Browse code

generate documentations by pkgdown

Zuguang Gu authored on 18/10/2019 11:34:02
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@@ -1,33 +0,0 @@
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-\name{columnAnnotation}
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-\alias{columnAnnotation}
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-\title{
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-Construct Column Annotations
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-}
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-\description{
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-Construct Column Annotations
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-}
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-\usage{
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-columnAnnotation(...)
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-}
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-\arguments{
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-
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-  \item{...}{Pass to \code{\link{HeatmapAnnotation}}.}
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-
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-}
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-\details{
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-The function is identical to
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-
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-  \preformatted{
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-    HeatmapAnnotation(..., which = "column")  }
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-}
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-\value{
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-A \code{\link{HeatmapAnnotation-class}} object.
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-}
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-\author{
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-Zuguang Gu <z.gu@dkfz.de>
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-}
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-\examples{
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-# There is no example
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-NULL
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-
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-}
Browse code

add jitter argument to Heatmap()

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

use pkgdown to build the doc site

Zuguang Gu authored on 24/09/2019 21:01:04
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@@ -29,5 +29,4 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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-
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 }
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set cluster_slice to FALSE for character matrix

Zuguang Gu authored on 18/01/2019 10:43:26
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@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
 \examples{
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 # There is no example
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 NULL
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+
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 }
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add NEWs

Zuguang Gu authored on 30/12/2018 08:12:22
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@@ -29,5 +29,4 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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-
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 }
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documentation checked

Zuguang Gu authored on 23/10/2018 19:59:12
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@@ -11,7 +11,7 @@ columnAnnotation(...)
11 11
 }
12 12
 \arguments{
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-  \item{...}{Pass to \code{\link{HeatmapAnnotation}}}
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+  \item{...}{Pass to \code{\link{HeatmapAnnotation}}.}
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 }
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 \details{
Browse code

fix some bugs

Zuguang Gu authored on 19/10/2018 19:08:59
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@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
 \examples{
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 # There is no example
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 NULL
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+
32 33
 }
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update

Zuguang Gu authored on 17/10/2018 06:09:36
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@@ -29,5 +29,4 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
 \examples{
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 # There is no example
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 NULL
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-
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 }
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R CMD check passed

Zuguang Gu authored on 12/10/2018 19:19:48
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@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
 \examples{
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 # There is no example
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 NULL
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+
32 33
 }
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update

jokergoo authored on 12/10/2018 15:28:37
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@@ -29,5 +29,4 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
 \examples{
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 # There is no example
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 NULL
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-
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 }
Browse code

vignette check passed

Zuguang Gu authored on 20/09/2018 22:09:48
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@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
 \examples{
30 30
 # There is no example
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 NULL
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+
32 33
 }
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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@@ -1,17 +1,17 @@
1 1
 \name{columnAnnotation}
2 2
 \alias{columnAnnotation}
3 3
 \title{
4
-Construct column annotations
4
+Construct Column Annotations
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 }
6 6
 \description{
7
-Construct column annotations
7
+Construct Column Annotations
8 8
 }
9 9
 \usage{
10 10
 columnAnnotation(...)
11 11
 }
12 12
 \arguments{
13 13
 
14
-  \item{...}{pass to \code{\link{HeatmapAnnotation}}}
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+  \item{...}{Pass to \code{\link{HeatmapAnnotation}}}
15 15
 
16 16
 }
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 \details{
... ...
@@ -27,7 +27,6 @@ A \code{\link{HeatmapAnnotation-class}} object.
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 Zuguang Gu <z.gu@dkfz.de>
28 28
 }
29 29
 \examples{
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-df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
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-ha = rowAnnotation(df = df)
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-
30
+# There is no example
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+NULL
33 32
 }
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
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1 1
old mode 100644
2 2
new mode 100755
Browse code

resolve conflict from master branch

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

z.gu authored on 03/09/2015 20:32:44
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@@ -18,7 +18,7 @@ columnAnnotation(...)
18 18
 The function is identical to
19 19
 
20 20
   \preformatted{
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-HeatmapAnnotation(..., which = "column")  }
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+    HeatmapAnnotation(..., which = "column")  }
22 22
 }
23 23
 \value{
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 A \code{\link{HeatmapAnnotation-class}} object.
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
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@@ -16,6 +16,7 @@ columnAnnotation(...)
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 }
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 \details{
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 The function is identical to
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+
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   \preformatted{
20 21
 HeatmapAnnotation(..., which = "column")  }
21 22
 }
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
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@@ -7,17 +7,17 @@ Construct column annotations
7 7
 Construct column annotations
8 8
 }
9 9
 \usage{
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-columnAnnotation(...)}
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+columnAnnotation(...)
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+}
11 12
 \arguments{
12 13
 
13 14
   \item{...}{pass to \code{\link{HeatmapAnnotation}}}
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+
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 }
15 17
 \details{
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 The function is identical to
17 19
   \preformatted{
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-HeatmapAnnotation(..., which = "column")
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-  }
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-
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+HeatmapAnnotation(..., which = "column")  }
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 }
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 \value{
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 A \code{\link{HeatmapAnnotation-class}} object.
... ...
@@ -28,4 +28,5 @@ Zuguang Gu <z.gu@dkfz.de>
28 28
 \examples{
29 29
 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
30 30
 ha = rowAnnotation(df = df)
31
+
31 32
 }
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
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@@ -2,11 +2,9 @@
2 2
 \alias{columnAnnotation}
3 3
 \title{
4 4
 Construct column annotations
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-
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 }
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 \description{
8 7
 Construct column annotations
9
-
10 8
 }
11 9
 \usage{
12 10
 columnAnnotation(...)}
... ...
@@ -16,32 +14,18 @@ columnAnnotation(...)}
16 14
 }
17 15
 \details{
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 The function is identical to
19
-
20 17
   \preformatted{
21
-    HeatmapAnnotation(..., which = "column")
18
+HeatmapAnnotation(..., which = "column")
22 19
   }
23 20
 
24 21
 }
25 22
 \value{
26 23
 A \code{\link{HeatmapAnnotation-class}} object.
27
-
28 24
 }
29 25
 \author{
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 Zuguang Gu <z.gu@dkfz.de>
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-
32 27
 }
33 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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 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
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-ha = rowAnnotation(df = df)}
30
+ha = rowAnnotation(df = df)
31
+}
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
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@@ -38,5 +38,10 @@ Zuguang Gu <z.gu@dkfz.de>
38 38
 
39 39
 
40 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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 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
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 ha = rowAnnotation(df = df)}
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
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@@ -37,5 +37,6 @@ Zuguang Gu <z.gu@dkfz.de>
37 37
 
38 38
 
39 39
 
40
+
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 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
41 42
 ha = rowAnnotation(df = df)}
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
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@@ -33,5 +33,9 @@ Zuguang Gu <z.gu@dkfz.de>
33 33
 \examples{
34 34
 
35 35
 
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+
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+
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+
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+
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 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
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 ha = rowAnnotation(df = df)}
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
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@@ -31,5 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
32 32
 }
33 33
 \examples{
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+
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+
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 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
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 ha = rowAnnotation(df = df)}
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
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@@ -31,6 +31,5 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
32 32
 }
33 33
 \examples{
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-
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 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
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 ha = rowAnnotation(df = df)}
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
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@@ -31,5 +31,6 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
32 32
 }
33 33
 \examples{
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+
34 35
 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
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 ha = rowAnnotation(df = df)}
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
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@@ -31,7 +31,5 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
32 32
 }
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 \examples{
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-
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-
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 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
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 ha = rowAnnotation(df = df)}
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
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@@ -31,5 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
32 32
 }
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 \examples{
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+
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+
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 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
35 37
 ha = rowAnnotation(df = df)}
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
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@@ -31,9 +31,5 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
32 32
 }
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 \examples{
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-
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-
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 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
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-ha = rowAnnotation(df = df)
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-
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-}
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+ha = rowAnnotation(df = df)}
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
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@@ -32,6 +32,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
33 33
 \examples{
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+
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 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
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 ha = rowAnnotation(df = df)
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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
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@@ -31,5 +31,8 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
32 32
 }
33 33
 \examples{
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+
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 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
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-ha = rowAnnotation(df = df)}
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+ha = rowAnnotation(df = df)
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+
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+}
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
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@@ -1,43 +1,35 @@
1 1
 \name{columnAnnotation}
2 2
 \alias{columnAnnotation}
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 \title{
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-Construct column annotations  
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+Construct column annotations
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 }
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 \description{
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-Construct column annotations  
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-
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 }
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 \usage{
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-}
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+columnAnnotation(...)}
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 \arguments{
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   \item{...}{pass to \code{\link{HeatmapAnnotation}}}
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-
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 }
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 \details{
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-The function is identical to  
18
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   \preformatted{
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     HeatmapAnnotation(..., which = "column")
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   }
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-
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 }
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 \value{
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-A \code{\link{HeatmapAnnotation-class}} object.  
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-
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 }
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 \author{
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-Zuguang Gu <z.gu@dkfz.de>  
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-
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+Zuguang Gu <z.gu@dkfz.de>
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 }
40 33
 \examples{
41 34
 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
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-ha = rowAnnotation(df = df)
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-}
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+ha = rowAnnotation(df = df)}
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
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@@ -1,35 +1,43 @@
1 1
 \name{columnAnnotation}
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 \alias{columnAnnotation}
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 \title{
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-Construct column annotations
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+Construct column annotations  
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 }
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 \description{
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-Construct column annotations
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+Construct column annotations  
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 }
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 \usage{
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 \arguments{
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   \item{...}{pass to \code{\link{HeatmapAnnotation}}}
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 }
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 \details{
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22
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19 23
 
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   \preformatted{
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     HeatmapAnnotation(..., which = "column")
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   }
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+
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 }
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 \value{
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-A \code{\link{HeatmapAnnotation-class}} object.
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+A \code{\link{HeatmapAnnotation-class}} object.  
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 }
29 35
 \author{
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-Zuguang Gu <z.gu@dkfz.de>
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+Zuguang Gu <z.gu@dkfz.de>  
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+
31 38
 
32 39
 }
33 40
 \examples{
34 41
 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
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-ha = rowAnnotation(df = df)}
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+ha = rowAnnotation(df = df)
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+}
Browse code

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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
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@@ -1,43 +1,35 @@
1 1
 \name{columnAnnotation}
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 \alias{columnAnnotation}
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 \title{
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-Construct column annotations  
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-
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+Construct column annotations
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 }
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 \description{
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-Construct column annotations  
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-
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+Construct column annotations
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 }
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 \usage{
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-columnAnnotation(...)
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-}
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+columnAnnotation(...)}
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 \arguments{
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   \item{...}{pass to \code{\link{HeatmapAnnotation}}}
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-
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 }
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 \details{
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-The function is identical to  
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+The function is identical to
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   \preformatted{
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     HeatmapAnnotation(..., which = "column")
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   }
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-
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 }
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 \value{
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-A \code{\link{HeatmapAnnotation-class}} object.  
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-
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+A \code{\link{HeatmapAnnotation-class}} object.
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 }
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 \author{
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-Zuguang Gu <z.gu@dkfz.de>  
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-
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+Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
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-ha = rowAnnotation(df = df)
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-}
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+ha = rowAnnotation(df = df)}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 7e3fe86f548acd2ed59cefc6d37be94adc29ce11

zero-column heatmap can be added to the heatmap list now



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@102673 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 18/04/2015 21:06:52
Showing1 changed files
... ...
@@ -37,3 +37,7 @@ Zuguang Gu <z.gu@dkfz.de>
37 37
 
38 38
 
39 39
 }
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+\examples{
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+df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
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+ha = rowAnnotation(df = df)
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+}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 3981fe02c795578b6314576278486fa5f88be6b8

merge from bioconductor


Commit id: 6811bed29d478afac5e518d7ea40819f5c649212

change version number


Commit id: 4785016520655b11334a5ea701eeb0b93778f205

change default value when the matrix has zeor column


Commit id: cf793440d71a2170d50b00564b6464fa92fe650c

fixed documentations


Commit id: 2fd8ba9a0ebf38c86fbe4eed604d37851e9bd91f

fixed bug when the heatmap list only contains zero column matrix



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@102662 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 18/04/2015 05:39:01
Showing1 changed files
1 1
new file mode 100644
... ...
@@ -0,0 +1,39 @@
1
+\name{columnAnnotation}
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+\alias{columnAnnotation}
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+\title{
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+Construct column annotations  
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+
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+
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+}
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+\description{
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+Construct column annotations  
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+
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+
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+}
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+\usage{
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+columnAnnotation(...)
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+}
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+\arguments{
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+
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+  \item{...}{pass to \code{\link{HeatmapAnnotation}}}
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+
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+}
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+\details{
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+The function is identical to  
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+
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+  \preformatted{
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+    HeatmapAnnotation(..., which = "column")
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+  }
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+
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+
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+}
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+\value{
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+A \code{\link{HeatmapAnnotation-class}} object.  
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+
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+
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+}
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+\author{
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+Zuguang Gu <z.gu@dkfz.de>  
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+
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+
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+}