Browse code

generate documentations by pkgdown

Zuguang Gu authored on 18/10/2019 11:34:02
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1 1
deleted file mode 100644
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@@ -1,33 +0,0 @@
1
-\name{draw-SingleAnnotation-method}
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-\alias{draw,SingleAnnotation-method}
3
-\title{
4
-Draw the Single Annotation
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-}
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-\description{
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-Draw the Single Annotation
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-}
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-\usage{
10
-\S4method{draw}{SingleAnnotation}(object, index, k = 1, n = 1, test = FALSE,
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-    anno_mark_param = list())
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-}
13
-\arguments{
14
-
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-  \item{object}{A \code{\link{SingleAnnotation-class}} object.}
16
-  \item{index}{A vector of indices.}
17
-  \item{k}{The index of the slice.}
18
-  \item{n}{Total number of slices. \code{k} and \code{n} are used to adjust annotation names. E.g. if \code{k} is 2 and \code{n} is 3, the annotation names are not drawn.}
19
-  \item{test}{Is it in test mode? The value can be logical or a text which is plotted as the title of plot.}
20
-  \item{anno_mark_param}{It contains specific parameters for drawing \code{\link{anno_mark}}.}
21
-
22
-}
23
-\value{
24
-No value is returned.
25
-}
26
-\author{
27
-Zuguang Gu <z.gu@dkfz.de>
28
-}
29
-\examples{
30
-# There is no example
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-NULL
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-
33
-}
Browse code

add jitter argument to Heatmap()

Zuguang Gu authored on 28/09/2019 08:37:13
Showing1 changed files
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@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
+
32 33
 }
Browse code

use pkgdown to build the doc site

Zuguang Gu authored on 24/09/2019 21:01:04
Showing1 changed files
... ...
@@ -29,5 +29,4 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
-
33 32
 }
Browse code

set cluster_slice to FALSE for character matrix

Zuguang Gu authored on 18/01/2019 10:43:26
Showing1 changed files
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@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
+
32 33
 }
Browse code

add NEWs

Zuguang Gu authored on 30/12/2018 08:12:22
Showing1 changed files
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@@ -29,5 +29,4 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
-
33 32
 }
Browse code

anno_mark() is calculated from mutiple slices

Zuguang Gu authored on 07/12/2018 14:41:15
Showing1 changed files
... ...
@@ -7,7 +7,8 @@ Draw the Single Annotation
7 7
 Draw the Single Annotation
8 8
 }
9 9
 \usage{
10
-\S4method{draw}{SingleAnnotation}(object, index, k = 1, n = 1, test = FALSE)
10
+\S4method{draw}{SingleAnnotation}(object, index, k = 1, n = 1, test = FALSE,
11
+    anno_mark_param = list())
11 12
 }
12 13
 \arguments{
13 14
 
... ...
@@ -16,6 +17,7 @@ Draw the Single Annotation
16 17
   \item{k}{The index of the slice.}
17 18
   \item{n}{Total number of slices. \code{k} and \code{n} are used to adjust annotation names. E.g. if \code{k} is 2 and \code{n} is 3, the annotation names are not drawn.}
18 19
   \item{test}{Is it in test mode? The value can be logical or a text which is plotted as the title of plot.}
20
+  \item{anno_mark_param}{It contains specific parameters for drawing \code{\link{anno_mark}}.}
19 21
 
20 22
 }
21 23
 \value{
Browse code

fix some bugs

Zuguang Gu authored on 19/10/2018 19:08:59
Showing1 changed files
... ...
@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
+
30 31
 }
Browse code

update

Zuguang Gu authored on 17/10/2018 06:09:36
Showing1 changed files
... ...
@@ -27,5 +27,4 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
-
31 30
 }
Browse code

R CMD check passed

Zuguang Gu authored on 12/10/2018 19:19:48
Showing1 changed files
... ...
@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
+
30 31
 }
Browse code

update

jokergoo authored on 12/10/2018 15:28:37
Showing1 changed files
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@@ -27,5 +27,4 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
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 NULL
30
-
31 30
 }
Browse code

vignette check passed

Zuguang Gu authored on 20/09/2018 22:09:48
Showing1 changed files
... ...
@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
+
30 31
 }
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
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@@ -1,26 +1,22 @@
1 1
 \name{draw-SingleAnnotation-method}
2 2
 \alias{draw,SingleAnnotation-method}
3 3
 \title{
4
-Draw the single annotation
4
+Draw the Single Annotation
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 }
6 6
 \description{
7
-Draw the single annotation
7
+Draw the Single Annotation
8 8
 }
9 9
 \usage{
10
-\S4method{draw}{SingleAnnotation}(object, index, k = NULL, n = NULL)
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+\S4method{draw}{SingleAnnotation}(object, index, k = 1, n = 1, test = FALSE)
11 11
 }
12 12
 \arguments{
13 13
 
14
-  \item{object}{a \code{\link{SingleAnnotation-class}} object.}
15
-  \item{index}{a vector of orders}
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-  \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the names of the viewport which contains the annotation graphics.}
17
-  \item{n}{total number of row slices}
14
+  \item{object}{A \code{\link{SingleAnnotation-class}} object.}
15
+  \item{index}{A vector of indices.}
16
+  \item{k}{The index of the slice.}
17
+  \item{n}{Total number of slices. \code{k} and \code{n} are used to adjust annotation names. E.g. if \code{k} is 2 and \code{n} is 3, the annotation names are not drawn.}
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+  \item{test}{Is it in test mode? The value can be logical or a text which is plotted as the title of plot.}
18 19
 
19
-}
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-\details{
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-A viewport is created.
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-
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-The graphics would be different depending the annotation is a row annotation or a column annotation.
24 20
 }
25 21
 \value{
26 22
 No value is returned.
... ...
@@ -29,27 +25,6 @@ No value is returned.
29 25
 Zuguang Gu <z.gu@dkfz.de>
30 26
 }
31 27
 \examples{
32
-anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
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-grid.newpage(); draw(anno, 1:5)
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-grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
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-
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-anno = SingleAnnotation(value = c("a", "a", "a", "b", "b", "b"), 
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-    col = c("a" = "red", "b" = "blue"))
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-grid.newpage(); draw(anno, 1:5)
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-grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
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-
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-anno = SingleAnnotation(value = c("a", "a", "a", "b", "b", "b"), 
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-    col = c("a" = "red", "b" = "blue"), which = "row")
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-grid.newpage(); draw(anno, 1:5)
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-
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-anno = SingleAnnotation(value = 1:10)
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-grid.newpage(); draw(anno, 1:10)
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-
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-require(circlize)
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-anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red")))
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-grid.newpage(); draw(anno, 1:10)
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-
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-anno = SingleAnnotation(fun = anno_points(1:10))
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-grid.newpage(); draw(anno, 1:10)
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-
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+# There is no example
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+NULL
55 30
 }
Browse code

merge by copy paste

Zuguang Gu authored on 17/10/2017 20:55:32
Showing1 changed files
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@@ -13,11 +13,7 @@ Draw the single annotation
13 13
 
14 14
   \item{object}{a \code{\link{SingleAnnotation-class}} object.}
15 15
   \item{index}{a vector of orders}
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-<<<<<<< HEAD
17 16
   \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the names of the viewport which contains the annotation graphics.}
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-=======
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-  \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewport which contains the annotation graphics.}
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->>>>>>> bioc/master
21 17
   \item{n}{total number of row slices}
22 18
 
23 19
 }
Zuguang Gu authored on 17/10/2017 19:44:53
Showing0 changed files
Browse code

fix typo

Zuguang Gu authored on 20/08/2017 05:56:30
Showing1 changed files
... ...
@@ -13,7 +13,7 @@ Draw the single annotation
13 13
 
14 14
   \item{object}{a \code{\link{SingleAnnotation-class}} object.}
15 15
   \item{index}{a vector of orders}
16
-  \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewport which contains the annotation graphics.}
16
+  \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the names of the viewport which contains the annotation graphics.}
17 17
   \item{n}{total number of row slices}
18 18
 
19 19
 }
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
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@@ -13,7 +13,7 @@ Draw the single annotation
13 13
 
14 14
   \item{object}{a \code{\link{SingleAnnotation-class}} object.}
15 15
   \item{index}{a vector of orders}
16
-  \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewportwhich contains the annotation graphics.}
16
+  \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewport which contains the annotation graphics.}
17 17
   \item{n}{total number of row slices}
18 18
 
19 19
 }
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
... ...
@@ -13,7 +13,7 @@ Draw the single annotation
13 13
 
14 14
   \item{object}{a \code{\link{SingleAnnotation-class}} object.}
15 15
   \item{index}{a vector of orders}
16
-  \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewportwhich contains the annotation graphics.}
16
+  \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewport which contains the annotation graphics.}
17 17
   \item{n}{total number of row slices}
18 18
 
19 19
 }
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

Commit made by the Bioconductor Git-SVN bridge.

Commit id: db263179df8a28bd25eb5afcf64aa9c37b2fdd32

refresh docs



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107358 bc3139a8-67e5-0310-9ffc-ced21a209358

Zuguang Gu authored on 12/08/2015 22:49:59
Showing1 changed files
... ...
@@ -19,6 +19,7 @@ Draw the single annotation
19 19
 }
20 20
 \details{
21 21
 A viewport is created.
22
+
22 23
 The graphics would be different depending the annotation is a row annotation or a column annotation.
23 24
 }
24 25
 \value{
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: db263179df8a28bd25eb5afcf64aa9c37b2fdd32

refresh docs



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107358 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 12/08/2015 22:49:59
Showing1 changed files
... ...
@@ -19,6 +19,7 @@ Draw the single annotation
19 19
 }
20 20
 \details{
21 21
 A viewport is created.
22
+
22 23
 The graphics would be different depending the annotation is a row annotation or a column annotation.
23 24
 }
24 25
 \value{
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
... ...
@@ -7,13 +7,15 @@ Draw the single annotation
7 7
 Draw the single annotation
8 8
 }
9 9
 \usage{
10
-\S4method{draw}{SingleAnnotation}(object, index, k = NULL, n = NULL)}
10
+\S4method{draw}{SingleAnnotation}(object, index, k = NULL, n = NULL)
11
+}
11 12
 \arguments{
12 13
 
13 14
   \item{object}{a \code{\link{SingleAnnotation-class}} object.}
14 15
   \item{index}{a vector of orders}
15 16
   \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewportwhich contains the annotation graphics.}
16 17
   \item{n}{total number of row slices}
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+
17 19
 }
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 \details{
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 A viewport is created.
... ...
@@ -48,4 +50,5 @@ grid.newpage(); draw(anno, 1:10)
48 50
 
49 51
 anno = SingleAnnotation(fun = anno_points(1:10))
50 52
 grid.newpage(); draw(anno, 1:10)
53
+
51 54
 }
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
... ...
@@ -7,13 +7,15 @@ Draw the single annotation
7 7
 Draw the single annotation
8 8
 }
9 9
 \usage{
10
-\S4method{draw}{SingleAnnotation}(object, index, k = NULL, n = NULL)}
10
+\S4method{draw}{SingleAnnotation}(object, index, k = NULL, n = NULL)
11
+}
11 12
 \arguments{
12 13
 
13 14
   \item{object}{a \code{\link{SingleAnnotation-class}} object.}
14 15
   \item{index}{a vector of orders}
15 16
   \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewportwhich contains the annotation graphics.}
16 17
   \item{n}{total number of row slices}
18
+
17 19
 }
18 20
 \details{
19 21
 A viewport is created.
... ...
@@ -48,4 +50,5 @@ grid.newpage(); draw(anno, 1:10)
48 50
 
49 51
 anno = SingleAnnotation(fun = anno_points(1:10))
50 52
 grid.newpage(); draw(anno, 1:10)
53
+
51 54
 }
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{draw,SingleAnnotation-method}
3 3
 \title{
4 4
 Draw the single annotation
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-
6 5
 }
7 6
 \description{
8 7
 Draw the single annotation
9
-
10 8
 }
11 9
 \usage{
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 \S4method{draw}{SingleAnnotation}(object, index, k = NULL, n = NULL)}
... ...
@@ -19,31 +17,15 @@ Draw the single annotation
19 17
 }
20 18
 \details{
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 A viewport is created.
22
-
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 The graphics would be different depending the annotation is a row annotation or a column annotation.
24
-
25 21
 }
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 \value{
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 No value is returned.
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-
29 24
 }
30 25
 \author{
31 26
 Zuguang Gu <z.gu@dkfz.de>
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-
33 27
 }
34 28
 \examples{
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
48 30
 grid.newpage(); draw(anno, 1:5)
49 31
 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
... ...
@@ -65,4 +47,5 @@ anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red"
65 47
 grid.newpage(); draw(anno, 1:10)
66 48
 
67 49
 anno = SingleAnnotation(fun = anno_points(1:10))
68
-grid.newpage(); draw(anno, 1:10)}
50
+grid.newpage(); draw(anno, 1:10)
51
+}
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{draw,SingleAnnotation-method}
3 3
 \title{
4 4
 Draw the single annotation
5
-
6 5
 }
7 6
 \description{
8 7
 Draw the single annotation
9
-
10 8
 }
11 9
 \usage{
12 10
 \S4method{draw}{SingleAnnotation}(object, index, k = NULL, n = NULL)}
... ...
@@ -19,31 +17,15 @@ Draw the single annotation
19 17
 }
20 18
 \details{
21 19
 A viewport is created.
22
-
23 20
 The graphics would be different depending the annotation is a row annotation or a column annotation.
24
-
25 21
 }
26 22
 \value{
27 23
 No value is returned.
28
-
29 24
 }
30 25
 \author{
31 26
 Zuguang Gu <z.gu@dkfz.de>
32
-
33 27
 }
34 28
 \examples{
35
-
36
-
37
-
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-
39
-
40
-
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-
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-
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-
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-
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-
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-
47 29
 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
48 30
 grid.newpage(); draw(anno, 1:5)
49 31
 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
... ...
@@ -65,4 +47,5 @@ anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red"
65 47
 grid.newpage(); draw(anno, 1:10)
66 48
 
67 49
 anno = SingleAnnotation(fun = anno_points(1:10))
68
-grid.newpage(); draw(anno, 1:10)}
50
+grid.newpage(); draw(anno, 1:10)
51
+}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 262e3960558c1f61b986f5be7a2ffd4599f704fa

comprehensive modifications



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

Zuguang Gu authored on 10/08/2015 22:17:54
Showing1 changed files
... ...
@@ -39,6 +39,11 @@ Zuguang Gu <z.gu@dkfz.de>
39 39
 
40 40
 
41 41
 
42
+
43
+
44
+
45
+
46
+
42 47
 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
43 48
 grid.newpage(); draw(anno, 1:5)
44 49
 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
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
... ...
@@ -39,6 +39,11 @@ Zuguang Gu <z.gu@dkfz.de>
39 39
 
40 40
 
41 41
 
42
+
43
+
44
+
45
+
46
+
42 47
 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
43 48
 grid.newpage(); draw(anno, 1:5)
44 49
 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 73171be89c157222e8e71e85daa8a37ce509a4e2

add border argument in anno_* family functions



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

Zuguang Gu authored on 06/08/2015 17:46:06
Showing1 changed files
... ...
@@ -38,6 +38,7 @@ Zuguang Gu <z.gu@dkfz.de>
38 38
 
39 39
 
40 40
 
41
+
41 42
 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
42 43
 grid.newpage(); draw(anno, 1:5)
43 44
 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
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
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@@ -38,6 +38,7 @@ Zuguang Gu <z.gu@dkfz.de>
38 38
 
39 39
 
40 40
 
41
+
41 42
 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
42 43
 grid.newpage(); draw(anno, 1:5)
43 44
 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
Browse code

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Commit id: 3429d28233ef2cbeafcd05307042d7c7aa54a2a2

add decorate* family functions



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

Zuguang Gu authored on 06/08/2015 16:40:59
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@@ -34,6 +34,10 @@ Zuguang Gu <z.gu@dkfz.de>
34 34
 \examples{
35 35
 
36 36
 
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+
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+
39
+
40
+
37 41
 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
38 42
 grid.newpage(); draw(anno, 1:5)
39 43
 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
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
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@@ -34,6 +34,10 @@ Zuguang Gu <z.gu@dkfz.de>
34 34
 \examples{
35 35
 
36 36
 
37
+
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+
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+
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+
37 41
 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
38 42
 grid.newpage(); draw(anno, 1:5)
39 43
 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: d5adc92bdbf27b45a6a4b5c7e29d2e4fe8380194

allow reordering



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

Zuguang Gu authored on 04/08/2015 20:24:37
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@@ -32,6 +32,8 @@ Zuguang Gu <z.gu@dkfz.de>
32 32
 
33 33
 }
34 34
 \examples{
35
+
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+
35 37
 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
36 38
 grid.newpage(); draw(anno, 1:5)
37 39
 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
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
 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
36 38
 grid.newpage(); draw(anno, 1:5)
37 39
 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 722ae931d95ad2242857b94a1383ad39650a6012

refresh documentations



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@106977 bc3139a8-67e5-0310-9ffc-ced21a209358

Zuguang Gu authored on 01/08/2015 18:51:11
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@@ -9,12 +9,13 @@ Draw the single annotation
9 9
 
10 10
 }
11 11
 \usage{
12
-\S4method{draw}{SingleAnnotation}(object, index, k = NULL)}
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+\S4method{draw}{SingleAnnotation}(object, index, k = NULL, n = NULL)}
13 13
 \arguments{
14 14
 
15 15
   \item{object}{a \code{\link{SingleAnnotation-class}} object.}
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   \item{index}{a vector of orders}
17 17
   \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewportwhich contains the annotation graphics.}
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+  \item{n}{total number of row slices}
18 19
 }
19 20
 \details{
20 21
 A viewport is created.
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 722ae931d95ad2242857b94a1383ad39650a6012

refresh documentations



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@106977 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 01/08/2015 18:51:11
Showing1 changed files
... ...
@@ -9,12 +9,13 @@ Draw the single annotation
9 9
 
10 10
 }
11 11
 \usage{
12
-\S4method{draw}{SingleAnnotation}(object, index, k = NULL)}
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+\S4method{draw}{SingleAnnotation}(object, index, k = NULL, n = NULL)}
13 13
 \arguments{
14 14
 
15 15
   \item{object}{a \code{\link{SingleAnnotation-class}} object.}
16 16
   \item{index}{a vector of orders}
17 17
   \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewportwhich contains the annotation graphics.}
18
+  \item{n}{total number of row slices}
18 19
 }
19 20
 \details{
20 21
 A viewport is created.
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
... ...
@@ -14,7 +14,7 @@ Draw the single annotation
14 14
 
15 15
   \item{object}{a \code{\link{SingleAnnotation-class}} object.}
16 16
   \item{index}{a vector of orders}
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-  \item{k}{if row annotation is splitted, the value identifies which row slice.}
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+  \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewportwhich contains the annotation graphics.}
18 18
 }
19 19
 \details{
20 20
 A viewport is created.
... ...
@@ -31,7 +31,6 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
32 32
 }
33 33
 \examples{
34
-
35 34
 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
36 35
 grid.newpage(); draw(anno, 1:5)
37 36
 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
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
... ...
@@ -14,7 +14,7 @@ Draw the single annotation
14 14
 
15 15
   \item{object}{a \code{\link{SingleAnnotation-class}} object.}
16 16
   \item{index}{a vector of orders}
17
-  \item{k}{if row annotation is splitted, the value identifies which row slice.}
17
+  \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewportwhich contains the annotation graphics.}
18 18
 }
19 19
 \details{
20 20
 A viewport is created.
... ...
@@ -31,7 +31,6 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
32 32
 }
33 33
 \examples{
34
-
35 34
 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
36 35
 grid.newpage(); draw(anno, 1:5)
37 36
 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
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: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@106487 bc3139a8-67e5-0310-9ffc-ced21a209358

Zuguang Gu authored on 16/07/2015 15:21:23
Showing1 changed files
... ...
@@ -31,6 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
32 32
 }
33 33
 \examples{
34
+
34 35
 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
35 36
 grid.newpage(); draw(anno, 1:5)
36 37
 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
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
... ...
@@ -31,6 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
32 32
 }
33 33
 \examples{
34
+
34 35
 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
35 36
 grid.newpage(); draw(anno, 1:5)
36 37
 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
Browse code

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Commit id: ff9ffa810ca9f16a253861d97301062962dbe38b

titles support expression now



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Zuguang Gu authored on 13/07/2015 21:26:16
Showing1 changed files
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@@ -31,8 +31,6 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
32 32
 }
33 33
 \examples{
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-
35
-
36 34
 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
37 35
 grid.newpage(); draw(anno, 1:5)
38 36
 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
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
... ...
@@ -31,8 +31,6 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
32 32
 }
33 33
 \examples{
34
-
35
-
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 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
37 35
 grid.newpage(); draw(anno, 1:5)
38 36
 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
Browse code

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Commit id: e811f8100ef035ff75c16312b3e5112cc82d4a49

continuous legend is supported



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

Zuguang Gu authored on 13/07/2015 10:21:55
Showing1 changed files
... ...
@@ -31,6 +31,8 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
32 32
 }
33 33
 \examples{
34
+
35
+
34 36
 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
35 37
 grid.newpage(); draw(anno, 1:5)
36 38
 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
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
... ...
@@ -31,6 +31,8 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
32 32
 }
33 33
 \examples{
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+
35
+
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 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
35 37
 grid.newpage(); draw(anno, 1:5)
36 38
 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
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: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105855 bc3139a8-67e5-0310-9ffc-ced21a209358

Zuguang Gu authored on 06/07/2015 22:31:19
Showing1 changed files
... ...
@@ -31,8 +31,6 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
32 32
 }
33 33
 \examples{
34
-
35
-
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 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
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 grid.newpage(); draw(anno, 1:5)
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 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
... ...
@@ -54,6 +52,4 @@ anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red"
54 52
 grid.newpage(); draw(anno, 1:10)
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56 54
 anno = SingleAnnotation(fun = anno_points(1:10))
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-grid.newpage(); draw(anno, 1:10)
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-
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-}
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+grid.newpage(); draw(anno, 1:10)}
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
... ...
@@ -31,8 +31,6 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
32 32
 }
33 33
 \examples{
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-
35
-
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 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
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 grid.newpage(); draw(anno, 1:5)
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 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
... ...
@@ -54,6 +52,4 @@ anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red"
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 grid.newpage(); draw(anno, 1:10)
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 anno = SingleAnnotation(fun = anno_points(1:10))
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-grid.newpage(); draw(anno, 1:10)
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-
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-}
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+grid.newpage(); draw(anno, 1:10)}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

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
... ...
@@ -32,6 +32,7 @@ Zuguang Gu <z.gu@dkfz.de>
32 32
 }
33 33
 \examples{
34 34
 
35
+
35 36
 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
36 37
 grid.newpage(); draw(anno, 1:5)
37 38
 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
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
... ...
@@ -32,6 +32,7 @@ Zuguang Gu <z.gu@dkfz.de>
32 32
 }
33 33
 \examples{
34 34
 
35
+
35 36
 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
36 37
 grid.newpage(); draw(anno, 1:5)
37 38
 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 1d5cea822fed8ed91d7ead49f520f719b3fecfd9

refreshed documentations



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

Zuguang Gu authored on 23/06/2015 08:33:59
Showing1 changed files
... ...
@@ -31,6 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
32 32
 }
33 33
 \examples{
34
+
34 35
 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
35 36
 grid.newpage(); draw(anno, 1:5)
36 37
 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
... ...
@@ -52,4 +53,6 @@ anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red"
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 grid.newpage(); draw(anno, 1:10)
53 54
 
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 anno = SingleAnnotation(fun = anno_points(1:10))
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-grid.newpage(); draw(anno, 1:10)}
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+grid.newpage(); draw(anno, 1:10)
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+
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+}
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
... ...
@@ -31,6 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
32 32
 }
33 33
 \examples{
34
+
34 35
 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
35 36
 grid.newpage(); draw(anno, 1:5)
36 37
 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
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@@ -52,4 +53,6 @@ anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red"
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 grid.newpage(); draw(anno, 1:10)
53 54
 
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 anno = SingleAnnotation(fun = anno_points(1:10))
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-grid.newpage(); draw(anno, 1:10)}
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+grid.newpage(); draw(anno, 1:10)
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+
58
+}
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
... ...
@@ -1,40 +1,33 @@
1 1
 \name{draw-SingleAnnotation-method}
2 2
 \alias{draw,SingleAnnotation-method}
3 3
 \title{
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-Draw the single annotation  
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-
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+Draw the single annotation
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7 6
 }
8 7
 \description{
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-Draw the single annotation  
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-
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+Draw the single annotation
11 9
 
12 10
 }
13 11
 \usage{
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-\S4method{draw}{SingleAnnotation}(object, index, k = NULL)
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-}
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+\S4method{draw}{SingleAnnotation}(object, index, k = NULL)}
16 13
 \arguments{
17 14
 
18 15
   \item{object}{a \code{\link{SingleAnnotation-class}} object.}
19 16
   \item{index}{a vector of orders}
20 17
   \item{k}{if row annotation is splitted, the value identifies which row slice.}
21
-
22 18
 }
23 19
 \details{
24
-A viewport is created.  
25
-
26
-The graphics would be different depending the annotation is a row annotation or a column annotation.  
20
+A viewport is created.
27 21
 
22
+The graphics would be different depending the annotation is a row annotation or a column annotation.
28 23
 
29 24
 }
30 25
 \value{
31
-No value is returned.  
32
-
26
+No value is returned.
33 27
 
34 28
 }
35 29
 \author{
36
-Zuguang Gu <z.gu@dkfz.de>  
37
-
30
+Zuguang Gu <z.gu@dkfz.de>
38 31
 
39 32
 }
40 33
 \examples{
... ...
@@ -59,5 +52,4 @@ anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red"
59 52
 grid.newpage(); draw(anno, 1:10)
60 53
 
61 54
 anno = SingleAnnotation(fun = anno_points(1:10))
62
-grid.newpage(); draw(anno, 1:10)
63
-}
55
+grid.newpage(); draw(anno, 1:10)}
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
... ...
@@ -1,40 +1,33 @@
1 1
 \name{draw-SingleAnnotation-method}
2 2
 \alias{draw,SingleAnnotation-method}
3 3
 \title{
4
-Draw the single annotation  
5
-
4
+Draw the single annotation
6 5
 
7 6
 }
8 7
 \description{
9
-Draw the single annotation  
10
-
8
+Draw the single annotation
11 9
 
12 10
 }
13 11
 \usage{
14
-\S4method{draw}{SingleAnnotation}(object, index, k = NULL)
15
-}
12
+\S4method{draw}{SingleAnnotation}(object, index, k = NULL)}
16 13
 \arguments{
17 14
 
18 15
   \item{object}{a \code{\link{SingleAnnotation-class}} object.}
19 16
   \item{index}{a vector of orders}
20 17
   \item{k}{if row annotation is splitted, the value identifies which row slice.}
21
-
22 18
 }
23 19
 \details{
24
-A viewport is created.  
25
-
26
-The graphics would be different depending the annotation is a row annotation or a column annotation.  
20
+A viewport is created.
27 21
 
22
+The graphics would be different depending the annotation is a row annotation or a column annotation.
28 23
 
29 24
 }
30 25
 \value{
31
-No value is returned.  
32
-
26
+No value is returned.
33 27
 
34 28
 }
35 29
 \author{
36
-Zuguang Gu <z.gu@dkfz.de>  
37
-
30
+Zuguang Gu <z.gu@dkfz.de>
38 31
 
39 32
 }
40 33
 \examples{
... ...
@@ -59,5 +52,4 @@ anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red"
59 52
 grid.newpage(); draw(anno, 1:10)
60 53
 
61 54
 anno = SingleAnnotation(fun = anno_points(1:10))
62
-grid.newpage(); draw(anno, 1:10)
63
-}
55
+grid.newpage(); draw(anno, 1:10)}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

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
... ...
@@ -1,33 +1,40 @@
1 1
 \name{draw-SingleAnnotation-method}
2 2
 \alias{draw,SingleAnnotation-method}
3 3
 \title{
4
-Draw the single annotation
4
+Draw the single annotation  
5
+
5 6
 
6 7
 }
7 8
 \description{
8
-Draw the single annotation
9
+Draw the single annotation  
10
+
9 11
 
10 12
 }
11 13
 \usage{
12
-\S4method{draw}{SingleAnnotation}(object, index, k = NULL)}
14
+\S4method{draw}{SingleAnnotation}(object, index, k = NULL)
15
+}
13 16
 \arguments{
14 17
 
15 18
   \item{object}{a \code{\link{SingleAnnotation-class}} object.}
16 19
   \item{index}{a vector of orders}
17 20
   \item{k}{if row annotation is splitted, the value identifies which row slice.}
21
+
18 22
 }
19 23
 \details{
20
-A viewport is created.
24
+A viewport is created.  
25
+
26
+The graphics would be different depending the annotation is a row annotation or a column annotation.  
21 27
 
22
-The graphics would be different depending the annotation is a row annotation or a column annotation.
23 28
 
24 29
 }
25 30
 \value{
26
-No value is returned.
31
+No value is returned.  
32
+
27 33
 
28 34
 }
29 35
 \author{
30
-Zuguang Gu <z.gu@dkfz.de>
36
+Zuguang Gu <z.gu@dkfz.de>  
37
+
31 38
 
32 39
 }
33 40
 \examples{
... ...
@@ -52,4 +59,5 @@ anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red"
52 59
 grid.newpage(); draw(anno, 1:10)
53 60
 
54 61
 anno = SingleAnnotation(fun = anno_points(1:10))
55
-grid.newpage(); draw(anno, 1:10)}
62
+grid.newpage(); draw(anno, 1:10)
63
+}
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
... ...
@@ -1,33 +1,40 @@
1 1
 \name{draw-SingleAnnotation-method}
2 2
 \alias{draw,SingleAnnotation-method}
3 3
 \title{
4
-Draw the single annotation
4
+Draw the single annotation  
5
+
5 6
 
6 7
 }
7 8
 \description{
8
-Draw the single annotation
9
+Draw the single annotation  
10
+
9 11
 
10 12
 }
11 13
 \usage{
12
-\S4method{draw}{SingleAnnotation}(object, index, k = NULL)}
14
+\S4method{draw}{SingleAnnotation}(object, index, k = NULL)
15
+}
13 16
 \arguments{
14 17
 
15 18
   \item{object}{a \code{\link{SingleAnnotation-class}} object.}
16 19
   \item{index}{a vector of orders}
17 20
   \item{k}{if row annotation is splitted, the value identifies which row slice.}
21
+
18 22
 }
19 23
 \details{
20
-A viewport is created.
24
+A viewport is created.  
25
+
26
+The graphics would be different depending the annotation is a row annotation or a column annotation.  
21 27
 
22
-The graphics would be different depending the annotation is a row annotation or a column annotation.
23 28
 
24 29
 }
25 30
 \value{
26
-No value is returned.
31
+No value is returned.  
32
+
27 33
 
28 34
 }
29 35
 \author{
30
-Zuguang Gu <z.gu@dkfz.de>
36
+Zuguang Gu <z.gu@dkfz.de>  
37
+
31 38
 
32 39
 }
33 40
 \examples{
... ...
@@ -52,4 +59,5 @@ anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red"
52 59
 grid.newpage(); draw(anno, 1:10)
53 60
 
54 61
 anno = SingleAnnotation(fun = anno_points(1:10))
55
-grid.newpage(); draw(anno, 1:10)}
62
+grid.newpage(); draw(anno, 1:10)
63
+}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 6cf15a1b2514d9c86295206a55c9d5efadc00f70

check row orders



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

Zuguang Gu authored on 21/06/2015 17:44:09
Showing1 changed files
... ...
@@ -1,40 +1,33 @@
1 1
 \name{draw-SingleAnnotation-method}
2 2
 \alias{draw,SingleAnnotation-method}
3 3
 \title{
4
-Draw the single annotation  
5
-
4
+Draw the single annotation
6 5
 
7 6
 }
8 7
 \description{
9
-Draw the single annotation  
10
-
8
+Draw the single annotation
11 9
 
12 10
 }
13 11
 \usage{
14
-\S4method{draw}{SingleAnnotation}(object, index, k = NULL)
15
-}
12
+\S4method{draw}{SingleAnnotation}(object, index, k = NULL)}
16 13
 \arguments{
17 14
 
18 15
   \item{object}{a \code{\link{SingleAnnotation-class}} object.}
19 16
   \item{index}{a vector of orders}
20 17
   \item{k}{if row annotation is splitted, the value identifies which row slice.}
21
-
22 18
 }
23 19
 \details{
24
-A viewport is created.  
25
-
26
-The graphics would be different depending the annotation is a row annotation or a column annotation.  
20
+A viewport is created.
27 21
 
22
+The graphics would be different depending the annotation is a row annotation or a column annotation.
28 23
 
29 24
 }
30 25
 \value{
31
-No value is returned.  
32
-
26
+No value is returned.
33 27
 
34 28
 }
35 29
 \author{
36
-Zuguang Gu <z.gu@dkfz.de>  
37
-
30
+Zuguang Gu <z.gu@dkfz.de>
38 31
 
39 32
 }
40 33
 \examples{
... ...
@@ -59,5 +52,4 @@ anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red"
59 52
 grid.newpage(); draw(anno, 1:10)
60 53
 
61 54
 anno = SingleAnnotation(fun = anno_points(1:10))
62
-grid.newpage(); draw(anno, 1:10)
63
-}
55
+grid.newpage(); draw(anno, 1:10)}
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
... ...
@@ -1,40 +1,33 @@
1 1
 \name{draw-SingleAnnotation-method}
2 2
 \alias{draw,SingleAnnotation-method}
3 3
 \title{
4
-Draw the single annotation  
5
-
4
+Draw the single annotation
6 5
 
7 6
 }
8 7
 \description{
9
-Draw the single annotation  
10
-
8
+Draw the single annotation
11 9
 
12 10
 }
13 11
 \usage{
14
-\S4method{draw}{SingleAnnotation}(object, index, k = NULL)
15
-}
12
+\S4method{draw}{SingleAnnotation}(object, index, k = NULL)}
16 13
 \arguments{
17 14
 
18 15
   \item{object}{a \code{\link{SingleAnnotation-class}} object.}
19 16
   \item{index}{a vector of orders}
20 17
   \item{k}{if row annotation is splitted, the value identifies which row slice.}
21
-
22 18
 }
23 19
 \details{
24
-A viewport is created.  
25
-
26
-The graphics would be different depending the annotation is a row annotation or a column annotation.  
20
+A viewport is created.
27 21
 
22
+The graphics would be different depending the annotation is a row annotation or a column annotation.
28 23
 
29 24
 }
30 25
 \value{
31
-No value is returned.  
32
-
26
+No value is returned.
33 27
 
34 28
 }
35 29
 \author{
36
-Zuguang Gu <z.gu@dkfz.de>  
37
-
30
+Zuguang Gu <z.gu@dkfz.de>
38 31
 
39 32
 }
40 33
 \examples{
... ...
@@ -59,5 +52,4 @@ anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red"
59 52
 grid.newpage(); draw(anno, 1:10)
60 53
 
61 54
 anno = SingleAnnotation(fun = anno_points(1:10))
62
-grid.newpage(); draw(anno, 1:10)
63
-}
55
+grid.newpage(); draw(anno, 1:10)}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 4769a51610e162e0f84b7fc1bb7bb69deb61c3e6

adjust component name and size



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105094 bc3139a8-67e5-0310-9ffc-ced21a209358

Zuguang Gu authored on 17/06/2015 20:03:45
Showing1 changed files
... ...
@@ -11,12 +11,13 @@ Draw the single annotation
11 11
 
12 12
 }
13 13
 \usage{
14
-\S4method{draw}{SingleAnnotation}(object, index)
14
+\S4method{draw}{SingleAnnotation}(object, index, k = NULL)
15 15
 }
16 16
 \arguments{
17 17
 
18 18
   \item{object}{a \code{\link{SingleAnnotation-class}} object.}
19 19
   \item{index}{a vector of orders}
20
+  \item{k}{if row annotation is splitted, the value identifies which row slice.}
20 21
 
21 22
 }
22 23
 \details{
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 4769a51610e162e0f84b7fc1bb7bb69deb61c3e6

adjust component name and size



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105094 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 17/06/2015 20:03:45
Showing1 changed files
... ...
@@ -11,12 +11,13 @@ Draw the single annotation
11 11
 
12 12
 }
13 13
 \usage{
14
-\S4method{draw}{SingleAnnotation}(object, index)
14
+\S4method{draw}{SingleAnnotation}(object, index, k = NULL)
15 15
 }
16 16
 \arguments{
17 17
 
18 18
   \item{object}{a \code{\link{SingleAnnotation-class}} object.}
19 19
   \item{index}{a vector of orders}
20
+  \item{k}{if row annotation is splitted, the value identifies which row slice.}
20 21
 
21 22
 }
22 23
 \details{
Browse code

add package to repository

ComplexHeatmap/ podkat/ RBM/


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

Sonali Arora authored on 31/03/2015 18:31:58
Showing1 changed files
1 1
new file mode 100644
... ...
@@ -0,0 +1,62 @@
1
+\name{draw-SingleAnnotation-method}
2
+\alias{draw,SingleAnnotation-method}
3
+\title{
4
+Draw the single annotation  
5
+
6
+
7
+}
8
+\description{
9
+Draw the single annotation  
10
+
11
+
12
+}
13
+\usage{
14
+\S4method{draw}{SingleAnnotation}(object, index)
15
+}
16
+\arguments{
17
+
18
+  \item{object}{a \code{\link{SingleAnnotation-class}} object.}
19
+  \item{index}{a vector of orders}
20
+
21
+}
22
+\details{
23
+A viewport is created.  
24
+
25
+The graphics would be different depending the annotation is a row annotation or a column annotation.  
26
+
27
+
28
+}
29
+\value{
30
+No value is returned.  
31
+
32
+
33
+}
34
+\author{
35
+Zuguang Gu <z.gu@dkfz.de>  
36
+
37
+
38
+}
39
+\examples{
40
+anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
41
+grid.newpage(); draw(anno, 1:5)
42
+grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
43
+
44
+anno = SingleAnnotation(value = c("a", "a", "a", "b", "b", "b"), 
45
+    col = c("a" = "red", "b" = "blue"))
46
+grid.newpage(); draw(anno, 1:5)
47
+grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
48
+
49
+anno = SingleAnnotation(value = c("a", "a", "a", "b", "b", "b"), 
50
+    col = c("a" = "red", "b" = "blue"), which = "row")
51
+grid.newpage(); draw(anno, 1:5)
52
+
53
+anno = SingleAnnotation(value = 1:10)
54
+grid.newpage(); draw(anno, 1:10)
55
+
56
+require(circlize)
57
+anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red")))
58
+grid.newpage(); draw(anno, 1:10)
59
+
60
+anno = SingleAnnotation(fun = anno_points(1:10))
61
+grid.newpage(); draw(anno, 1:10)
62
+}
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 +1,62 @@
1
+\name{draw-SingleAnnotation-method}
2
+\alias{draw,SingleAnnotation-method}
3
+\title{
4
+Draw the single annotation  
5
+
6
+
7
+}
8
+\description{
9
+Draw the single annotation  
10
+
11
+
12
+}
13
+\usage{
14
+\S4method{draw}{SingleAnnotation}(object, index)
15
+}
16
+\arguments{
17
+
18
+  \item{object}{a \code{\link{SingleAnnotation-class}} object.}
19
+  \item{index}{a vector of orders}
20
+
21
+}
22
+\details{
23
+A viewport is created.  
24
+
25
+The graphics would be different depending the annotation is a row annotation or a column annotation.  
26
+
27
+
28
+}
29
+\value{
30
+No value is returned.  
31
+
32
+
33
+}
34
+\author{
35
+Zuguang Gu <z.gu@dkfz.de>  
36
+
37
+
38
+}
39
+\examples{
40
+anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
41
+grid.newpage(); draw(anno, 1:5)
42
+grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
43
+
44
+anno = SingleAnnotation(value = c("a", "a", "a", "b", "b", "b"), 
45
+    col = c("a" = "red", "b" = "blue"))
46
+grid.newpage(); draw(anno, 1:5)
47
+grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
48
+
49
+anno = SingleAnnotation(value = c("a", "a", "a", "b", "b", "b"), 
50
+    col = c("a" = "red", "b" = "blue"), which = "row")
51
+grid.newpage(); draw(anno, 1:5)
52
+
53
+anno = SingleAnnotation(value = 1:10)
54
+grid.newpage(); draw(anno, 1:10)
55
+
56
+require(circlize)
57
+anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red")))
58
+grid.newpage(); draw(anno, 1:10)
59
+
60
+anno = SingleAnnotation(fun = anno_points(1:10))
61
+grid.newpage(); draw(anno, 1:10)
62
+}