1. ComplexHeatmap
  2. man
  3. anno_boxplot.rd
Browse code

generate documentations by pkgdown

Zuguang Gu authored on 18/10/2019 11:34:02
Showing1 changed files
man/anno_boxplot.rd
History View file @1cb7fea
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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
man/anno_boxplot.rd
History View file @41afe8b
... ... 
@@ -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
man/anno_boxplot.rd
History View file @3c40a7c
... ... 
@@ -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
man/anno_boxplot.rd
History View file @1a56796
... ... 
@@ -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
man/anno_boxplot.rd
History View file @ad35494
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
man/anno_boxplot.rd
History View file @289e2e9
... ... 
@@ -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
man/anno_boxplot.rd
History View file @dc0ec14
... ... 
@@ -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
man/anno_boxplot.rd
History View file @bbf9015
... ... 
@@ -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
man/anno_boxplot.rd
History View file @40fd807
... ... 
@@ -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
man/anno_boxplot.rd
History View file @8e55abf
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
man/anno_boxplot.rd
History View file @ba8a507
... ... 
@@ -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
man/anno_boxplot.rd
History View file @f597719
... ... 
@@ -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
man/anno_boxplot.rd
History View file @5ab2cb8
... ... 
@@ -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
man/anno_boxplot.rd
History View file @aee203e
... ... 
@@ -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
man/anno_boxplot.rd
History View file @7f268ee
... ... 
@@ -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
man/anno_boxplot.rd
History View file @dc0f5a9
... ... 
@@ -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
man/anno_boxplot.rd
History View file @b08d7ba
... ... 
@@ -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
man/anno_boxplot.rd
History View file @3bb5581
... ... 
@@ -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
man/anno_boxplot.rd
History View file @0725063
... ... 
@@ -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

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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
man/anno_boxplot.rd
History View file @2224e09
... ... 
@@ -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
man/anno_boxplot.rd
History View file @07961c6
... ... 
@@ -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
man/anno_boxplot.rd
History View file @10b246c
... ... 
@@ -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
man/anno_boxplot.rd
History View file @7f6dddf
... ... 
@@ -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
man/anno_boxplot.rd
History View file @6f1307c
... ... 
@@ -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
man/anno_boxplot.rd
History View file @4818ea9
... ... 
@@ -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}
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   \item{axis_side}{value in "left", "right", "bottom" and "top"}
24 27 
   \item{axis_gp}{graphic parameters for axis}
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+
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
man/anno_boxplot.rd
History View file @f0eb7a9
... ... 
@@ -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
man/anno_boxplot.rd
History View file @11a77c8
... ... 
@@ -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
man/anno_boxplot.rd
History View file @d1da987
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 
+}