. - clustering_distance_columns}
60
+  \item{cluster_columns}{Whether cluster columns (here clustered by density values)? Normally we don't cluster columns.}
61
+  \item{clustering_distance_columns}{-clustering_distance_columns}
61 62
   \item{clustering_method_columns}{-clustering_method_columns}
62 63
   \item{...}{pass to \code{\link{Heatmap}}.}
63 64
 
Browse code

fix some bugs

Zuguang Gu authored on 19/10/2018 19:08:59
Showing1 changed files
... ...
@@ -31,6 +31,9 @@ densityHeatmap(data,
31 31
     column_names_rot = 90,
32 32
     
33 33
     cluster_columns = FALSE,
34
+    clustering_distance_columns = "ks",
35
+    clustering_method_columns = "complete",
36
+    
34 37
     ...)
35 38
 }
36 39
 \arguments{
... ...
@@ -54,7 +57,8 @@ densityHeatmap(data,
54 57
   \item{column_names_max_height}{Pass to \code{\link{Heatmap}}.}
55 58
   \item{column_names_gp}{Pass to \code{\link{Heatmap}}.}
56 59
   \item{column_names_rot}{Pass to \code{\link{Heatmap}}.}
57
-  \item{cluster_columns}{Whether cluster columns (here clustered by density values)? Normally we don't cluster columns.}
60
+  \item{cluster_columns}{Whether cluster columns (here clustered by density values)? Normally we don't cluster columns. - clustering_distance_columns}
61
+  \item{clustering_method_columns}{-clustering_method_columns}
58 62
   \item{...}{pass to \code{\link{Heatmap}}.}
59 63
 
60 64
 }
Browse code

update

jokergoo authored on 12/10/2018 15:28:37
Showing1 changed files
... ...
@@ -35,7 +35,7 @@ densityHeatmap(data,
35 35
 }
36 36
 \arguments{
37 37
 
38
-  \item{data}{A matrix or a list. If it is a matrix, density will be calculated by columns.}
38
+  \item{data}{A matrix or a list. If it is a matrix, density is calculated by columns.}
39 39
   \item{density_param}{Parameters send to \code{\link[stats]{density}}, \code{na.rm} is enforced to be \code{TRUE}.}
40 40
   \item{col}{A vector of colors that density values are mapped to.}
41 41
   \item{color_space}{The color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}
... ...
@@ -47,7 +47,7 @@ densityHeatmap(data,
47 47
   \item{title_gp}{= gpar(fontsize = 14),}
48 48
   \item{ylab_gp}{= gpar(fontsize = 12),}
49 49
   \item{tick_label_gp}{= gpar(fontsize = 10),}
50
-  \item{quantile_gp}{= gpar(fontsize = 10),# -column_order Order of columns.}
50
+  \item{quantile_gp}{= gpar(fontsize = 10),}
51 51
   \item{column_order}{column_order}
52 52
   \item{column_names_side}{Pass to \code{\link{Heatmap}}.}
53 53
   \item{show_column_names}{Pass to \code{\link{Heatmap}}.}
... ...
@@ -59,13 +59,15 @@ densityHeatmap(data,
59 59
 
60 60
 }
61 61
 \details{
62
-To visualize data distribution in a matrix or in a list, sometimes we use boxplot or beanplot.
63
-Here we use colors to map the density values and visualize distribution of values
64
-in each column (or each vector in the list) through a heatmap. It is useful if you have huge number 
65
-of columns in \code{data} to visualize.
62
+To visualize data distribution in a matrix or in a list, we normally use
63
+boxplot or violinplot. We can also use colors to map the density values and
64
+visualize distribution of values through a heatmap. It is useful if you have
65
+huge number of columns in \code{data} to visualize.
66 66
 
67
-The density matrix is generated with 500 rows ranging between the maximun and minimal values in all densities.
68
-The density values in each row are linearly intepolated between the two density values at the two nearest bounds.
67
+The density matrix is generated with 500 rows ranging between the maximun
68
+and minimal values in all densities. The density values in each row are
69
+linearly intepolated between the two density values at the two nearest
70
+bounds.
69 71
 }
70 72
 \value{
71 73
 A \code{\link{HeatmapList-class}} object with only one heatmap, but it can only add other heatmaps/annotations vertically.
... ...
@@ -77,10 +79,11 @@ Zuguang Gu <z.gu@dkfz.de>
77 79
 matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10]
78 80
 densityHeatmap(matrix)
79 81
 
82
+lt = list(rnorm(10), rnorm(10))
83
+densityHeatmap(lt)
84
+
80 85
 ha = HeatmapAnnotation(points = anno_points(runif(10)),
81 86
     anno = rep(c("A", "B"), each = 5), col = list(anno = c("A" = "red", "B" = "blue")))
82 87
 densityHeatmap(matrix, top_annotation = ha)
83
-
84
-lt = list(rnorm(10), rnorm(10))
85
-densityHeatmap(lt)
88
+densityHeatmap(matrix, top_annotation = ha) %v% Heatmap(matrix, height = unit(6, "cm"))
86 89
 }
Browse code

beta release

Zuguang Gu authored on 22/09/2018 10:01:44
Showing1 changed files
... ...
@@ -12,8 +12,6 @@ densityHeatmap(data,
12 12
     
13 13
     col = rev(brewer.pal(11, "Spectral")),
14 14
     color_space = "LAB",
15
-    top_annotation = NULL,
16
-    bottom_annotation = NULL,
17 15
     ylab = deparse(substitute(data)),
18 16
     column_title = paste0("Density heatmap of ", deparse(substitute(data))),
19 17
     title = column_title,
... ...
@@ -41,8 +39,6 @@ densityHeatmap(data,
41 39
   \item{density_param}{Parameters send to \code{\link[stats]{density}}, \code{na.rm} is enforced to be \code{TRUE}.}
42 40
   \item{col}{A vector of colors that density values are mapped to.}
43 41
   \item{color_space}{The color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}
44
-  \item{top_annotation}{A \code{\link{HeatmapAnnotation-class}} object which is put on top of the heatmap.}
45
-  \item{bottom_annotation}{A \code{\link{HeatmapAnnotation-class}} object which is put at bottom of the heatmap.}
46 42
   \item{ylab}{Label on y-axis.}
47 43
   \item{column_title}{Title of the heatmap.}
48 44
   \item{title}{Same as \code{column_title}.}
Browse code

R CMD check passed

Zuguang Gu authored on 20/09/2018 12:48:08
Showing1 changed files
1 1
old mode 100755
2 2
new mode 100644
... ...
@@ -1,59 +1,65 @@
1 1
 \name{densityHeatmap}
2 2
 \alias{densityHeatmap}
3 3
 \title{
4
-Use colors to represent density distribution
4
+Visualize Density Distribution by Heatmap
5 5
 }
6 6
 \description{
7
-Use colors to represent density distribution
7
+Visualize Density Distribution by Heatmap
8 8
 }
9 9
 \usage{
10 10
 densityHeatmap(data,
11
-    col = rev(brewer.pal(11, "Spectral")),
12 11
     density_param = list(na.rm = TRUE),
12
+    
13
+    col = rev(brewer.pal(11, "Spectral")),
13 14
     color_space = "LAB",
14
-    anno = NULL,
15
+    top_annotation = NULL,
16
+    bottom_annotation = NULL,
15 17
     ylab = deparse(substitute(data)),
16
-    title = paste0("Density heatmap of ", deparse(substitute(data))),
17
-    range = c(-Inf, Inf),
18
-    cluster_columns = FALSE,
19
-    clustering_distance_columns = "euclidean",
20
-    clustering_method_columns = "complete",
21
-    column_dend_side = "top",
22
-    column_dend_height = unit(10, "mm"),
23
-    show_column_dend = FALSE,
24
-    column_dend_gp = gpar(),
25
-    column_dend_reorder = TRUE,
26
-    column_names_side = c("bottom", "top"),
18
+    column_title = paste0("Density heatmap of ", deparse(substitute(data))),
19
+    title = column_title,
20
+    ylim = c(-Inf, Inf),
21
+    range = ylim,
22
+    
23
+    title_gp = gpar(fontsize = 14),
24
+    ylab_gp = gpar(fontsize = 12),
25
+    tick_label_gp = gpar(fontsize = 10),
26
+    quantile_gp = gpar(fontsize = 10),
27
+    
28
+    column_order = NULL,
29
+    column_names_side = "bottom",
27 30
     show_column_names = TRUE,
28
-    column_names_max_height = unit(4, "cm"),
31
+    column_names_max_height = unit(6, "cm"),
29 32
     column_names_gp = gpar(fontsize = 12),
30
-    column_order = NULL,
33
+    column_names_rot = 90,
34
+    
35
+    cluster_columns = FALSE,
31 36
     ...)
32 37
 }
33 38
 \arguments{
34 39
 
35
-  \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns.}
36
-  \item{col}{a list of colors that density values are mapped to.}
37
-  \item{density_param}{parameters send to \code{\link[stats]{density}}, \code{na.rm} is enforced to \code{TRUE}.}
38
-  \item{color_space}{the color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}
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.}
40
-  \item{ylab}{label on y-axis in the plot}
41
-  \item{title}{title of the plot}
42
-  \item{range}{ranges on the y-axis. By default the range is between 1th quantile and 99th quantile of the data.}
43
-  \item{cluster_columns}{whether cluster columns (here cluster by density distributions)}
44
-  \item{clustering_distance_columns}{pass to \code{\link{Heatmap}}}
45
-  \item{clustering_method_columns}{pass to \code{\link{Heatmap}}}
46
-  \item{column_dend_side}{pass to \code{\link{Heatmap}}}
47
-  \item{column_dend_height}{pass to \code{\link{Heatmap}}}
48
-  \item{show_column_dend}{pass to \code{\link{Heatmap}}}
49
-  \item{column_dend_gp}{pass to \code{\link{Heatmap}}}
50
-  \item{column_dend_reorder}{pass to \code{\link{Heatmap}}}
51
-  \item{column_names_side}{pass to \code{\link{Heatmap}}}
52
-  \item{show_column_names}{pass to \code{\link{Heatmap}}}
53
-  \item{column_names_max_height}{pass to \code{\link{Heatmap}}}
54
-  \item{column_names_gp}{pass to \code{\link{Heatmap}}}
55
-  \item{column_order}{order of columns}
56
-  \item{...}{pass to \code{\link{draw,HeatmapList-method}}}
40
+  \item{data}{A matrix or a list. If it is a matrix, density will be calculated by columns.}
41
+  \item{density_param}{Parameters send to \code{\link[stats]{density}}, \code{na.rm} is enforced to be \code{TRUE}.}
42
+  \item{col}{A vector of colors that density values are mapped to.}
43
+  \item{color_space}{The color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}
44
+  \item{top_annotation}{A \code{\link{HeatmapAnnotation-class}} object which is put on top of the heatmap.}
45
+  \item{bottom_annotation}{A \code{\link{HeatmapAnnotation-class}} object which is put at bottom of the heatmap.}
46
+  \item{ylab}{Label on y-axis.}
47
+  \item{column_title}{Title of the heatmap.}
48
+  \item{title}{Same as \code{column_title}.}
49
+  \item{ylim}{Ranges on the y-axis. By default the range is between 1th quantile and 99th quantile of the data.}
50
+  \item{range}{Same as \code{ylim}.}
51
+  \item{title_gp}{= gpar(fontsize = 14),}
52
+  \item{ylab_gp}{= gpar(fontsize = 12),}
53
+  \item{tick_label_gp}{= gpar(fontsize = 10),}
54
+  \item{quantile_gp}{= gpar(fontsize = 10),# -column_order Order of columns.}
55
+  \item{column_order}{column_order}
56
+  \item{column_names_side}{Pass to \code{\link{Heatmap}}.}
57
+  \item{show_column_names}{Pass to \code{\link{Heatmap}}.}
58
+  \item{column_names_max_height}{Pass to \code{\link{Heatmap}}.}
59
+  \item{column_names_gp}{Pass to \code{\link{Heatmap}}.}
60
+  \item{column_names_rot}{Pass to \code{\link{Heatmap}}.}
61
+  \item{cluster_columns}{Whether cluster columns (here clustered by density values)? Normally we don't cluster columns.}
62
+  \item{...}{pass to \code{\link{Heatmap}}.}
57 63
 
58 64
 }
59 65
 \details{
... ...
@@ -66,7 +72,7 @@ The density matrix is generated with 500 rows ranging between the maximun and mi
66 72
 The density values in each row are linearly intepolated between the two density values at the two nearest bounds.
67 73
 }
68 74
 \value{
69
-No value is returned.
75
+A \code{\link{HeatmapList-class}} object with only one heatmap, but it can only add other heatmaps/annotations vertically.
70 76
 }
71 77
 \author{
72 78
 Zuguang Gu <z.gu@dkfz.de>
... ...
@@ -74,12 +80,10 @@ Zuguang Gu <z.gu@dkfz.de>
74 80
 \examples{
75 81
 matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10]
76 82
 densityHeatmap(matrix)
77
-densityHeatmap(matrix, anno = rep(c("A", "B"), each = 5))
78
-densityHeatmap(matrix, col = c("white", "red"), anno = rep(c("A", "B"), each = 5))
79 83
 
80 84
 ha = HeatmapAnnotation(points = anno_points(runif(10)),
81 85
     anno = rep(c("A", "B"), each = 5), col = list(anno = c("A" = "red", "B" = "blue")))
82
-densityHeatmap(matrix, anno = ha)
86
+densityHeatmap(matrix, top_annotation = ha)
83 87
 
84 88
 lt = list(rnorm(10), rnorm(10))
85 89
 densityHeatmap(lt)
Browse code

merge by copy paste

Zuguang Gu authored on 17/10/2017 20:55:32
Showing1 changed files
... ...
@@ -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.
Zuguang Gu authored on 17/10/2017 19:44:53
Showing0 changed files
Browse code

various updates

Zuguang Gu authored on 23/06/2017 21:05:07
Showing0 changed files
Browse code

resolve conflict

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@118270 bc3139a8-67e5-0310-9ffc-ced21a209358

Zuguang Gu authored on 07/06/2016 21:28:32
Showing1 changed files
... ...
@@ -14,6 +14,18 @@ densityHeatmap(data,
14 14
     ylab = deparse(substitute(data)),
15 15
     title = paste0("Density heatmap of ", deparse(substitute(data))),
16 16
     range = c(-Inf, Inf),
17
+    cluster_columns = FALSE,
18
+    clustering_distance_columns = "euclidean",
19
+    clustering_method_columns = "complete",
20
+    column_dend_side = "top",
21
+    column_dend_height = unit(10, "mm"),
22
+    show_column_dend = FALSE,
23
+    column_dend_gp = gpar(),
24
+    column_dend_reorder = TRUE,
25
+    column_names_side = c("bottom", "top"),
26
+    show_column_names = TRUE,
27
+    column_names_max_height = unit(4, "cm"),
28
+    column_names_gp = gpar(fontsize = 12),
17 29
     column_order = NULL,
18 30
     ...)
19 31
 }
... ...
@@ -26,6 +38,18 @@ densityHeatmap(data,
26 38
   \item{ylab}{label on y-axis in the plot}
27 39
   \item{title}{title of the plot}
28 40
   \item{range}{ranges on the y-axis. By default the range is between 1th quantile and 99th quantile of the data.}
41
+  \item{cluster_columns}{whether cluster columns (here cluster by density distributions)}
42
+  \item{clustering_distance_columns}{pass to \code{\link{Heatmap}}}
43
+  \item{clustering_method_columns}{pass to \code{\link{Heatmap}}}
44
+  \item{column_dend_side}{pass to \code{\link{Heatmap}}}
45
+  \item{column_dend_height}{pass to \code{\link{Heatmap}}}
46
+  \item{show_column_dend}{pass to \code{\link{Heatmap}}}
47
+  \item{column_dend_gp}{pass to \code{\link{Heatmap}}}
48
+  \item{column_dend_reorder}{pass to \code{\link{Heatmap}}}
49
+  \item{column_names_side}{pass to \code{\link{Heatmap}}}
50
+  \item{show_column_names}{pass to \code{\link{Heatmap}}}
51
+  \item{column_names_max_height}{pass to \code{\link{Heatmap}}}
52
+  \item{column_names_gp}{pass to \code{\link{Heatmap}}}
29 53
   \item{column_order}{order of columns}
30 54
   \item{...}{pass to \code{\link{draw,HeatmapList-method}}}
31 55
 
Browse code

add import in NAMESPACE

jokergoo authored on 30/05/2016 14:31:40
Showing1 changed files
... ...
@@ -50,7 +50,6 @@ densityHeatmap(data,
50 50
   \item{show_column_names}{pass to \code{\link{Heatmap}}}
51 51
   \item{column_names_max_height}{pass to \code{\link{Heatmap}}}
52 52
   \item{column_names_gp}{pass to \code{\link{Heatmap}}}
53
-  \item{column_order}{pass to \code{\link{Heatmap}}}
54 53
   \item{column_order}{order of columns}
55 54
   \item{...}{pass to \code{\link{draw,HeatmapList-method}}}
56 55
 
Browse code

add more column settings in densityHeatmap()

jokergoo authored on 30/05/2016 09:58:40
Showing1 changed files
... ...
@@ -14,6 +14,18 @@ densityHeatmap(data,
14 14
     ylab = deparse(substitute(data)),
15 15
     title = paste0("Density heatmap of ", deparse(substitute(data))),
16 16
     range = c(-Inf, Inf),
17
+    cluster_columns = FALSE,
18
+    clustering_distance_columns = "euclidean",
19
+    clustering_method_columns = "complete",
20
+    column_dend_side = "top",
21
+    column_dend_height = unit(10, "mm"),
22
+    show_column_dend = FALSE,
23
+    column_dend_gp = gpar(),
24
+    column_dend_reorder = TRUE,
25
+    column_names_side = c("bottom", "top"),
26
+    show_column_names = TRUE,
27
+    column_names_max_height = unit(4, "cm"),
28
+    column_names_gp = gpar(fontsize = 12),
17 29
     column_order = NULL,
18 30
     ...)
19 31
 }
... ...
@@ -26,6 +38,19 @@ densityHeatmap(data,
26 38
   \item{ylab}{label on y-axis in the plot}
27 39
   \item{title}{title of the plot}
28 40
   \item{range}{ranges on the y-axis. By default the range is between 1th quantile and 99th quantile of the data.}
41
+  \item{cluster_columns}{whether cluster columns (here cluster by density distributions)}
42
+  \item{clustering_distance_columns}{pass to \code{\link{Heatmap}}}
43
+  \item{clustering_method_columns}{pass to \code{\link{Heatmap}}}
44
+  \item{column_dend_side}{pass to \code{\link{Heatmap}}}
45
+  \item{column_dend_height}{pass to \code{\link{Heatmap}}}
46
+  \item{show_column_dend}{pass to \code{\link{Heatmap}}}
47
+  \item{column_dend_gp}{pass to \code{\link{Heatmap}}}
48
+  \item{column_dend_reorder}{pass to \code{\link{Heatmap}}}
49
+  \item{column_names_side}{pass to \code{\link{Heatmap}}}
50
+  \item{show_column_names}{pass to \code{\link{Heatmap}}}
51
+  \item{column_names_max_height}{pass to \code{\link{Heatmap}}}
52
+  \item{column_names_gp}{pass to \code{\link{Heatmap}}}
53
+  \item{column_order}{pass to \code{\link{Heatmap}}}
29 54
   \item{column_order}{order of columns}
30 55
   \item{...}{pass to \code{\link{draw,HeatmapList-method}}}
31 56
 
Browse code

refreshed documentations

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@115000 bc3139a8-67e5-0310-9ffc-ced21a209358

Zuguang Gu authored on 19/03/2016 18:00:20
Showing1 changed files
... ...
@@ -14,6 +14,7 @@ densityHeatmap(data,
14 14
     ylab = deparse(substitute(data)),
15 15
     title = paste0("Density heatmap of ", deparse(substitute(data))),
16 16
     range = c(-Inf, Inf),
17
+    column_order = NULL,
17 18
     ...)
18 19
 }
19 20
 \arguments{
... ...
@@ -25,6 +26,7 @@ densityHeatmap(data,
25 26
   \item{ylab}{label on y-axis in the plot}
26 27
   \item{title}{title of the plot}
27 28
   \item{range}{ranges on the y-axis. By default the range is between 1th quantile and 99th quantile of the data.}
29
+  \item{column_order}{order of columns}
28 30
   \item{...}{pass to \code{\link{draw,HeatmapList-method}}}
29 31
 
30 32
 }
Browse code

revised documentations

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@114991 bc3139a8-67e5-0310-9ffc-ced21a209358

Zuguang Gu authored on 19/03/2016 17:59:18
Showing1 changed files
... ...
@@ -19,12 +19,12 @@ densityHeatmap(data,
19 19
 \arguments{
20 20
 
21 21
   \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns.}
22
-  \item{col}{a list of colors that density values are scaled to.}
22
+  \item{col}{a list of colors that density values are mapped to.}
23 23
   \item{color_space}{the color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}
24
-  \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame.  It can also be a \code{\link{HeatmapAnnotation-class}} object.}
24
+  \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.}
25 25
   \item{ylab}{label on y-axis in the plot}
26 26
   \item{title}{title of the plot}
27
-  \item{range}{ranges on the y-axis. The lower bound is the maximul value between \code{range[[1]]} and minimal value in the data and the upper bound is the minimal value between \code{range[[2]]} and maximul value in the data.}
27
+  \item{range}{ranges on the y-axis. By default the range is between 1th quantile and 99th quantile of the data.}
28 28
   \item{...}{pass to \code{\link{draw,HeatmapList-method}}}
29 29
 
30 30
 }
... ...
@@ -46,7 +46,8 @@ densityHeatmap(matrix)
46 46
 densityHeatmap(matrix, anno = rep(c("A", "B"), each = 5))
47 47
 densityHeatmap(matrix, col = c("white", "red"), anno = rep(c("A", "B"), each = 5))
48 48
 
49
-ha = HeatmapAnnotation(points = anno_points(runif(10)))
49
+ha = HeatmapAnnotation(points = anno_points(runif(10)),
50
+    anno = rep(c("A", "B"), each = 5), col = list(anno = c("A" = "red", "B" = "blue")))
50 51
 densityHeatmap(matrix, anno = ha)
51 52
 
52 53
 lt = list(rnorm(10), rnorm(10))
Browse code

refreshed documentations

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@114986 bc3139a8-67e5-0310-9ffc-ced21a209358

Zuguang Gu authored on 19/03/2016 17:58:37
Showing1 changed files
... ...
@@ -13,6 +13,7 @@ densityHeatmap(data,
13 13
     anno = NULL,
14 14
     ylab = deparse(substitute(data)),
15 15
     title = paste0("Density heatmap of ", deparse(substitute(data))),
16
+    range = c(-Inf, Inf),
16 17
     ...)
17 18
 }
18 19
 \arguments{
... ...
@@ -23,8 +24,7 @@ densityHeatmap(data,
23 24
   \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame.  It can also be a \code{\link{HeatmapAnnotation-class}} object.}
24 25
   \item{ylab}{label on y-axis in the plot}
25 26
   \item{title}{title of the plot}
26
-  \item{range}{ranges on the y-axis. The lower bound is the maximul value between \code{range[[1]]} and minimal value
27
-       in the data and the upper bound is the minimal value between \code{range[[2]]} and maximul value in the data.}
27
+  \item{range}{ranges on the y-axis. The lower bound is the maximul value between \code{range[[1]]} and minimal value in the data and the upper bound is the minimal value between \code{range[[2]]} and maximul value in the data.}
28 28
   \item{...}{pass to \code{\link{draw,HeatmapList-method}}}
29 29
 
30 30
 }
Browse code

add 'range' option in densithHeatmap()

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@114984 bc3139a8-67e5-0310-9ffc-ced21a209358

Zuguang Gu authored on 19/03/2016 17:58:24
Showing1 changed files
... ...
@@ -23,6 +23,8 @@ densityHeatmap(data,
23 23
   \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame.  It can also be a \code{\link{HeatmapAnnotation-class}} object.}
24 24
   \item{ylab}{label on y-axis in the plot}
25 25
   \item{title}{title of the plot}
26
+  \item{range}{ranges on the y-axis. The lower bound is the maximul value between \code{range[[1]]} and minimal value
27
+       in the data and the upper bound is the minimal value between \code{range[[2]]} and maximul value in the data.}
26 28
   \item{...}{pass to \code{\link{draw,HeatmapList-method}}}
27 29
 
28 30
 }
Browse code

refreshed documentations

Zuguang Gu authored on 17/03/2016 17:10:15
Showing1 changed files
... ...
@@ -14,6 +14,7 @@ densityHeatmap(data,
14 14
     ylab = deparse(substitute(data)),
15 15
     title = paste0("Density heatmap of ", deparse(substitute(data))),
16 16
     range = c(-Inf, Inf),
17
+    column_order = NULL,
17 18
     ...)
18 19
 }
19 20
 \arguments{
... ...
@@ -25,6 +26,7 @@ densityHeatmap(data,
25 26
   \item{ylab}{label on y-axis in the plot}
26 27
   \item{title}{title of the plot}
27 28
   \item{range}{ranges on the y-axis. By default the range is between 1th quantile and 99th quantile of the data.}
29
+  \item{column_order}{order of columns}
28 30
   \item{...}{pass to \code{\link{draw,HeatmapList-method}}}
29 31
 
30 32
 }
Browse code

revised documentations

Zuguang Gu authored on 06/03/2016 13:15:14
Showing1 changed files
... ...
@@ -19,12 +19,12 @@ densityHeatmap(data,
19 19
 \arguments{
20 20
 
21 21
   \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns.}
22
-  \item{col}{a list of colors that density values are scaled to.}
22
+  \item{col}{a list of colors that density values are mapped to.}
23 23
   \item{color_space}{the color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}
24
-  \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame.  It can also be a \code{\link{HeatmapAnnotation-class}} object.}
24
+  \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.}
25 25
   \item{ylab}{label on y-axis in the plot}
26 26
   \item{title}{title of the plot}
27
-  \item{range}{ranges on the y-axis. The lower bound is the maximul value between \code{range[[1]]} and minimal value in the data and the upper bound is the minimal value between \code{range[[2]]} and maximul value in the data.}
27
+  \item{range}{ranges on the y-axis. By default the range is between 1th quantile and 99th quantile of the data.}
28 28
   \item{...}{pass to \code{\link{draw,HeatmapList-method}}}
29 29
 
30 30
 }
... ...
@@ -46,7 +46,8 @@ densityHeatmap(matrix)
46 46
 densityHeatmap(matrix, anno = rep(c("A", "B"), each = 5))
47 47
 densityHeatmap(matrix, col = c("white", "red"), anno = rep(c("A", "B"), each = 5))
48 48
 
49
-ha = HeatmapAnnotation(points = anno_points(runif(10)))
49
+ha = HeatmapAnnotation(points = anno_points(runif(10)),
50
+    anno = rep(c("A", "B"), each = 5), col = list(anno = c("A" = "red", "B" = "blue")))
50 51
 densityHeatmap(matrix, anno = ha)
51 52
 
52 53
 lt = list(rnorm(10), rnorm(10))
Browse code

refreshed documentations

Zuguang Gu authored on 17/01/2016 21:59:07
Showing1 changed files
... ...
@@ -13,6 +13,7 @@ densityHeatmap(data,
13 13
     anno = NULL,
14 14
     ylab = deparse(substitute(data)),
15 15
     title = paste0("Density heatmap of ", deparse(substitute(data))),
16
+    range = c(-Inf, Inf),
16 17
     ...)
17 18
 }
18 19
 \arguments{
... ...
@@ -23,8 +24,7 @@ densityHeatmap(data,
23 24
   \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame.  It can also be a \code{\link{HeatmapAnnotation-class}} object.}
24 25
   \item{ylab}{label on y-axis in the plot}
25 26
   \item{title}{title of the plot}
26
-  \item{range}{ranges on the y-axis. The lower bound is the maximul value between \code{range[[1]]} and minimal value
27
-       in the data and the upper bound is the minimal value between \code{range[[2]]} and maximul value in the data.}
27
+  \item{range}{ranges on the y-axis. The lower bound is the maximul value between \code{range[[1]]} and minimal value in the data and the upper bound is the minimal value between \code{range[[2]]} and maximul value in the data.}
28 28
   \item{...}{pass to \code{\link{draw,HeatmapList-method}}}
29 29
 
30 30
 }
Browse code

add 'range' option in densithHeatmap()

jokergoo authored on 15/01/2016 09:37:40
Showing1 changed files
... ...
@@ -23,6 +23,8 @@ densityHeatmap(data,
23 23
   \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame.  It can also be a \code{\link{HeatmapAnnotation-class}} object.}
24 24
   \item{ylab}{label on y-axis in the plot}
25 25
   \item{title}{title of the plot}
26
+  \item{range}{ranges on the y-axis. The lower bound is the maximul value between \code{range[[1]]} and minimal value
27
+       in the data and the upper bound is the minimal value between \code{range[[2]]} and maximul value in the data.}
26 28
   \item{...}{pass to \code{\link{draw,HeatmapList-method}}}
27 29
 
28 30
 }
Browse code

name assigned to vp with data ranges

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@111675 bc3139a8-67e5-0310-9ffc-ced21a209358

Zuguang Gu authored on 20/12/2015 21:18:10
Showing1 changed files
... ...
@@ -12,7 +12,8 @@ densityHeatmap(data,
12 12
     color_space = "LAB",
13 13
     anno = NULL,
14 14
     ylab = deparse(substitute(data)),
15
-    title = paste0("Density heatmap of ", deparse(substitute(data))))
15
+    title = paste0("Density heatmap of ", deparse(substitute(data))),
16
+    ...)
16 17
 }
17 18
 \arguments{
18 19
 
... ...
@@ -22,6 +23,7 @@ densityHeatmap(data,
22 23
   \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame.  It can also be a \code{\link{HeatmapAnnotation-class}} object.}
23 24
   \item{ylab}{label on y-axis in the plot}
24 25
   \item{title}{title of the plot}
26
+  \item{...}{pass to \code{\link{draw,HeatmapList-method}}}
25 27
 
26 28
 }
27 29
 \details{
... ...
@@ -41,8 +43,10 @@ matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10]
41 43
 densityHeatmap(matrix)
42 44
 densityHeatmap(matrix, anno = rep(c("A", "B"), each = 5))
43 45
 densityHeatmap(matrix, col = c("white", "red"), anno = rep(c("A", "B"), each = 5))
46
+
44 47
 ha = HeatmapAnnotation(points = anno_points(runif(10)))
45 48
 densityHeatmap(matrix, anno = ha)
49
+
46 50
 lt = list(rnorm(10), rnorm(10))
47 51
 densityHeatmap(lt)
48 52
 }
Browse code

name assigned to vp with data ranges

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@111675 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 20/12/2015 21:18:10
Showing1 changed files
... ...
@@ -12,7 +12,8 @@ densityHeatmap(data,
12 12
     color_space = "LAB",
13 13
     anno = NULL,
14 14
     ylab = deparse(substitute(data)),
15
-    title = paste0("Density heatmap of ", deparse(substitute(data))))
15
+    title = paste0("Density heatmap of ", deparse(substitute(data))),
16
+    ...)
16 17
 }
17 18
 \arguments{
18 19
 
... ...
@@ -22,6 +23,7 @@ densityHeatmap(data,
22 23
   \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame.  It can also be a \code{\link{HeatmapAnnotation-class}} object.}
23 24
   \item{ylab}{label on y-axis in the plot}
24 25
   \item{title}{title of the plot}
26
+  \item{...}{pass to \code{\link{draw,HeatmapList-method}}}
25 27
 
26 28
 }
27 29
 \details{
... ...
@@ -41,8 +43,10 @@ matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10]
41 43
 densityHeatmap(matrix)
42 44
 densityHeatmap(matrix, anno = rep(c("A", "B"), each = 5))
43 45
 densityHeatmap(matrix, col = c("white", "red"), anno = rep(c("A", "B"), each = 5))
46
+
44 47
 ha = HeatmapAnnotation(points = anno_points(runif(10)))
45 48
 densityHeatmap(matrix, anno = ha)
49
+
46 50
 lt = list(rnorm(10), rnorm(10))
47 51
 densityHeatmap(lt)
48 52
 }
Browse code

Merge branch 'master' into devel

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@110567 bc3139a8-67e5-0310-9ffc-ced21a209358

Zuguang Gu authored on 12/11/2015 10:07:49
Showing1 changed files
... ...
@@ -19,7 +19,7 @@ densityHeatmap(data,
19 19
   \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns.}
20 20
   \item{col}{a list of colors that density values are scaled to.}
21 21
   \item{color_space}{the color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}
22
-  \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame. It can also be a \code{\link{HeatmapAnnotation-class}} object.}
22
+  \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame.  It can also be a \code{\link{HeatmapAnnotation-class}} object.}
23 23
   \item{ylab}{label on y-axis in the plot}
24 24
   \item{title}{title of the plot}
25 25
 
Browse code

Merge branch 'master' into devel

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@110567 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 12/11/2015 10:07:49
Showing1 changed files
... ...
@@ -19,7 +19,7 @@ densityHeatmap(data,
19 19
   \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns.}
20 20
   \item{col}{a list of colors that density values are scaled to.}
21 21
   \item{color_space}{the color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}
22
-  \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame. It can also be a \code{\link{HeatmapAnnotation-class}} object.}
22
+  \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame.  It can also be a \code{\link{HeatmapAnnotation-class}} object.}
23 23
   \item{ylab}{label on y-axis in the plot}
24 24
   \item{title}{title of the plot}
25 25
 
Browse code

Merge branch 'master' into devel

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@108253 bc3139a8-67e5-0310-9ffc-ced21a209358

Zuguang Gu authored on 07/09/2015 20:39:32
Showing1 changed files
1 1
old mode 100644
2 2
new mode 100755
Browse code

Merge branch 'master' into devel

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@108253 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 07/09/2015 20:39:32
Showing1 changed files
1 1
old mode 100644
2 2
new mode 100755
Browse code

resolve conflict from master branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@108131 bc3139a8-67e5-0310-9ffc-ced21a209358

Zuguang Gu authored on 03/09/2015 20:32:44
Showing1 changed files
... ...
@@ -7,8 +7,11 @@ Use colors to represent density distribution
7 7
 Use colors to represent density distribution
8 8
 }
9 9
 \usage{
10
-densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),
11
-    color_space = "RGB", anno = NULL, ylab = deparse(substitute(data)),
10
+densityHeatmap(data,
11
+    col = rev(brewer.pal(11, "Spectral")),
12
+    color_space = "LAB",
13
+    anno = NULL,
14
+    ylab = deparse(substitute(data)),
12 15
     title = paste0("Density heatmap of ", deparse(substitute(data))))
13 16
 }
14 17
 \arguments{
... ...
@@ -16,19 +19,23 @@ densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),
16 19
   \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns.}
17 20
   \item{col}{a list of colors that density values are scaled to.}
18 21
   \item{color_space}{the color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}
19
-  \item{anno}{annotation for matrix columns or list. The value should be a vector or a data frame. It can also be a \code{\link{HeatmapAnnotation-class}} object.}
22
+  \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame. It can also be a \code{\link{HeatmapAnnotation-class}} object.}
20 23
   \item{ylab}{label on y-axis in the plot}
21 24
   \item{title}{title of the plot}
22 25
 
23 26
 }
24 27
 \details{
25
-To visualize distribution of columns in a matrix or in a list, sometimes we use boxplot or beanplot.
26
-Here we use colors to map to the density values and visualize distribution of values
27
-in each column (or each element in the list) through a heatmap. It is useful if you have huge number of columns in \code{data} to visualize.
28
+To visualize data distribution in a matrix or in a list, sometimes we use boxplot or beanplot.
29
+Here we use colors to map the density values and visualize distribution of values
30
+in each column (or each vector in the list) through a heatmap. It is useful if you have huge number 
31
+of columns in \code{data} to visualize.
28 32
 }
29 33
 \value{
30 34
 No value is returned.
31 35
 }
36
+\author{
37
+Zuguang Gu <z.gu@dkfz.de>
38
+}
32 39
 \examples{
33 40
 matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10]
34 41
 densityHeatmap(matrix)
Browse code

resolve conflict from master branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@108131 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 03/09/2015 20:32:44
Showing1 changed files
... ...
@@ -7,8 +7,11 @@ Use colors to represent density distribution
7 7
 Use colors to represent density distribution
8 8
 }
9 9
 \usage{
10
-densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),
11
-    color_space = "RGB", anno = NULL, ylab = deparse(substitute(data)),
10
+densityHeatmap(data,
11
+    col = rev(brewer.pal(11, "Spectral")),
12
+    color_space = "LAB",
13
+    anno = NULL,
14
+    ylab = deparse(substitute(data)),
12 15
     title = paste0("Density heatmap of ", deparse(substitute(data))))
13 16
 }
14 17
 \arguments{
... ...
@@ -16,19 +19,23 @@ densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),
16 19
   \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns.}
17 20
   \item{col}{a list of colors that density values are scaled to.}
18 21
   \item{color_space}{the color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}
19
-  \item{anno}{annotation for matrix columns or list. The value should be a vector or a data frame. It can also be a \code{\link{HeatmapAnnotation-class}} object.}
22
+  \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame. It can also be a \code{\link{HeatmapAnnotation-class}} object.}
20 23
   \item{ylab}{label on y-axis in the plot}
21 24
   \item{title}{title of the plot}
22 25
 
23 26
 }
24 27
 \details{
25
-To visualize distribution of columns in a matrix or in a list, sometimes we use boxplot or beanplot.
26
-Here we use colors to map to the density values and visualize distribution of values
27
-in each column (or each element in the list) through a heatmap. It is useful if you have huge number of columns in \code{data} to visualize.
28
+To visualize data distribution in a matrix or in a list, sometimes we use boxplot or beanplot.
29
+Here we use colors to map the density values and visualize distribution of values
30
+in each column (or each vector in the list) through a heatmap. It is useful if you have huge number 
31
+of columns in \code{data} to visualize.
28 32
 }
29 33
 \value{
30 34
 No value is returned.
31 35
 }
36
+\author{
37
+Zuguang Gu <z.gu@dkfz.de>
38
+}
32 39
 \examples{
33 40
 matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10]
34 41
 densityHeatmap(matrix)
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 25191b4dc0bd4242c260ef5abd112d4bdd0ea887

add oncoPrint() function



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107561 bc3139a8-67e5-0310-9ffc-ced21a209358

Zuguang Gu authored on 18/08/2015 22:21:59
Showing1 changed files
... ...
@@ -8,13 +8,14 @@ Use colors to represent density distribution
8 8
 }
9 9
 \usage{
10 10
 densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),
11
-    anno = NULL, ylab = deparse(substitute(data)),
11
+    color_space = "RGB", anno = NULL, ylab = deparse(substitute(data)),
12 12
     title = paste0("Density heatmap of ", deparse(substitute(data))))
13 13
 }
14 14
 \arguments{
15 15
 
16 16
   \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns.}
17 17
   \item{col}{a list of colors that density values are scaled to.}
18
+  \item{color_space}{the color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}
18 19
   \item{anno}{annotation for matrix columns or list. The value should be a vector or a data frame. It can also be a \code{\link{HeatmapAnnotation-class}} object.}
19 20
   \item{ylab}{label on y-axis in the plot}
20 21
   \item{title}{title of the plot}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 25191b4dc0bd4242c260ef5abd112d4bdd0ea887

add oncoPrint() function



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107561 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 18/08/2015 22:21:59
Showing1 changed files
... ...
@@ -8,13 +8,14 @@ Use colors to represent density distribution
8 8
 }
9 9
 \usage{
10 10
 densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),
11
-    anno = NULL, ylab = deparse(substitute(data)),
11
+    color_space = "RGB", anno = NULL, ylab = deparse(substitute(data)),
12 12
     title = paste0("Density heatmap of ", deparse(substitute(data))))
13 13
 }
14 14
 \arguments{
15 15
 
16 16
   \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns.}
17 17
   \item{col}{a list of colors that density values are scaled to.}
18
+  \item{color_space}{the color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}
18 19
   \item{anno}{annotation for matrix columns or list. The value should be a vector or a data frame. It can also be a \code{\link{HeatmapAnnotation-class}} object.}
19 20
   \item{ylab}{label on y-axis in the plot}
20 21
   \item{title}{title of the plot}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 1de356e1d1343725223e03ff696f931d80b2842b

Merge branch 'master' of https://github.com/jokergoo/mheatmap


Commit id: 478962957a34b7a5e87c8336989bae3df54f9559

change default colors



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107356 bc3139a8-67e5-0310-9ffc-ced21a209358

Zuguang Gu authored on 12/08/2015 22:03:22
Showing1 changed files
... ...
@@ -9,7 +9,8 @@ Use colors to represent density distribution
9 9
 \usage{
10 10
 densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),
11 11
     anno = NULL, ylab = deparse(substitute(data)),
12
-    title = paste0("Density heatmap of ", deparse(substitute(data))))}
12
+    title = paste0("Density heatmap of ", deparse(substitute(data))))
13
+}
13 14
 \arguments{
14 15
 
15 16
   \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns.}
... ...
@@ -17,6 +18,7 @@ densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),
17 18
   \item{anno}{annotation for matrix columns or list. The value should be a vector or a data frame. It can also be a \code{\link{HeatmapAnnotation-class}} object.}
18 19
   \item{ylab}{label on y-axis in the plot}
19 20
   \item{title}{title of the plot}
21
+
20 22
 }
21 23
 \details{
22 24
 To visualize distribution of columns in a matrix or in a list, sometimes we use boxplot or beanplot.
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 1de356e1d1343725223e03ff696f931d80b2842b

Merge branch 'master' of https://github.com/jokergoo/mheatmap


Commit id: 478962957a34b7a5e87c8336989bae3df54f9559

change default colors



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107356 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 12/08/2015 22:03:22
Showing1 changed files
... ...
@@ -9,7 +9,8 @@ Use colors to represent density distribution
9 9
 \usage{
10 10
 densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),
11 11
     anno = NULL, ylab = deparse(substitute(data)),
12
-    title = paste0("Density heatmap of ", deparse(substitute(data))))}
12
+    title = paste0("Density heatmap of ", deparse(substitute(data))))
13
+}
13 14
 \arguments{
14 15
 
15 16
   \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns.}
... ...
@@ -17,6 +18,7 @@ densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),
17 18
   \item{anno}{annotation for matrix columns or list. The value should be a vector or a data frame. It can also be a \code{\link{HeatmapAnnotation-class}} object.}
18 19
   \item{ylab}{label on y-axis in the plot}
19 20
   \item{title}{title of the plot}
21
+
20 22
 }
21 23
 \details{
22 24
 To visualize distribution of columns in a matrix or in a list, sometimes we use boxplot or beanplot.
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: f1b195419490dad46029cf7b681508ed21ba8c60

refreshed documentations



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107316 bc3139a8-67e5-0310-9ffc-ced21a209358

Zuguang Gu authored on 11/08/2015 10:42:08
Showing1 changed files
... ...
@@ -2,11 +2,9 @@
2 2
 \alias{densityHeatmap}
3 3
 \title{
4 4
 Use colors to represent density distribution
5
-
6 5
 }
7 6
 \description{
8 7
 Use colors to represent density distribution
9
-
10 8
 }
11 9
 \usage{
12 10
 densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),
... ...
@@ -24,22 +22,17 @@ densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),
24 22
 To visualize distribution of columns in a matrix or in a list, sometimes we use boxplot or beanplot.
25 23
 Here we use colors to map to the density values and visualize distribution of values
26 24
 in each column (or each element in the list) through a heatmap. It is useful if you have huge number of columns in \code{data} to visualize.
27
-
28 25
 }
29 26
 \value{
30 27
 No value is returned.
31
-
32 28
 }
33 29
 \examples{
34 30
 matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10]
35 31
 densityHeatmap(matrix)
36 32
 densityHeatmap(matrix, anno = rep(c("A", "B"), each = 5))
37 33
 densityHeatmap(matrix, col = c("white", "red"), anno = rep(c("A", "B"), each = 5))
38
-
39 34
 ha = HeatmapAnnotation(points = anno_points(runif(10)))
40 35
 densityHeatmap(matrix, anno = ha)
41
-
42 36
 lt = list(rnorm(10), rnorm(10))
43 37
 densityHeatmap(lt)
44
-
45 38
 }
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: f1b195419490dad46029cf7b681508ed21ba8c60

refreshed documentations



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107316 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 11/08/2015 10:42:08
Showing1 changed files
... ...
@@ -2,11 +2,9 @@
2 2
 \alias{densityHeatmap}
3 3
 \title{
4 4
 Use colors to represent density distribution
5
-
6 5
 }
7 6
 \description{
8 7
 Use colors to represent density distribution
9
-
10 8
 }
11 9
 \usage{
12 10
 densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),
... ...
@@ -24,22 +22,17 @@ densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),
24 22
 To visualize distribution of columns in a matrix or in a list, sometimes we use boxplot or beanplot.
25 23
 Here we use colors to map to the density values and visualize distribution of values
26 24
 in each column (or each element in the list) through a heatmap. It is useful if you have huge number of columns in \code{data} to visualize.
27
-
28 25
 }
29 26
 \value{
30 27
 No value is returned.
31
-
32 28
 }
33 29
 \examples{
34 30
 matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10]
35 31
 densityHeatmap(matrix)
36 32
 densityHeatmap(matrix, anno = rep(c("A", "B"), each = 5))
37 33
 densityHeatmap(matrix, col = c("white", "red"), anno = rep(c("A", "B"), each = 5))
38
-
39 34
 ha = HeatmapAnnotation(points = anno_points(runif(10)))
40 35
 densityHeatmap(matrix, anno = ha)
41
-
42 36
 lt = list(rnorm(10), rnorm(10))
43 37
 densityHeatmap(lt)
44
-
45 38
 }
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 174dbdcbcad3be858d664784793f1b2424acc2c0

remove plot.HeatmapList and print.HeatmapList



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@106530 bc3139a8-67e5-0310-9ffc-ced21a209358

Zuguang Gu authored on 18/07/2015 18:14:29
Showing1 changed files
... ...
@@ -11,19 +11,19 @@ Use colors to represent density distribution
11 11
 \usage{
12 12
 densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),
13 13
     anno = NULL, ylab = deparse(substitute(data)),
14
-    title = paste0("density heatmap of ", deparse(substitute(data))))}
14
+    title = paste0("Density heatmap of ", deparse(substitute(data))))}
15 15
 \arguments{
16 16
 
17
-  \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns}
18
-  \item{col}{a list of colors that density values are mapped to}
19
-  \item{anno}{annotation for matrix columns or list, a vector or a data frame. The order of elements or rows corresponding to the orders of elements of rows of \code{data}}
17
+  \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns.}
18
+  \item{col}{a list of colors that density values are scaled to.}
19
+  \item{anno}{annotation for matrix columns or list. The value should be a vector or a data frame. It can also be a \code{\link{HeatmapAnnotation-class}} object.}
20 20
   \item{ylab}{label on y-axis in the plot}
21 21
   \item{title}{title of the plot}
22 22
 }
23 23
 \details{
24 24
 To visualize distribution of columns in a matrix or in a list, sometimes we use boxplot or beanplot.
25 25
 Here we use colors to map to the density values and visualize distribution of values
26
-in each column (or each list element) through a heatmap. It is useful if you have huge number of columns in \code{data} to visualize.
26
+in each column (or each element in the list) through a heatmap. It is useful if you have huge number of columns in \code{data} to visualize.
27 27
 
28 28
 }
29 29
 \value{
... ...
@@ -36,6 +36,9 @@ densityHeatmap(matrix)
36 36
 densityHeatmap(matrix, anno = rep(c("A", "B"), each = 5))
37 37
 densityHeatmap(matrix, col = c("white", "red"), anno = rep(c("A", "B"), each = 5))
38 38
 
39
+ha = HeatmapAnnotation(points = anno_points(runif(10)))
40
+densityHeatmap(matrix, anno = ha)
41
+
39 42
 lt = list(rnorm(10), rnorm(10))
40 43
 densityHeatmap(lt)
41 44
 
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 174dbdcbcad3be858d664784793f1b2424acc2c0

remove plot.HeatmapList and print.HeatmapList



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@106530 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 18/07/2015 18:14:29
Showing1 changed files
... ...
@@ -11,19 +11,19 @@ Use colors to represent density distribution
11 11
 \usage{
12 12
 densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),
13 13
     anno = NULL, ylab = deparse(substitute(data)),
14
-    title = paste0("density heatmap of ", deparse(substitute(data))))}
14
+    title = paste0("Density heatmap of ", deparse(substitute(data))))}
15 15
 \arguments{
16 16
 
17
-  \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns}
18
-  \item{col}{a list of colors that density values are mapped to}
19
-  \item{anno}{annotation for matrix columns or list, a vector or a data frame. The order of elements or rows corresponding to the orders of elements of rows of \code{data}}
17
+  \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns.}
18
+  \item{col}{a list of colors that density values are scaled to.}
19
+  \item{anno}{annotation for matrix columns or list. The value should be a vector or a data frame. It can also be a \code{\link{HeatmapAnnotation-class}} object.}
20 20
   \item{ylab}{label on y-axis in the plot}
21 21
   \item{title}{title of the plot}
22 22
 }
23 23
 \details{
24 24
 To visualize distribution of columns in a matrix or in a list, sometimes we use boxplot or beanplot.
25 25
 Here we use colors to map to the density values and visualize distribution of values
26
-in each column (or each list element) through a heatmap. It is useful if you have huge number of columns in \code{data} to visualize.
26
+in each column (or each element in the list) through a heatmap. It is useful if you have huge number of columns in \code{data} to visualize.
27 27
 
28 28
 }
29 29
 \value{
... ...
@@ -36,6 +36,9 @@ densityHeatmap(matrix)
36 36
 densityHeatmap(matrix, anno = rep(c("A", "B"), each = 5))
37 37
 densityHeatmap(matrix, col = c("white", "red"), anno = rep(c("A", "B"), each = 5))
38 38
 
39
+ha = HeatmapAnnotation(points = anno_points(runif(10)))
40
+densityHeatmap(matrix, anno = ha)
41
+
39 42
 lt = list(rnorm(10), rnorm(10))
40 43
 densityHeatmap(lt)
41 44
 
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: dbcd94f09a509b142af23817e40c5b7b9e434c26

improved text in vignettes



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105881 bc3139a8-67e5-0310-9ffc-ced21a209358

Zuguang Gu authored on 07/07/2015 18:03:11
Showing1 changed files
... ...
@@ -1,11 +1,11 @@
1 1
 \name{densityHeatmap}
2 2
 \alias{densityHeatmap}
3 3
 \title{
4
-use colors to represent density distribution
4
+Use colors to represent density distribution
5 5
 
6 6
 }
7 7
 \description{
8
-use colors to represent density distribution
8
+Use colors to represent density distribution
9 9
 
10 10
 }
11 11
 \usage{
... ...
@@ -15,15 +15,15 @@ densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),
15 15
 \arguments{
16 16
 
17 17
   \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns}
18
-  \item{col}{a list of colors that density values are to be mapped to}
19
-  \item{anno}{annotation for matrix columns or list, a vector or a data frame}
18
+  \item{col}{a list of colors that density values are mapped to}
19
+  \item{anno}{annotation for matrix columns or list, a vector or a data frame. The order of elements or rows corresponding to the orders of elements of rows of \code{data}}
20 20
   \item{ylab}{label on y-axis in the plot}
21 21
   \item{title}{title of the plot}
22 22
 }
23 23
 \details{
24 24
 To visualize distribution of columns in a matrix or in a list, sometimes we use boxplot or beanplot.
25 25
 Here we use colors to map to the density values and visualize distribution of values
26
-in each column (or each list element) through a heatmap.
26
+in each column (or each list element) through a heatmap. It is useful if you have huge number of columns in \code{data} to visualize.
27 27
 
28 28
 }
29 29
 \value{
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: dbcd94f09a509b142af23817e40c5b7b9e434c26

improved text in vignettes



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105881 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 07/07/2015 18:03:11
Showing1 changed files
... ...
@@ -1,11 +1,11 @@
1 1
 \name{densityHeatmap}
2 2
 \alias{densityHeatmap}
3 3
 \title{
4
-use colors to represent density distribution
4
+Use colors to represent density distribution
5 5
 
6 6
 }
7 7
 \description{
8
-use colors to represent density distribution
8
+Use colors to represent density distribution
9 9
 
10 10
 }
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 \usage{
... ...
@@ -15,15 +15,15 @@ densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),
15 15
 \arguments{
16 16
 
17 17
   \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns}
18
-  \item{col}{a list of colors that density values are to be mapped to}
19
-  \item{anno}{annotation for matrix columns or list, a vector or a data frame}
18
+  \item{col}{a list of colors that density values are mapped to}
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+  \item{anno}{annotation for matrix columns or list, a vector or a data frame. The order of elements or rows corresponding to the orders of elements of rows of \code{data}}
20 20
   \item{ylab}{label on y-axis in the plot}
21 21
   \item{title}{title of the plot}
22 22
 }
23 23
 \details{
24 24
 To visualize distribution of columns in a matrix or in a list, sometimes we use boxplot or beanplot.
25 25
 Here we use colors to map to the density values and visualize distribution of values
26
-in each column (or each list element) through a heatmap.
26
+in each column (or each list element) through a heatmap. It is useful if you have huge number of columns in \code{data} to visualize.
27 27
 
28 28
 }
29 29
 \value{
Browse code

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Commit id: 9d7fc297a370b44dd3bfb12696ed9eac33aed48a

refreshed documentations



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105365 bc3139a8-67e5-0310-9ffc-ced21a209358

Zuguang Gu authored on 23/06/2015 10:24:06
Showing1 changed files
... ...
@@ -25,6 +25,10 @@ To visualize distribution of columns in a matrix or in a list, sometimes we use
25 25
 Here we use colors to map to the density values and visualize distribution of values
26 26
 in each column (or each list element) through a heatmap.
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+}
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+\value{
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+No value is returned.
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+
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 }
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 \examples{
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 matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10]
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 9d7fc297a370b44dd3bfb12696ed9eac33aed48a

refreshed documentations



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105365 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 23/06/2015 10:24:06
Showing1 changed files
... ...
@@ -25,6 +25,10 @@ To visualize distribution of columns in a matrix or in a list, sometimes we use
25 25
 Here we use colors to map to the density values and visualize distribution of values
26 26
 in each column (or each list element) through a heatmap.
27 27
 
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+}
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+\value{
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+No value is returned.
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+
28 32
 }
29 33
 \examples{
30 34
 matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10]
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 00f8f84d3541cad55bc6dac494ff6a9f65d593da

refreshed documentations



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105347 bc3139a8-67e5-0310-9ffc-ced21a209358

Zuguang Gu authored on 22/06/2015 22:30:44
Showing1 changed files
... ...
@@ -26,10 +26,6 @@ Here we use colors to map to the density values and visualize distribution of va
26 26
 in each column (or each list element) through a heatmap.
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28 28
 }
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-\section{Example}{
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-matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10] densityHeatmap(matrix) densityHeatmap(matrix, anno = rep(c("A", "B"), each = 5)) densityHeatmap(matrix, col = c("white", "red"), anno = rep(c("A", "B"), each = 5))  
31
-
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-lt = list(rnorm(10), rnorm(10)) densityHeatmap(lt)}
33 29
 \examples{
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 matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10]
35 31
 densityHeatmap(matrix)
Browse code

Commit made by the Bioconductor Git-SVN bridge.

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refreshed documentations



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105347 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 22/06/2015 22:30:44
Showing1 changed files
... ...
@@ -26,10 +26,6 @@ Here we use colors to map to the density values and visualize distribution of va
26 26
 in each column (or each list element) through a heatmap.
27 27
 
28 28
 }
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-\section{Example}{
30
-matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10] densityHeatmap(matrix) densityHeatmap(matrix, anno = rep(c("A", "B"), each = 5)) densityHeatmap(matrix, col = c("white", "red"), anno = rep(c("A", "B"), each = 5))  
31
-
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-lt = list(rnorm(10), rnorm(10)) densityHeatmap(lt)}
33 29
 \examples{
34 30
 matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10]
35 31
 densityHeatmap(matrix)
Browse code

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Commit id: 1682e4aed696b8fa901530ebc6b9d67ad2a013ad

refresh documentations and NAMESPACE



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105345 bc3139a8-67e5-0310-9ffc-ced21a209358

Zuguang Gu authored on 22/06/2015 21:57:04
Showing1 changed files
... ...
@@ -1,20 +1,17 @@
1 1
 \name{densityHeatmap}
2 2
 \alias{densityHeatmap}
3 3
 \title{
4
-use colors to represent density distribution  
5
-
4
+use colors to represent density distribution
6 5
 
7 6
 }
8 7
 \description{
9
-use colors to represent density distribution  
10
-
8
+use colors to represent density distribution
11 9
 
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 }
13 11
 \usage{
14 12
 densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),
15 13
     anno = NULL, ylab = deparse(substitute(data)),
16
-    title = paste0("density heatmap of ", deparse(substitute(data))))
17
-}
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+    title = paste0("density heatmap of ", deparse(substitute(data))))}
18 15
 \arguments{
19 16
 
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   \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns}
... ...
@@ -22,20 +19,17 @@ densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),
22 19
   \item{anno}{annotation for matrix columns or list, a vector or a data frame}
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   \item{ylab}{label on y-axis in the plot}
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   \item{title}{title of the plot}
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-
26 22
 }
27 23
 \details{
28
-To visualize distribution of columns in a matrix or in a list, sometimes we use boxplot or beanplot. Here we use colors to map to the density values and visualize distribution of values in each column (or each list element) through a heatmap.  
29
-
24
+To visualize distribution of columns in a matrix or in a list, sometimes we use boxplot or beanplot.
25
+Here we use colors to map to the density values and visualize distribution of values
26
+in each column (or each list element) through a heatmap.
30 27
 
31 28
 }
32 29
 \section{Example}{
33 30
 matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10] densityHeatmap(matrix) densityHeatmap(matrix, anno = rep(c("A", "B"), each = 5)) densityHeatmap(matrix, col = c("white", "red"), anno = rep(c("A", "B"), each = 5))  
34 31
 
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-lt = list(rnorm(10), rnorm(10)) densityHeatmap(lt)  
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-
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-
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-}
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+lt = list(rnorm(10), rnorm(10)) densityHeatmap(lt)}
39 33
 \examples{
40 34
 matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10]
41 35
 densityHeatmap(matrix)
... ...
@@ -44,4 +38,5 @@ densityHeatmap(matrix, col = c("white", "red"), anno = rep(c("A", "B"), each = 5
44 38
 
45 39
 lt = list(rnorm(10), rnorm(10))
46 40
 densityHeatmap(lt)
41
+
47 42
 }
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 1682e4aed696b8fa901530ebc6b9d67ad2a013ad

refresh documentations and NAMESPACE



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105345 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 22/06/2015 21:57:04
Showing1 changed files
... ...
@@ -1,20 +1,17 @@
1 1
 \name{densityHeatmap}
2 2
 \alias{densityHeatmap}
3 3
 \title{
4
-use colors to represent density distribution  
5
-
4
+use colors to represent density distribution
6 5
 
7 6
 }
8 7
 \description{
9
-use colors to represent density distribution  
10
-
8
+use colors to represent density distribution
11 9
 
12 10
 }
13 11
 \usage{
14 12
 densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),
15 13
     anno = NULL, ylab = deparse(substitute(data)),
16
-    title = paste0("density heatmap of ", deparse(substitute(data))))
17
-}
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+    title = paste0("density heatmap of ", deparse(substitute(data))))}
18 15
 \arguments{
19 16
 
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   \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns}
... ...
@@ -22,20 +19,17 @@ densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),
22 19
   \item{anno}{annotation for matrix columns or list, a vector or a data frame}
23 20
   \item{ylab}{label on y-axis in the plot}
24 21
   \item{title}{title of the plot}
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-
26 22
 }
27 23
 \details{
28
-To visualize distribution of columns in a matrix or in a list, sometimes we use boxplot or beanplot. Here we use colors to map to the density values and visualize distribution of values in each column (or each list element) through a heatmap.  
29
-
24
+To visualize distribution of columns in a matrix or in a list, sometimes we use boxplot or beanplot.
25
+Here we use colors to map to the density values and visualize distribution of values
26
+in each column (or each list element) through a heatmap.
30 27
 
31 28
 }
32 29
 \section{Example}{
33 30
 matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10] densityHeatmap(matrix) densityHeatmap(matrix, anno = rep(c("A", "B"), each = 5)) densityHeatmap(matrix, col = c("white", "red"), anno = rep(c("A", "B"), each = 5))  
34 31
 
35
-lt = list(rnorm(10), rnorm(10)) densityHeatmap(lt)  
36
-
37
-
38
-}
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+lt = list(rnorm(10), rnorm(10)) densityHeatmap(lt)}
39 33
 \examples{
40 34
 matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10]
41 35
 densityHeatmap(matrix)
... ...
@@ -44,4 +38,5 @@ densityHeatmap(matrix, col = c("white", "red"), anno = rep(c("A", "B"), each = 5
44 38
 
45 39
 lt = list(rnorm(10), rnorm(10))
46 40
 densityHeatmap(lt)
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+
47 42
 }
Browse code

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Commit id: ff6ad79beeef75c709dc08588bb942ad86de9761

rotation for heatmap title supported



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105315 bc3139a8-67e5-0310-9ffc-ced21a209358

Zuguang Gu authored on 22/06/2015 15:09:06
Showing1 changed files
... ...
@@ -1,17 +1,20 @@
1 1
 \name{densityHeatmap}
2 2
 \alias{densityHeatmap}
3 3
 \title{
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-use colors to represent density distribution
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+use colors to represent density distribution  
5
+
5 6
 
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 }
7 8
 \description{
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-use colors to represent density distribution
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+use colors to represent density distribution  
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+
9 11
 
10 12
 }
11 13
 \usage{
12 14
 densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),
13 15
     anno = NULL, ylab = deparse(substitute(data)),
14
-    title = paste0("density heatmap of ", deparse(substitute(data))))}
16
+    title = paste0("density heatmap of ", deparse(substitute(data))))
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+}
15 18
 \arguments{
16 19
 
17 20
   \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns}
... ...
@@ -19,17 +22,20 @@ densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),
19 22
   \item{anno}{annotation for matrix columns or list, a vector or a data frame}
20 23
   \item{ylab}{label on y-axis in the plot}
21 24
   \item{title}{title of the plot}
25
+
22 26
 }
23 27
 \details{
24
-To visualize distribution of columns in a matrix or in a list, sometimes we use boxplot or beanplot.
25
-Here we use colors to map to the density values and visualize distribution of values
26
-in each column (or each list element) through a heatmap.
28
+To visualize distribution of columns in a matrix or in a list, sometimes we use boxplot or beanplot. Here we use colors to map to the density values and visualize distribution of values in each column (or each list element) through a heatmap.  
29
+
27 30
 
28 31