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
... ...
@@ -1,47 +0,0 @@
1
-\name{anno_boxplot}
2
-\alias{anno_boxplot}
3
-\title{
4
-Boxplot Annotation
5
-}
6
-\description{
7
-Boxplot Annotation
8
-}
9
-\usage{
10
-anno_boxplot(x, which = c("column", "row"), border = TRUE,
11
-    gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, outline = TRUE, box_width = 0.6,
12
-    pch = 1, size = unit(2, "mm"), axis = TRUE, axis_param = default_axis_param(which),
13
-    width = NULL, height = NULL, ...)
14
-}
15
-\arguments{
16
-
17
-  \item{x}{A matrix or a list. If \code{x} is a matrix and if \code{which} is \code{column}, statistics for boxplots are calculated by columns, if \code{which} is \code{row}, the calculation is done by rows.}
18
-  \item{which}{Whether it is a column annotation or a row annotation?}
19
-  \item{border}{Wether draw borders of the annotation region?}
20
-  \item{gp}{Graphic parameters for the boxes. The length of the graphic parameters should be one or the number of observations.}
21
-  \item{ylim}{Data ranges.}
22
-  \item{extend}{The extension to both side of \code{ylim}. The value is a percent value corresponding to \code{ylim[2] - ylim[1]}.}
23
-  \item{outline}{Whether draw outline of boxplots?}
24
-  \item{box_width}{Relative width of boxes. The value should be smaller than one.}
25
-  \item{pch}{Point style.}
26
-  \item{size}{Point size.}
27
-  \item{axis}{Whether to add axis?}
28
-  \item{axis_param}{parameters for controlling axis. See \code{\link{default_axis_param}} for all possible settings and default parameters.}
29
-  \item{width}{Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.}
30
-  \item{height}{Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.}
31
-  \item{...}{Other arguments.}
32
-
33
-}
34
-\value{
35
-An annotation function which can be used in \code{\link{HeatmapAnnotation}}.
36
-}
37
-\seealso{
38
-\url{https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#box-annotation}
39
-}
40
-\examples{
41
-set.seed(123)
42
-m = matrix(rnorm(100), 10)
43
-anno = anno_boxplot(m, height = unit(4, "cm"))
44
-draw(anno, test = "anno_boxplot")
45
-anno = anno_boxplot(m, height = unit(4, "cm"), gp = gpar(fill = 1:10))
46
-draw(anno, test = "anno_boxplot with gp")
47
-}
Browse code

check arguments from old versions

jokergoo authored on 02/11/2018 11:11:30
Showing1 changed files
... ...
@@ -10,7 +10,7 @@ Boxplot Annotation
10 10
 anno_boxplot(x, which = c("column", "row"), border = TRUE,
11 11
     gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, outline = TRUE, box_width = 0.6,
12 12
     pch = 1, size = unit(2, "mm"), axis = TRUE, axis_param = default_axis_param(which),
13
-    width = NULL, height = NULL)
13
+    width = NULL, height = NULL, ...)
14 14
 }
15 15
 \arguments{
16 16
 
... ...
@@ -28,6 +28,7 @@ anno_boxplot(x, which = c("column", "row"), border = TRUE,
28 28
   \item{axis_param}{parameters for controlling axis. See \code{\link{default_axis_param}} for all possible settings and default parameters.}
29 29
   \item{width}{Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.}
30 30
   \item{height}{Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.}
31
+  \item{...}{Other arguments.}
31 32
 
32 33
 }
33 34
 \value{
Browse code

documentation checked

Zuguang Gu authored on 23/10/2018 19:59:12
Showing1 changed files
... ...
@@ -33,6 +33,9 @@ anno_boxplot(x, which = c("column", "row"), border = TRUE,
33 33
 \value{
34 34
 An annotation function which can be used in \code{\link{HeatmapAnnotation}}.
35 35
 }
36
+\seealso{
37
+\url{https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#box-annotation}
38
+}
36 39
 \examples{
37 40
 set.seed(123)
38 41
 m = matrix(rnorm(100), 10)
Browse code

update

jokergoo authored on 12/10/2018 15:28:37
Showing1 changed files
... ...
@@ -26,8 +26,8 @@ anno_boxplot(x, which = c("column", "row"), border = TRUE,
26 26
   \item{size}{Point size.}
27 27
   \item{axis}{Whether to add axis?}
28 28
   \item{axis_param}{parameters for controlling axis. See \code{\link{default_axis_param}} for all possible settings and default parameters.}
29
-  \item{width}{Width of the annotation.}
30
-  \item{height}{Height of the annotation.}
29
+  \item{width}{Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.}
30
+  \item{height}{Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.}
31 31
 
32 32
 }
33 33
 \value{
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
... ...
@@ -1,49 +1,43 @@
1 1
 \name{anno_boxplot}
2 2
 \alias{anno_boxplot}
3 3
 \title{
4
-Using boxplot as annotation
4
+Boxplot Annotation
5 5
 }
6 6
 \description{
7
-Using boxplot as annotation
7
+Boxplot Annotation
8 8
 }
9 9
 \usage{
10 10
 anno_boxplot(x, which = c("column", "row"), border = TRUE,
11
-    gp = gpar(fill = "#CCCCCC"), ylim = NULL, outline = TRUE,
12
-    pch = 16, size = unit(2, "mm"), axis = FALSE, axis_side = NULL,
13
-    axis_gp = gpar(fontsize = 8), axis_direction = c("normal", "reverse"))
11
+    gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, outline = TRUE, box_width = 0.6,
12
+    pch = 1, size = unit(2, "mm"), axis = TRUE, axis_param = default_axis_param(which),
13
+    width = NULL, height = NULL)
14 14
 }
15 15
 \arguments{
16 16
 
17
-  \item{x}{a matrix or a list. If \code{x} is a matrix and if \code{which} is \code{column}, statistics for boxplot is calculated by columns, if \code{which} is \code{row}, the calculation is by rows.}
18
-  \item{which}{is the annotation a column annotation or a row annotation?}
19
-  \item{border}{whether show border of the annotation compoment}
20
-  \item{gp}{graphic parameters}
21
-  \item{ylim}{data ranges.}
22
-  \item{outline}{whether draw outliers}
23
-  \item{pch}{point type}
24
-  \item{size}{point size}
25
-  \item{axis}{whether add axis}
26
-  \item{axis_side}{if it is placed as column annotation, value can only be "left" or "right". If it is placed as row annotation, value can only be "bottom" or "top".}
27
-  \item{axis_gp}{graphic parameters for axis}
28
-  \item{axis_direction}{if the annotation is row annotation, should the axis be from left to right (default) or follow the reversed direction?}
17
+  \item{x}{A matrix or a list. If \code{x} is a matrix and if \code{which} is \code{column}, statistics for boxplots are calculated by columns, if \code{which} is \code{row}, the calculation is done by rows.}
18
+  \item{which}{Whether it is a column annotation or a row annotation?}
19
+  \item{border}{Wether draw borders of the annotation region?}
20
+  \item{gp}{Graphic parameters for the boxes. The length of the graphic parameters should be one or the number of observations.}
21
+  \item{ylim}{Data ranges.}
22
+  \item{extend}{The extension to both side of \code{ylim}. The value is a percent value corresponding to \code{ylim[2] - ylim[1]}.}
23
+  \item{outline}{Whether draw outline of boxplots?}
24
+  \item{box_width}{Relative width of boxes. The value should be smaller than one.}
25
+  \item{pch}{Point style.}
26
+  \item{size}{Point size.}
27
+  \item{axis}{Whether to add axis?}
28
+  \item{axis_param}{parameters for controlling axis. See \code{\link{default_axis_param}} for all possible settings and default parameters.}
29
+  \item{width}{Width of the annotation.}
30
+  \item{height}{Height of the annotation.}
29 31
 
30 32
 }
31 33
 \value{
32
-A graphic function which can be set in \code{\link{HeatmapAnnotation}} constructor method.
33
-}
34
-\author{
35
-Zuguang Gu <z.gu@dkfz.de>
34
+An annotation function which can be used in \code{\link{HeatmapAnnotation}}.
36 35
 }
37 36
 \examples{
38
-mat = matrix(rnorm(32), nrow = 4)
39
-f = anno_boxplot(mat)
40
-grid.newpage(); f(1:8)
41
-
42
-f = anno_boxplot(mat, which = "row")
43
-grid.newpage(); f(1:4)
44
-
45
-lt = lapply(1:4, function(i) rnorm(8))
46
-f = anno_boxplot(lt)
47
-grid.newpage(); f(1:4)
48
-
37
+set.seed(123)
38
+m = matrix(rnorm(100), 10)
39
+anno = anno_boxplot(m, height = unit(4, "cm"))
40
+draw(anno, test = "anno_boxplot")
41
+anno = anno_boxplot(m, height = unit(4, "cm"), gp = gpar(fill = 1:10))
42
+draw(anno, test = "anno_boxplot with gp")
49 43
 }
Browse code

alter_fun in oncoPrint supports a single function

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@114989 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 19/03/2016 17:58:59
Showing1 changed files
... ...
@@ -8,7 +8,7 @@ Using boxplot as annotation
8 8
 }
9 9
 \usage{
10 10
 anno_boxplot(x, which = c("column", "row"), border = TRUE,
11
-    gp = gpar(fill = "#CCCCCC"), ylim = NULL,
11
+    gp = gpar(fill = "#CCCCCC"), ylim = NULL, outline = TRUE,
12 12
     pch = 16, size = unit(2, "mm"), axis = FALSE, axis_side = NULL,
13 13
     axis_gp = gpar(fontsize = 8), axis_direction = c("normal", "reverse"))
14 14
 }
... ...
@@ -19,6 +19,7 @@ anno_boxplot(x, which = c("column", "row"), border = TRUE,
19 19
   \item{border}{whether show border of the annotation compoment}
20 20
   \item{gp}{graphic parameters}
21 21
   \item{ylim}{data ranges.}
22
+  \item{outline}{whether draw outliers}
22 23
   \item{pch}{point type}
23 24
   \item{size}{point size}
24 25
   \item{axis}{whether add axis}
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
... ...
@@ -8,7 +8,7 @@ Using boxplot as annotation
8 8
 }
9 9
 \usage{
10 10
 anno_boxplot(x, which = c("column", "row"), border = TRUE,
11
-    gp = gpar(fill = "#CCCCCC"), lim = NULL,
11
+    gp = gpar(fill = "#CCCCCC"), ylim = NULL,
12 12
     pch = 16, size = unit(2, "mm"), axis = FALSE, axis_side = NULL,
13 13
     axis_gp = gpar(fontsize = 8), axis_direction = c("normal", "reverse"))
14 14
 }
... ...
@@ -18,7 +18,7 @@ anno_boxplot(x, which = c("column", "row"), border = TRUE,
18 18
   \item{which}{is the annotation a column annotation or a row annotation?}
19 19
   \item{border}{whether show border of the annotation compoment}
20 20
   \item{gp}{graphic parameters}
21
-  \item{lim}{data ranges.}
21
+  \item{ylim}{data ranges.}
22 22
   \item{pch}{point type}
23 23
   \item{size}{point size}
24 24
   \item{axis}{whether add axis}
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
... ...
@@ -14,7 +14,7 @@ anno_boxplot(x, which = c("column", "row"), border = TRUE,
14 14
 }
15 15
 \arguments{
16 16
 
17
-  \item{x}{a matrix or a list. If \code{x} is a matrix and if \code{which} is \code{column}, statistics for boxplotis calculated by columns, if \code{which} is \code{row}, the calculation is by rows.}
17
+  \item{x}{a matrix or a list. If \code{x} is a matrix and if \code{which} is \code{column}, statistics for boxplot is calculated by columns, if \code{which} is \code{row}, the calculation is by rows.}
18 18
   \item{which}{is the annotation a column annotation or a row annotation?}
19 19
   \item{border}{whether show border of the annotation compoment}
20 20
   \item{gp}{graphic parameters}
... ...
@@ -22,7 +22,7 @@ anno_boxplot(x, which = c("column", "row"), border = TRUE,
22 22
   \item{pch}{point type}
23 23
   \item{size}{point size}
24 24
   \item{axis}{whether add axis}
25
-  \item{axis_side}{if it is placed as column annotation, value can only be "left" or "right".If it is placed as row annotation, value can only be "bottom" or "top".}
25
+  \item{axis_side}{if it is placed as column annotation, value can only be "left" or "right". If it is placed as row annotation, value can only be "bottom" or "top".}
26 26
   \item{axis_gp}{graphic parameters for axis}
27 27
   \item{axis_direction}{if the annotation is row annotation, should the axis be from left to right (default) or follow the reversed direction?}
28 28
 
Browse code

Merge branch 'master' into devel

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@109144 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 03/10/2015 10:32:07
Showing1 changed files
... ...
@@ -8,7 +8,7 @@ Using boxplot as annotation
8 8
 }
9 9
 \usage{
10 10
 anno_boxplot(x, which = c("column", "row"), border = TRUE,
11
-    gp = gpar(fill = "#CCCCCC"),
11
+    gp = gpar(fill = "#CCCCCC"), lim = NULL,
12 12
     pch = 16, size = unit(2, "mm"), axis = FALSE, axis_side = NULL,
13 13
     axis_gp = gpar(fontsize = 8), axis_direction = c("normal", "reverse"))
14 14
 }
... ...
@@ -18,6 +18,7 @@ anno_boxplot(x, which = c("column", "row"), border = TRUE,
18 18
   \item{which}{is the annotation a column annotation or a row annotation?}
19 19
   \item{border}{whether show border of the annotation compoment}
20 20
   \item{gp}{graphic parameters}
21
+  \item{lim}{data ranges.}
21 22
   \item{pch}{point type}
22 23
   \item{size}{point size}
23 24
   \item{axis}{whether add axis}
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

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
... ...
@@ -10,7 +10,8 @@ Using boxplot as annotation
10 10
 anno_boxplot(x, which = c("column", "row"), border = TRUE,
11 11
     gp = gpar(fill = "#CCCCCC"),
12 12
     pch = 16, size = unit(2, "mm"), axis = FALSE, axis_side = NULL,
13
-    axis_gp = gpar(fontsize = 8), axis_direction = c("normal", "reverse"))}
13
+    axis_gp = gpar(fontsize = 8), axis_direction = c("normal", "reverse"))
14
+}
14 15
 \arguments{
15 16
 
16 17
   \item{x}{a matrix or a list. If \code{x} is a matrix and if \code{which} is \code{column}, statistics for boxplotis calculated by columns, if \code{which} is \code{row}, the calculation is by rows.}
... ...
@@ -23,6 +24,7 @@ anno_boxplot(x, which = c("column", "row"), border = TRUE,
23 24
   \item{axis_side}{if it is placed as column annotation, value can only be "left" or "right".If it is placed as row annotation, value can only be "bottom" or "top".}
24 25
   \item{axis_gp}{graphic parameters for axis}
25 26
   \item{axis_direction}{if the annotation is row annotation, should the axis be from left to right (default) or follow the reversed direction?}
27
+
26 28
 }
27 29
 \value{
28 30
 A graphic function which can be set in \code{\link{HeatmapAnnotation}} constructor method.
... ...
@@ -41,4 +43,5 @@ grid.newpage(); f(1:4)
41 43
 lt = lapply(1:4, function(i) rnorm(8))
42 44
 f = anno_boxplot(lt)
43 45
 grid.newpage(); f(1:4)
46
+
44 47
 }
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{anno_boxplot}
3 3
 \title{
4 4
 Using boxplot as annotation
5
-
6 5
 }
7 6
 \description{
8 7
 Using boxplot as annotation
9
-
10 8
 }
11 9
 \usage{
12 10
 anno_boxplot(x, which = c("column", "row"), border = TRUE,
... ...
@@ -28,25 +26,11 @@ anno_boxplot(x, which = c("column", "row"), border = TRUE,
28 26
 }
29 27
 \value{
30 28
 A graphic function which can be set in \code{\link{HeatmapAnnotation}} constructor method.
31
-
32 29
 }
33 30
 \author{
34 31
 Zuguang Gu <z.gu@dkfz.de>
35
-
36 32
 }
37 33
 \examples{
38
-
39
-
40
-
41
-
42
-
43
-
44
-
45
-
46
-
47
-
48
-
49
-
50 34
 mat = matrix(rnorm(32), nrow = 4)
51 35
 f = anno_boxplot(mat)
52 36
 grid.newpage(); f(1:8)
... ...
@@ -56,4 +40,5 @@ grid.newpage(); f(1:4)
56 40
 
57 41
 lt = lapply(1:4, function(i) rnorm(8))
58 42
 f = anno_boxplot(lt)
59
-grid.newpage(); f(1:4)}
43
+grid.newpage(); f(1:4)
44
+}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 262e3960558c1f61b986f5be7a2ffd4599f704fa

comprehensive modifications



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107311 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 10/08/2015 22:17:54
Showing1 changed files
... ...
@@ -12,7 +12,7 @@ Using boxplot as annotation
12 12
 anno_boxplot(x, which = c("column", "row"), border = TRUE,
13 13
     gp = gpar(fill = "#CCCCCC"),
14 14
     pch = 16, size = unit(2, "mm"), axis = FALSE, axis_side = NULL,
15
-    axis_gp = gpar(fontsize = 8))}
15
+    axis_gp = gpar(fontsize = 8), axis_direction = c("normal", "reverse"))}
16 16
 \arguments{
17 17
 
18 18
   \item{x}{a matrix or a list. If \code{x} is a matrix and if \code{which} is \code{column}, statistics for boxplotis calculated by columns, if \code{which} is \code{row}, the calculation is by rows.}
... ...
@@ -24,6 +24,7 @@ anno_boxplot(x, which = c("column", "row"), border = TRUE,
24 24
   \item{axis}{whether add axis}
25 25
   \item{axis_side}{if it is placed as column annotation, value can only be "left" or "right".If it is placed as row annotation, value can only be "bottom" or "top".}
26 26
   \item{axis_gp}{graphic parameters for axis}
27
+  \item{axis_direction}{if the annotation is row annotation, should the axis be from left to right (default) or follow the reversed direction?}
27 28
 }
28 29
 \value{
29 30
 A graphic function which can be set in \code{\link{HeatmapAnnotation}} constructor method.
... ...
@@ -41,6 +42,11 @@ Zuguang Gu <z.gu@dkfz.de>
41 42
 
42 43
 
43 44
 
45
+
46
+
47
+
48
+
49
+
44 50
 mat = matrix(rnorm(32), nrow = 4)
45 51
 f = anno_boxplot(mat)
46 52
 grid.newpage(); f(1:8)
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 73171be89c157222e8e71e85daa8a37ce509a4e2

add border argument in anno_* family functions



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107201 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 06/08/2015 17:46:06
Showing1 changed files
... ...
@@ -9,13 +9,15 @@ Using boxplot as annotation
9 9
 
10 10
 }
11 11
 \usage{
12
-anno_boxplot(x, which = c("column", "row"), gp = gpar(fill = "#CCCCCC"),
12
+anno_boxplot(x, which = c("column", "row"), border = TRUE,
13
+    gp = gpar(fill = "#CCCCCC"),
13 14
     pch = 16, size = unit(2, "mm"), axis = FALSE, axis_side = NULL,
14 15
     axis_gp = gpar(fontsize = 8))}
15 16
 \arguments{
16 17
 
17 18
   \item{x}{a matrix or a list. If \code{x} is a matrix and if \code{which} is \code{column}, statistics for boxplotis calculated by columns, if \code{which} is \code{row}, the calculation is by rows.}
18 19
   \item{which}{is the annotation a column annotation or a row annotation?}
20
+  \item{border}{whether show border of the annotation compoment}
19 21
   \item{gp}{graphic parameters}
20 22
   \item{pch}{point type}
21 23
   \item{size}{point size}
... ...
@@ -38,6 +40,7 @@ Zuguang Gu <z.gu@dkfz.de>
38 40
 
39 41
 
40 42
 
43
+
41 44
 mat = matrix(rnorm(32), nrow = 4)
42 45
 f = anno_boxplot(mat)
43 46
 grid.newpage(); f(1:8)
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 3429d28233ef2cbeafcd05307042d7c7aa54a2a2

add decorate* family functions



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107197 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 06/08/2015 16:40:59
Showing1 changed files
... ...
@@ -34,6 +34,10 @@ Zuguang Gu <z.gu@dkfz.de>
34 34
 \examples{
35 35
 
36 36
 
37
+
38
+
39
+
40
+
37 41
 mat = matrix(rnorm(32), nrow = 4)
38 42
 f = anno_boxplot(mat)
39 43
 grid.newpage(); f(1:8)
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: d5adc92bdbf27b45a6a4b5c7e29d2e4fe8380194

allow reordering



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107130 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 04/08/2015 20:24:37
Showing1 changed files
... ...
@@ -32,6 +32,8 @@ Zuguang Gu <z.gu@dkfz.de>
32 32
 
33 33
 }
34 34
 \examples{
35
+
36
+
35 37
 mat = matrix(rnorm(32), nrow = 4)
36 38
 f = anno_boxplot(mat)
37 39
 grid.newpage(); f(1:8)
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
... ...
@@ -20,7 +20,7 @@ anno_boxplot(x, which = c("column", "row"), gp = gpar(fill = "#CCCCCC"),
20 20
   \item{pch}{point type}
21 21
   \item{size}{point size}
22 22
   \item{axis}{whether add axis}
23
-  \item{axis_side}{value in "left", "right", "bottom" and "top"}
23
+  \item{axis_side}{if it is placed as column annotation, value can only be "left" or "right".If it is placed as row annotation, value can only be "bottom" or "top".}
24 24
   \item{axis_gp}{graphic parameters for axis}
25 25
 }
26 26
 \value{
... ...
@@ -32,7 +32,6 @@ Zuguang Gu <z.gu@dkfz.de>
32 32
 
33 33
 }
34 34
 \examples{
35
-
36 35
 mat = matrix(rnorm(32), nrow = 4)
37 36
 f = anno_boxplot(mat)
38 37
 grid.newpage(); f(1:8)
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 4cbce102eabb1633fc8980b1374795bfb44507df

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


Commit id: a15bbec76c85c15bc27273ce15f5118ea087132f

refreshed documentatinos


Commit id: b1fe0a94aa09a4a47e5a02383ce662580f057bdc

ColorMapping object has default value for name slot



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@106487 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 16/07/2015 15:21:23
Showing1 changed files
... ...
@@ -32,6 +32,7 @@ Zuguang Gu <z.gu@dkfz.de>
32 32
 
33 33
 }
34 34
 \examples{
35
+
35 36
 mat = matrix(rnorm(32), nrow = 4)
36 37
 f = anno_boxplot(mat)
37 38
 grid.newpage(); f(1:8)
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: ff9ffa810ca9f16a253861d97301062962dbe38b

titles support expression now



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@106147 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 13/07/2015 21:26:16
Showing1 changed files
... ...
@@ -32,8 +32,6 @@ Zuguang Gu <z.gu@dkfz.de>
32 32
 
33 33
 }
34 34
 \examples{
35
-
36
-
37 35
 mat = matrix(rnorm(32), nrow = 4)
38 36
 f = anno_boxplot(mat)
39 37
 grid.newpage(); f(1:8)
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: e811f8100ef035ff75c16312b3e5112cc82d4a49

continuous legend is supported



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@106027 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 13/07/2015 10:21:55
Showing1 changed files
... ...
@@ -32,6 +32,8 @@ Zuguang Gu <z.gu@dkfz.de>
32 32
 
33 33
 }
34 34
 \examples{
35
+
36
+
35 37
 mat = matrix(rnorm(32), nrow = 4)
36 38
 f = anno_boxplot(mat)
37 39
 grid.newpage(); f(1:8)
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 2786dac4ddaa97c69cc24e29e121ed1a1624cdf4

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


Commit id: a61c101325601aa0d4d3ba81e10c33d4a8b34c63

rows can be split if providing a clustering object



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105855 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 06/07/2015 22:31:19
Showing1 changed files
... ...
@@ -32,8 +32,6 @@ Zuguang Gu <z.gu@dkfz.de>
32 32
 
33 33
 }
34 34
 \examples{
35
-
36
-
37 35
 mat = matrix(rnorm(32), nrow = 4)
38 36
 f = anno_boxplot(mat)
39 37
 grid.newpage(); f(1:8)
... ...
@@ -43,6 +41,4 @@ grid.newpage(); f(1:4)
43 41
 
44 42
 lt = lapply(1:4, function(i) rnorm(8))
45 43
 f = anno_boxplot(lt)
46
-grid.newpage(); f(1:4)
47
-
48
-}
44
+grid.newpage(); f(1:4)}
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
... ...
@@ -33,6 +33,7 @@ Zuguang Gu <z.gu@dkfz.de>
33 33
 }
34 34
 \examples{
35 35
 
36
+
36 37
 mat = matrix(rnorm(32), nrow = 4)
37 38
 f = anno_boxplot(mat)
38 39
 grid.newpage(); f(1:8)
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 1d5cea822fed8ed91d7ead49f520f719b3fecfd9

refreshed documentations



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105355 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 23/06/2015 08:33:59
Showing1 changed files
... ...
@@ -32,6 +32,7 @@ Zuguang Gu <z.gu@dkfz.de>
32 32
 
33 33
 }
34 34
 \examples{
35
+
35 36
 mat = matrix(rnorm(32), nrow = 4)
36 37
 f = anno_boxplot(mat)
37 38
 grid.newpage(); f(1:8)
... ...
@@ -41,4 +42,6 @@ grid.newpage(); f(1:4)
41 42
 
42 43
 lt = lapply(1:4, function(i) rnorm(8))
43 44
 f = anno_boxplot(lt)
44
-grid.newpage(); f(1:4)}
45
+grid.newpage(); f(1:4)
46
+
47
+}
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
... ...
@@ -1,23 +1,20 @@
1 1
 \name{anno_boxplot}
2 2
 \alias{anno_boxplot}
3 3
 \title{
4
-Using boxplot as annotation  
5
-
4
+Using boxplot as annotation
6 5
 
7 6
 }
8 7
 \description{
9
-Using boxplot as annotation  
10
-
8
+Using boxplot as annotation
11 9
 
12 10
 }
13 11
 \usage{
14 12
 anno_boxplot(x, which = c("column", "row"), gp = gpar(fill = "#CCCCCC"),
15 13
     pch = 16, size = unit(2, "mm"), axis = FALSE, axis_side = NULL,
16
-    axis_gp = gpar(fontsize = 8))
17
-}
14
+    axis_gp = gpar(fontsize = 8))}
18 15
 \arguments{
19 16
 
20
-  \item{x}{a matrix or a list. If \code{x} is a matrix and if \code{which} is \code{column}, statistics for boxplot is calculated by columns, if \code{which} is \code{row}, the calculation is by rows.}
17
+  \item{x}{a matrix or a list. If \code{x} is a matrix and if \code{which} is \code{column}, statistics for boxplotis calculated by columns, if \code{which} is \code{row}, the calculation is by rows.}
21 18
   \item{which}{is the annotation a column annotation or a row annotation?}
22 19
   \item{gp}{graphic parameters}
23 20
   \item{pch}{point type}
... ...
@@ -25,16 +22,13 @@ anno_boxplot(x, which = c("column", "row"), gp = gpar(fill = "#CCCCCC"),
25 22
   \item{axis}{whether add axis}
26 23
   \item{axis_side}{value in "left", "right", "bottom" and "top"}
27 24
   \item{axis_gp}{graphic parameters for axis}
28
-
29 25
 }
30 26
 \value{
31
-A graphic function which can be set in \code{\link{HeatmapAnnotation}} constructor method.  
32
-
27
+A graphic function which can be set in \code{\link{HeatmapAnnotation}} constructor method.
33 28
 
34 29
 }
35 30
 \author{
36
-Zuguang Gu <z.gu@dkfz.de>  
37
-
31
+Zuguang Gu <z.gu@dkfz.de>
38 32
 
39 33
 }
40 34
 \examples{
... ...
@@ -47,5 +41,4 @@ grid.newpage(); f(1:4)
47 41
 
48 42
 lt = lapply(1:4, function(i) rnorm(8))
49 43
 f = anno_boxplot(lt)
50
-grid.newpage(); f(1:4)
51
-}
44
+grid.newpage(); f(1:4)}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: ff6ad79beeef75c709dc08588bb942ad86de9761

rotation for heatmap title supported



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

z.gu authored on 22/06/2015 15:09:06
Showing1 changed files
... ...
@@ -1,20 +1,23 @@
1 1
 \name{anno_boxplot}
2 2
 \alias{anno_boxplot}
3 3
 \title{
4
-Using boxplot as annotation
4
+Using boxplot as annotation  
5
+
5 6
 
6 7
 }
7 8
 \description{
8
-Using boxplot as annotation
9
+Using boxplot as annotation  
10
+
9 11
 
10 12
 }
11 13
 \usage{
12 14
 anno_boxplot(x, which = c("column", "row"), gp = gpar(fill = "#CCCCCC"),
13 15
     pch = 16, size = unit(2, "mm"), axis = FALSE, axis_side = NULL,
14
-    axis_gp = gpar(fontsize = 8))}
16
+    axis_gp = gpar(fontsize = 8))
17
+}
15 18
 \arguments{
16 19
 
17
-  \item{x}{a matrix or a list. If \code{x} is a matrix and if \code{which} is \code{column}, statistics for boxplotis calculated by columns, if \code{which} is \code{row}, the calculation is by rows.}
20
+  \item{x}{a matrix or a list. If \code{x} is a matrix and if \code{which} is \code{column}, statistics for boxplot is calculated by columns, if \code{which} is \code{row}, the calculation is by rows.}
18 21
   \item{which}{is the annotation a column annotation or a row annotation?}
19 22
   \item{gp}{graphic parameters}
20 23
   \item{pch}{point type}
... ...
@@ -22,13 +25,16 @@ anno_boxplot(x, which = c("column", "row"), gp = gpar(fill = "#CCCCCC"),
22 25
   \item{axis}{whether add axis}
23 26
   \item{axis_side}{value in "left", "right", "bottom" and "top"}
24 27
   \item{axis_gp}{graphic parameters for axis}
28
+
25 29
 }
26 30
 \value{
27
-A graphic function which can be set in \code{\link{HeatmapAnnotation}} constructor method.
31
+A graphic function which can be set in \code{\link{HeatmapAnnotation}} constructor method.  
32
+
28 33
 
29 34
 }
30 35
 \author{
31
-Zuguang Gu <z.gu@dkfz.de>
36
+Zuguang Gu <z.gu@dkfz.de>  
37
+
32 38
 
33 39
 }
34 40
 \examples{
... ...
@@ -41,4 +47,5 @@ grid.newpage(); f(1:4)
41 47
 
42 48
 lt = lapply(1:4, function(i) rnorm(8))
43 49
 f = anno_boxplot(lt)
44
-grid.newpage(); f(1:4)}
50
+grid.newpage(); f(1:4)
51
+}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 6cf15a1b2514d9c86295206a55c9d5efadc00f70

check row orders



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105276 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 21/06/2015 17:44:09
Showing1 changed files
... ...
@@ -1,23 +1,20 @@
1 1
 \name{anno_boxplot}
2 2
 \alias{anno_boxplot}
3 3
 \title{
4
-Using boxplot as annotation  
5
-
4
+Using boxplot as annotation
6 5
 
7 6
 }
8 7
 \description{
9
-Using boxplot as annotation  
10
-
8
+Using boxplot as annotation
11 9
 
12 10
 }
13 11
 \usage{
14 12
 anno_boxplot(x, which = c("column", "row"), gp = gpar(fill = "#CCCCCC"),
15 13
     pch = 16, size = unit(2, "mm"), axis = FALSE, axis_side = NULL,
16
-    axis_gp = gpar(fontsize = 8))
17
-}
14
+    axis_gp = gpar(fontsize = 8))}
18 15
 \arguments{
19 16
 
20
-  \item{x}{a matrix or a list. If \code{x} is a matrix and if \code{which} is \code{column}, statistics for boxplot is calculated by columns, if \code{which} is \code{row}, the calculation is by rows.}
17
+  \item{x}{a matrix or a list. If \code{x} is a matrix and if \code{which} is \code{column}, statistics for boxplotis calculated by columns, if \code{which} is \code{row}, the calculation is by rows.}
21 18
   \item{which}{is the annotation a column annotation or a row annotation?}
22 19
   \item{gp}{graphic parameters}
23 20
   \item{pch}{point type}
... ...
@@ -25,16 +22,13 @@ anno_boxplot(x, which = c("column", "row"), gp = gpar(fill = "#CCCCCC"),
25 22
   \item{axis}{whether add axis}
26 23
   \item{axis_side}{value in "left", "right", "bottom" and "top"}
27 24
   \item{axis_gp}{graphic parameters for axis}
28
-
29 25
 }
30 26
 \value{
31
-A graphic function which can be set in \code{\link{HeatmapAnnotation}} constructor method.  
32
-
27
+A graphic function which can be set in \code{\link{HeatmapAnnotation}} constructor method.
33 28
 
34 29
 }
35 30
 \author{
36
-Zuguang Gu <z.gu@dkfz.de>  
37
-
31
+Zuguang Gu <z.gu@dkfz.de>
38 32
 
39 33
 }
40 34
 \examples{
... ...
@@ -47,5 +41,4 @@ grid.newpage(); f(1:4)
47 41
 
48 42
 lt = lapply(1:4, function(i) rnorm(8))
49 43
 f = anno_boxplot(lt)
50
-grid.newpage(); f(1:4)
51
-}
44
+grid.newpage(); f(1:4)}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 72c5e9c3243eaf6a26e529a2a16fa77af40a1291

axes are supported in annotations



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@104323 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 28/05/2015 14:20:38
Showing1 changed files
... ...
@@ -12,7 +12,8 @@ Using boxplot as annotation
12 12
 }
13 13
 \usage{
14 14
 anno_boxplot(x, which = c("column", "row"), gp = gpar(fill = "#CCCCCC"),
15
-    pch = 16, size = unit(2, "mm"))
15
+    pch = 16, size = unit(2, "mm"), axis = FALSE, axis_side = NULL,
16
+    axis_gp = gpar(fontsize = 8))
16 17
 }
17 18
 \arguments{
18 19
 
... ...
@@ -21,6 +22,9 @@ anno_boxplot(x, which = c("column", "row"), gp = gpar(fill = "#CCCCCC"),
21 22
   \item{gp}{graphic parameters}
22 23
   \item{pch}{point type}
23 24
   \item{size}{point size}
25
+  \item{axis}{whether add axis}
26
+  \item{axis_side}{value in "left", "right", "bottom" and "top"}
27
+  \item{axis_gp}{graphic parameters for axis}
24 28
 
25 29
 }
26 30
 \value{
Browse code

add package to repository

ComplexHeatmap/ podkat/ RBM/


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@101658 bc3139a8-67e5-0310-9ffc-ced21a209358

s.arora authored on 31/03/2015 18:31:58
Showing1 changed files
1 1
new file mode 100644
... ...
@@ -0,0 +1,47 @@
1
+\name{anno_boxplot}
2
+\alias{anno_boxplot}
3
+\title{
4
+Using boxplot as annotation  
5
+
6
+
7
+}
8
+\description{
9
+Using boxplot as annotation  
10
+
11
+
12
+}
13
+\usage{
14
+anno_boxplot(x, which = c("column", "row"), gp = gpar(fill = "#CCCCCC"),
15
+    pch = 16, size = unit(2, "mm"))
16
+}
17
+\arguments{
18
+
19
+  \item{x}{a matrix or a list. If \code{x} is a matrix and if \code{which} is \code{column}, statistics for boxplot is calculated by columns, if \code{which} is \code{row}, the calculation is by rows.}
20
+  \item{which}{is the annotation a column annotation or a row annotation?}
21
+  \item{gp}{graphic parameters}
22
+  \item{pch}{point type}
23
+  \item{size}{point size}
24
+
25
+}
26
+\value{
27
+A graphic function which can be set in \code{\link{HeatmapAnnotation}} constructor method.  
28
+
29
+
30
+}
31
+\author{
32
+Zuguang Gu <z.gu@dkfz.de>  
33
+
34
+
35
+}
36
+\examples{
37
+mat = matrix(rnorm(32), nrow = 4)
38
+f = anno_boxplot(mat)
39
+grid.newpage(); f(1:8)
40
+
41
+f = anno_boxplot(mat, which = "row")
42
+grid.newpage(); f(1:4)
43
+
44
+lt = lapply(1:4, function(i) rnorm(8))
45
+f = anno_boxplot(lt)
46
+grid.newpage(); f(1:4)
47
+}