#### generate documentations by pkgdown

Zuguang Gu authored on 18/10/2019 11:34:02
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 1 1 deleted file mode 100644 ... ... @@ -1,32 +0,0 @@ 1 -\name{SingleAnnotation-class} 2 -\docType{class} 3 -\alias{SingleAnnotation-class} 4 -\title{ 5 -Class for a Single Annotation 6 -} 7 -\description{ 8 -Class for a Single Annotation 9 -} 10 -\details{ 11 -The \code{\link{SingleAnnotation-class}} is used for storing data for a single annotation and provides 12 -methods for drawing annotation graphics. 13 -} 14 -\section{Methods}{ 15 -The \code{\link{SingleAnnotation-class}} provides following methods: 16 - 17 -\itemize{ 18 - \item \code{\link{SingleAnnotation}}: constructor method 19 - \item \code{\link{draw,SingleAnnotation-method}}: draw the single annotation. 20 -}} 21 -\seealso{ 22 -The \code{\link{SingleAnnotation-class}} is always used internally. The public \code{\link{HeatmapAnnotation-class}} 23 -contains a list of \code{\link{SingleAnnotation-class}} objects and is used to add annotation graphics on heatmaps. 24 -} 25 -\author{ 26 -Zuguang Gu  27 -} 28 -\examples{ 29 -# There is no example 30 -NULL 31 - 32 -}

#### add jitter argument to Heatmap()

Zuguang Gu authored on 28/09/2019 08:37:13
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 ... ... @@ -28,4 +28,5 @@ Zuguang Gu  28 28  \examples{ 29 29  # There is no example 30 30  NULL 31 + 31 32  }

#### use pkgdown to build the doc site

Zuguang Gu authored on 24/09/2019 21:01:04
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 ... ... @@ -28,5 +28,4 @@ Zuguang Gu  28 28  \examples{ 29 29  # There is no example 30 30  NULL 31 - 32 31  }

#### set cluster_slice to FALSE for character matrix

Zuguang Gu authored on 18/01/2019 10:43:26
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 ... ... @@ -28,4 +28,5 @@ Zuguang Gu  28 28  \examples{ 29 29  # There is no example 30 30  NULL 31 + 31 32  }

Zuguang Gu authored on 30/12/2018 08:12:22
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 ... ... @@ -28,5 +28,4 @@ Zuguang Gu  28 28  \examples{ 29 29  # There is no example 30 30  NULL 31 - 32 31  }

#### fix some bugs

Zuguang Gu authored on 19/10/2018 19:08:59
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 ... ... @@ -28,4 +28,5 @@ Zuguang Gu  28 28  \examples{ 29 29  # There is no example 30 30  NULL 31 + 31 32  }

#### update

Zuguang Gu authored on 17/10/2018 06:09:36
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 ... ... @@ -28,5 +28,4 @@ Zuguang Gu  28 28  \examples{ 29 29  # There is no example 30 30  NULL 31 - 32 31  }

#### R CMD check passed

Zuguang Gu authored on 12/10/2018 19:19:48
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 ... ... @@ -28,4 +28,5 @@ Zuguang Gu  28 28  \examples{ 29 29  # There is no example 30 30  NULL 31 + 31 32  }

#### update

jokergoo authored on 12/10/2018 15:28:37
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 ... ... @@ -28,5 +28,4 @@ Zuguang Gu  28 28  \examples{ 29 29  # There is no example 30 30  NULL 31 - 32 31  }

#### vignette check passed

Zuguang Gu authored on 20/09/2018 22:09:48
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 ... ... @@ -28,4 +28,5 @@ Zuguang Gu  28 28  \examples{ 29 29  # There is no example 30 30  NULL 31 + 31 32  }

#### R CMD check passed

Zuguang Gu authored on 20/09/2018 12:48:08
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 1 1 old mode 100755 2 2 new mode 100644 ... ... @@ -2,18 +2,12 @@ 2 2  \docType{class} 3 3  \alias{SingleAnnotation-class} 4 4  \title{ 5 -Class for a single annotation 5 +Class for a Single Annotation 6 6  } 7 7  \description{ 8 -Class for a single annotation 8 +Class for a Single Annotation 9 9  } 10 10  \details{ 11 -A complex heatmap always has more than one annotations on rows and columns. Here 12 -the \code{\link{SingleAnnotation-class}} defines the basic unit of annotations. 13 -The most simple annotation is one row or one column grids in which different colors 14 -represent different classes of the data. The annotation can also be more complex 15 -graphics, such as a boxplot that shows data distribution in corresponding row or column. 16 - 17 11  The \code{\link{SingleAnnotation-class}} is used for storing data for a single annotation and provides 18 12  methods for drawing annotation graphics. 19 13  } ... ... @@ -32,7 +26,6 @@ contains a list of \code{\link{SingleAnnotation-class}} objects and is used to a 32 26  Zuguang Gu  33 27  } 34 28  \examples{ 35 -# for examples, please go to SingleAnnotation method page 29 +# There is no example 36 30  NULL 37 - 38 31  }

#### Merge branch 'master' into devel

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

#### Commit made by the Bioconductor Git-SVN bridge.

Commit id: db263179df8a28bd25eb5afcf64aa9c37b2fdd32

refresh docs

z.gu authored on 12/08/2015 22:49:59
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 ... ... @@ -13,11 +13,13 @@ the \code{\link{SingleAnnotation-class}} defines the basic unit of annotations. 13 13  The most simple annotation is one row or one column grids in which different colors 14 14  represent different classes of the data. The annotation can also be more complex 15 15  graphics, such as a boxplot that shows data distribution in corresponding row or column. 16 + 16 17  The \code{\link{SingleAnnotation-class}} is used for storing data for a single annotation and provides 17 18  methods for drawing annotation graphics. 18 19  } 19 20  \section{Methods}{ 20 21  The \code{\link{SingleAnnotation-class}} provides following methods: 22 + 21 23  \itemize{ 22 24  \item \code{\link{SingleAnnotation}}: constructor method 23 25  \item \code{\link{draw,SingleAnnotation-method}}: draw the single annotation.

#### 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

z.gu authored on 12/08/2015 22:03:22
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 ... ... @@ -21,9 +21,7 @@ The \code{\link{SingleAnnotation-class}} provides following methods: 21 21  \itemize{ 22 22  \item \code{\link{SingleAnnotation}}: constructor method 23 23  \item \code{\link{draw,SingleAnnotation-method}}: draw the single annotation. 24 -} 25 - 26 -} 24 +}} 27 25  \seealso{ 28 26  The \code{\link{SingleAnnotation-class}} is always used internally. The public \code{\link{HeatmapAnnotation-class}} 29 27  contains a list of \code{\link{SingleAnnotation-class}} objects and is used to add annotation graphics on heatmaps. ... ... @@ -34,4 +32,5 @@ Zuguang Gu  34 32  \examples{ 35 33  # for examples, please go to SingleAnnotation method page 36 34  NULL 35 + 37 36  }

#### Commit made by the Bioconductor Git-SVN bridge.

refreshed documentations

z.gu authored on 11/08/2015 10:42:08
Showing1 changed files
 ... ... @@ -3,11 +3,9 @@ 3 3  \alias{SingleAnnotation-class} 4 4  \title{ 5 5  Class for a single annotation 6 - 7 6  } 8 7  \description{ 9 8  Class for a single annotation 10 - 11 9  } 12 10  \details{ 13 11  A complex heatmap always has more than one annotations on rows and columns. Here ... ... @@ -15,14 +13,11 @@ the \code{\link{SingleAnnotation-class}} defines the basic unit of annotations. 15 13  The most simple annotation is one row or one column grids in which different colors 16 14  represent different classes of the data. The annotation can also be more complex 17 15  graphics, such as a boxplot that shows data distribution in corresponding row or column. 18 - 19 16  The \code{\link{SingleAnnotation-class}} is used for storing data for a single annotation and provides 20 17  methods for drawing annotation graphics. 21 - 22 18  } 23 19  \section{Methods}{ 24 20  The \code{\link{SingleAnnotation-class}} provides following methods: 25 - 26 21  \itemize{ 27 22  \item \code{\link{SingleAnnotation}}: constructor method 28 23  \item \code{\link{draw,SingleAnnotation-method}}: draw the single annotation. ... ... @@ -32,24 +27,11 @@ The \code{\link{SingleAnnotation-class}} provides following methods: 32 27  \seealso{ 33 28  The \code{\link{SingleAnnotation-class}} is always used internally. The public \code{\link{HeatmapAnnotation-class}} 34 29  contains a list of \code{\link{SingleAnnotation-class}} objects and is used to add annotation graphics on heatmaps. 35 - 36 30  } 37 31  \author{ 38 32  Zuguang Gu  39 - 40 33  } 41 34  \examples{ 42 - 43 - 44 - 45 - 46 - 47 - 48 - 49 - 50 - 51 - 52 - 53 - 54 35  # for examples, please go to SingleAnnotation method page 55 -NULL} 36 +NULL 37 +}

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comprehensive modifications

z.gu authored on 10/08/2015 22:17:54
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 ... ... @@ -46,5 +46,10 @@ Zuguang Gu  46 46   47 47   48 48   49 + 50 + 51 + 52 + 53 + 49 54  # for examples, please go to SingleAnnotation method page 50 55  NULL}

#### Commit made by the Bioconductor Git-SVN bridge.

Commit id: 73171be89c157222e8e71e85daa8a37ce509a4e2

add border argument in anno_* family functions

z.gu authored on 06/08/2015 17:46:06
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 ... ... @@ -45,5 +45,6 @@ Zuguang Gu  45 45   46 46   47 47   48 + 48 49  # for examples, please go to SingleAnnotation method page 49 50  NULL}

#### Commit made by the Bioconductor Git-SVN bridge.

Commit id: 3429d28233ef2cbeafcd05307042d7c7aa54a2a2

z.gu authored on 06/08/2015 16:40:59
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 ... ... @@ -41,5 +41,9 @@ Zuguang Gu  41 41  \examples{ 42 42   43 43   44 + 45 + 46 + 47 + 44 48  # for examples, please go to SingleAnnotation method page 45 49  NULL}

#### Commit made by the Bioconductor Git-SVN bridge.

allow reordering

z.gu authored on 04/08/2015 20:24:37
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 ... ... @@ -39,5 +39,7 @@ Zuguang Gu  39 39   40 40  } 41 41  \examples{ 42 + 43 + 42 44  # for examples, please go to SingleAnnotation method page 43 45  NULL}

#### Commit made by the Bioconductor Git-SVN bridge.

remove plot.HeatmapList and print.HeatmapList

z.gu authored on 18/07/2015 18:14:29
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 ... ... @@ -39,6 +39,5 @@ Zuguang Gu  39 39   40 40  } 41 41  \examples{ 42 - 43 42  # for examples, please go to SingleAnnotation method page 44 43  NULL}

#### 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

z.gu authored on 16/07/2015 15:21:23
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 ... ... @@ -39,5 +39,6 @@ Zuguang Gu  39 39   40 40  } 41 41  \examples{ 42 + 42 43  # for examples, please go to SingleAnnotation method page 43 44  NULL}

#### Commit made by the Bioconductor Git-SVN bridge.

Commit id: ff9ffa810ca9f16a253861d97301062962dbe38b

titles support expression now

z.gu authored on 13/07/2015 21:26:16
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 ... ... @@ -39,7 +39,5 @@ Zuguang Gu  39 39   40 40  } 41 41  \examples{ 42 - 43 - 44 42  # for examples, please go to SingleAnnotation method page 45 43  NULL}

#### Commit made by the Bioconductor Git-SVN bridge.

Commit id: e811f8100ef035ff75c16312b3e5112cc82d4a49

continuous legend is supported

z.gu authored on 13/07/2015 10:21:55
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 ... ... @@ -39,5 +39,7 @@ Zuguang Gu  39 39   40 40  } 41 41  \examples{ 42 + 43 + 42 44  # for examples, please go to SingleAnnotation method page 43 45  NULL}

#### 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

z.gu authored on 06/07/2015 22:31:19
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 ... ... @@ -39,9 +39,5 @@ Zuguang Gu  39 39   40 40  } 41 41  \examples{ 42 - 43 - 44 42  # for examples, please go to SingleAnnotation method page 45 -NULL 46 - 47 -} 43 +NULL}

#### Commit made by the Bioconductor Git-SVN bridge.

Commit id: 9d7fc297a370b44dd3bfb12696ed9eac33aed48a

refreshed documentations

z.gu authored on 23/06/2015 10:24:06
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 ... ... @@ -40,6 +40,7 @@ Zuguang Gu  40 40  } 41 41  \examples{ 42 42   43 + 43 44  # for examples, please go to SingleAnnotation method page 44 45  NULL 45 46 

#### Commit made by the Bioconductor Git-SVN bridge.

refreshed documentations

z.gu authored on 23/06/2015 08:33:59
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 ... ... @@ -39,5 +39,8 @@ Zuguang Gu  39 39   40 40  } 41 41  \examples{ 42 + 42 43  # for examples, please go to SingleAnnotation method page 43 -NULL} 44 +NULL 45 + 46 +}

#### Commit made by the Bioconductor Git-SVN bridge.

refresh documentations and NAMESPACE

z.gu authored on 22/06/2015 21:57:04
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 ... ... @@ -2,43 +2,42 @@ 2 2  \docType{class} 3 3  \alias{SingleAnnotation-class} 4 4  \title{ 5 -Class for a single annotation  6 - 5 +Class for a single annotation 7 6   8 7  } 9 8  \description{ 10 -Class for a single annotation  11 - 9 +Class for a single annotation 12 10   13 11  } 14 12  \details{ 15 -A complex heatmap always has more than one annotations on rows and columns. Here the \code{\link{SingleAnnotation-class}} defines the basic unit of annotations. The most simple annotation is one row or one column grids in which different colors represent different classes of the data. The annotation can also be more complex graphics, such as a boxplot that shows data distribution in corresponding row or column.  16 - 17 -The \code{\link{SingleAnnotation-class}} is used for storing data for a single annotation and provides methods for drawing annotation graphics.  13 +A complex heatmap always has more than one annotations on rows and columns. Here 14 +the \code{\link{SingleAnnotation-class}} defines the basic unit of annotations. 15 +The most simple annotation is one row or one column grids in which different colors 16 +represent different classes of the data. The annotation can also be more complex 17 +graphics, such as a boxplot that shows data distribution in corresponding row or column. 18 18   19 +The \code{\link{SingleAnnotation-class}} is used for storing data for a single annotation and provides 20 +methods for drawing annotation graphics. 19 21   20 22  } 21 23  \section{Methods}{ 22 -The \code{\link{SingleAnnotation-class}} provides following methods:  24 +The \code{\link{SingleAnnotation-class}} provides following methods: 23 25   24 26  \itemize{ 25 27  \item \code{\link{SingleAnnotation}}: constructor method 26 28  \item \code{\link{draw,SingleAnnotation-method}}: draw the single annotation. 27 29  } 28 30   29 - 30 31  } 31 32  \seealso{ 32 -The \code{\link{SingleAnnotation-class}} is always used internally. The public \code{\link{HeatmapAnnotation-class}} contains a list of \code{\link{SingleAnnotation-class}} objects and is used to add annotation graphics on heatmaps.  33 - 33 +The \code{\link{SingleAnnotation-class}} is always used internally. The public \code{\link{HeatmapAnnotation-class}} 34 +contains a list of \code{\link{SingleAnnotation-class}} objects and is used to add annotation graphics on heatmaps. 34 35   35 36  } 36 37  \author{ 37 -Zuguang Gu  38 - 38 +Zuguang Gu  39 39   40 40  } 41 41  \examples{ 42 42  # for examples, please go to SingleAnnotation method page 43 -NULL 44 -} 43 +NULL}

#### Commit made by the Bioconductor Git-SVN bridge.

rotation for heatmap title supported

z.gu authored on 22/06/2015 15:09:06
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 ... ... @@ -2,42 +2,43 @@ 2 2  \docType{class} 3 3  \alias{SingleAnnotation-class} 4 4  \title{ 5 -Class for a single annotation 5 +Class for a single annotation  6 + 6 7   7 8  } 8 9  \description{ 9 -Class for a single annotation 10 +Class for a single annotation  11 + 10 12   11 13  } 12 14  \details{ 13 -A complex heatmap always has more than one annotations on rows and columns. Here 14 -the \code{\link{SingleAnnotation-class}} defines the basic unit of annotations. 15 -The most simple annotation is one row or one column grids in which different colors 16 -represent different classes of the data. The annotation can also be more complex 17 -graphics, such as a boxplot that shows data distribution in corresponding row or column. 15 +A complex heatmap always has more than one annotations on rows and columns. Here the \code{\link{SingleAnnotation-class}} defines the basic unit of annotations. The most simple annotation is one row or one column grids in which different colors represent different classes of the data. The annotation can also be more complex graphics, such as a boxplot that shows data distribution in corresponding row or column.  16 + 17 +The \code{\link{SingleAnnotation-class}} is used for storing data for a single annotation and provides methods for drawing annotation graphics.  18 18   19 -The \code{\link{SingleAnnotation-class}} is used for storing data for a single annotation and provides 20 -methods for drawing annotation graphics. 21 19   22 20  } 23 21  \section{Methods}{ 24 -The \code{\link{SingleAnnotation-class}} provides following methods: 22 +The \code{\link{SingleAnnotation-class}} provides following methods:  25 23   26 24  \itemize{ 27 25  \item \code{\link{SingleAnnotation}}: constructor method 28 26  \item \code{\link{draw,SingleAnnotation-method}}: draw the single annotation. 29 27  } 30 28   29 + 31 30  } 32 31  \seealso{ 33 -The \code{\link{SingleAnnotation-class}} is always used internally. The public \code{\link{HeatmapAnnotation-class}} 34 -contains a list of \code{\link{SingleAnnotation-class}} objects and is used to add annotation graphics on heatmaps. 32 +The \code{\link{SingleAnnotation-class}} is always used internally. The public \code{\link{HeatmapAnnotation-class}} contains a list of \code{\link{SingleAnnotation-class}} objects and is used to add annotation graphics on heatmaps.  33 + 35 34   36 35  } 37 36  \author{ 38 -Zuguang Gu  37 +Zuguang Gu  38 + 39 39   40 40  } 41 41  \examples{ 42 42  # for examples, please go to SingleAnnotation method page 43 -NULL} 43 +NULL 44 +}

#### Commit made by the Bioconductor Git-SVN bridge.

check row orders

z.gu authored on 21/06/2015 17:44:09
Showing1 changed files
 ... ... @@ -2,43 +2,42 @@ 2 2  \docType{class} 3 3  \alias{SingleAnnotation-class} 4 4  \title{ 5 -Class for a single annotation  6 - 5 +Class for a single annotation 7 6   8 7  } 9 8  \description{ 10 -Class for a single annotation  11 - 9 +Class for a single annotation 12 10   13 11  } 14 12  \details{ 15 -A complex heatmap always has more than one annotations on rows and columns. Here the \code{\link{SingleAnnotation-class}} defines the basic unit of annotations. The most simple annotation is one row or one column grids in which different colors represent different classes of the data. The annotation can also be more complex graphics, such as a boxplot that shows data distribution in corresponding row or column.  16 - 17 -The \code{\link{SingleAnnotation-class}} is used for storing data for a single annotation and provides methods for drawing annotation graphics.  13 +A complex heatmap always has more than one annotations on rows and columns. Here 14 +the \code{\link{SingleAnnotation-class}} defines the basic unit of annotations. 15 +The most simple annotation is one row or one column grids in which different colors 16 +represent different classes of the data. The annotation can also be more complex 17 +graphics, such as a boxplot that shows data distribution in corresponding row or column. 18 18   19 +The \code{\link{SingleAnnotation-class}} is used for storing data for a single annotation and provides 20 +methods for drawing annotation graphics. 19 21   20 22  } 21 23  \section{Methods}{ 22 -The \code{\link{SingleAnnotation-class}} provides following methods:  24 +The \code{\link{SingleAnnotation-class}} provides following methods: 23 25   24 26  \itemize{ 25 27  \item \code{\link{SingleAnnotation}}: constructor method 26 28  \item \code{\link{draw,SingleAnnotation-method}}: draw the single annotation. 27 29  } 28 30   29 - 30 31  } 31 32  \seealso{ 32 -The \code{\link{SingleAnnotation-class}} is always used internally. The public \code{\link{HeatmapAnnotation-class}} contains a list of \code{\link{SingleAnnotation-class}} objects and is used to add annotation graphics on heatmaps.  33 - 33 +The \code{\link{SingleAnnotation-class}} is always used internally. The public \code{\link{HeatmapAnnotation-class}} 34 +contains a list of \code{\link{SingleAnnotation-class}} objects and is used to add annotation graphics on heatmaps. 34 35   35 36  } 36 37  \author{ 37 -Zuguang Gu  38 - 38 +Zuguang Gu  39 39   40 40  } 41 41  \examples{ 42 42  # for examples, please go to SingleAnnotation method page 43 -NULL 44 -} 43 +NULL}

 1 1 new file mode 100644 ... ... @@ -0,0 +1,44 @@ 1 +\name{SingleAnnotation-class} 2 +\docType{class} 3 +\alias{SingleAnnotation-class} 4 +\title{ 5 +Class for a single annotation  6 + 7 + 8 +} 9 +\description{ 10 +Class for a single annotation  11 + 12 + 13 +} 14 +\details{ 15 +A complex heatmap always has more than one annotations on rows and columns. Here the \code{\link{SingleAnnotation-class}} defines the basic unit of annotations. The most simple annotation is one row or one column grids in which different colors represent different classes of the data. The annotation can also be more complex graphics, such as a boxplot that shows data distribution in corresponding row or column.  16 + 17 +The \code{\link{SingleAnnotation-class}} is used for storing data for a single annotation and provides methods for drawing annotation graphics.  18 + 19 + 20 +} 21 +\section{Methods}{ 22 +The \code{\link{SingleAnnotation-class}} provides following methods:  23 + 24 +\itemize{ 25 + \item \code{\link{SingleAnnotation}}: constructor method 26 + \item \code{\link{draw,SingleAnnotation-method}}: draw the single annotation. 27 +} 28 + 29 + 30 +} 31 +\seealso{ 32 +The \code{\link{SingleAnnotation-class}} is always used internally. The public \code{\link{HeatmapAnnotation-class}} contains a list of \code{\link{SingleAnnotation-class}} objects and is used to add annotation graphics on heatmaps.  33 + 34 + 35 +} 36 +\author{ 37 +Zuguang Gu  38 + 39 + 40 +} 41 +\examples{ 42 +# for examples, please go to SingleAnnotation method page 43 +NULL 44 +}