#### generate documentations by pkgdown

Zuguang Gu authored on 18/10/2019 11:34:02
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 1 1 deleted file mode 100644 ... ... @@ -1,44 +0,0 @@ 1 -\name{ComplexHeatmap-package} 2 -\docType{package} 3 -\alias{ComplexHeatmap-package} 4 -\title{ 5 -Make complex heatmaps 6 -} 7 -\description{ 8 -Make complex heatmaps 9 -} 10 -\details{ 11 -This package aims to provide a simple and flexible way to arrange 12 -multiple heatmaps as well as flexible annotation graphics. 13 - 14 -The package is implemented in an object-oriented way.  15 -The heatmap lists are abstracted into several classes. 16 - 17 -\itemize{ 18 - \item \code{\link{Heatmap-class}}: a single heatmap containing heatmap body, row/column names, titles, dendrograms and annotations. 19 - \item \code{\link{HeatmapList-class}}: a list of heatmaps and annotations. 20 - \item \code{\link{HeatmapAnnotation-class}}: a list of row/column annotations. 21 -} 22 - 23 -There are also several internal classes: 24 - 25 -\itemize{ 26 - \item \code{\link{SingleAnnotation-class}}: a single row annotation or column annotation. 27 - \item \code{\link{ColorMapping-class}}: mapping from values to colors. 28 - \item \code{\link{AnnotationFunction-class}}: construct an annotation function which allows subsetting. 29 -} 30 - 31 -Following two high-level functions take use of functionality of complex heatmaps: 32 - 33 -\itemize{ 34 - \item \code{\link{oncoPrint}}: oncoPrint plot which visualize genomic alterations in a set of genes. 35 - \item \code{\link{densityHeatmap}}: use heatmaps to visualize density distributions. 36 -} 37 - 38 -The complete reference of ComplexHeatmap package is available at \url{http://jokergoo.github.io/ComplexHeatmap-reference/book.} 39 -} 40 -\examples{ 41 -# There is no example 42 -NULL 43 - 44 -}

#### add jitter argument to Heatmap()

Zuguang Gu authored on 28/09/2019 08:37:13
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 ... ... @@ -40,4 +40,5 @@ The complete reference of ComplexHeatmap package is available at \url{http://jok 40 40  \examples{ 41 41  # There is no example 42 42  NULL 43 + 43 44  }

#### use pkgdown to build the doc site

Zuguang Gu authored on 24/09/2019 21:01:04
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 ... ... @@ -40,5 +40,4 @@ The complete reference of ComplexHeatmap package is available at \url{http://jok 40 40  \examples{ 41 41  # There is no example 42 42  NULL 43 - 44 43  }

#### set cluster_slice to FALSE for character matrix

Zuguang Gu authored on 18/01/2019 10:43:26
Showing1 changed files
 ... ... @@ -40,4 +40,5 @@ The complete reference of ComplexHeatmap package is available at \url{http://jok 40 40  \examples{ 41 41  # There is no example 42 42  NULL 43 + 43 44  }

Zuguang Gu authored on 30/12/2018 08:12:22
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 ... ... @@ -40,5 +40,4 @@ The complete reference of ComplexHeatmap package is available at \url{http://jok 40 40  \examples{ 41 41  # There is no example 42 42  NULL 43 - 44 43  }

#### documentation checked

Zuguang Gu authored on 23/10/2018 19:59:12
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 ... ... @@ -12,11 +12,11 @@ This package aims to provide a simple and flexible way to arrange 12 12  multiple heatmaps as well as flexible annotation graphics. 13 13   14 14  The package is implemented in an object-oriented way.  15 -Components of heatmap lists are abstracted into several classes. 15 +The heatmap lists are abstracted into several classes. 16 16   17 17  \itemize{ 18 - \item \code{\link{Heatmap-class}}: a single heatmap containing heatmap body, row/column names, titles, dendrograms and column annotations. 19 - \item \code{\link{HeatmapList-class}}: a list of heatmaps and row/column annotations. 18 + \item \code{\link{Heatmap-class}}: a single heatmap containing heatmap body, row/column names, titles, dendrograms and annotations. 19 + \item \code{\link{HeatmapList-class}}: a list of heatmaps and annotations. 20 20  \item \code{\link{HeatmapAnnotation-class}}: a list of row/column annotations. 21 21  } 22 22   ... ... @@ -28,10 +28,14 @@ There are also several internal classes: 28 28  \item \code{\link{AnnotationFunction-class}}: construct an annotation function which allows subsetting. 29 29  } 30 30   31 -For plotting one single heatmap, please go to the documentation page of \code{\link{Heatmap}}. 32 -For plotting multiple heatmaps, please go to \code{\link{HeatmapList-class}}, \code{+.AdditiveUnit} and \code{\%v\%.AdditiveUnit}. 31 +Following two high-level functions take use of functionality of complex heatmaps: 33 32   34 -You can refer to the ComplexHeatmap Complete Reference for all the information of this package (). 33 +\itemize{ 34 + \item \code{\link{oncoPrint}}: oncoPrint plot which visualize genomic alterations in a set of genes. 35 + \item \code{\link{densityHeatmap}}: use heatmaps to visualize density distributions. 36 +} 37 + 38 +The complete reference of ComplexHeatmap package is available at \url{http://jokergoo.github.io/ComplexHeatmap-reference/book.} 35 39  } 36 40  \examples{ 37 41  # There is no example

#### fix some bugs

Zuguang Gu authored on 19/10/2018 19:08:59
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 ... ... @@ -36,4 +36,5 @@ You can refer to the ComplexHeatmap Complete Reference for all the information o 36 36  \examples{ 37 37  # There is no example 38 38  NULL 39 + 39 40  }

#### update

Zuguang Gu authored on 17/10/2018 06:09:36
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 ... ... @@ -36,5 +36,4 @@ You can refer to the ComplexHeatmap Complete Reference for all the information o 36 36  \examples{ 37 37  # There is no example 38 38  NULL 39 - 40 39  }

#### R CMD check passed

Zuguang Gu authored on 12/10/2018 19:19:48
Showing1 changed files
 ... ... @@ -36,4 +36,5 @@ You can refer to the ComplexHeatmap Complete Reference for all the information o 36 36  \examples{ 37 37  # There is no example 38 38  NULL 39 + 39 40  }

#### update

jokergoo authored on 12/10/2018 15:28:37
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 ... ... @@ -2,22 +2,22 @@ 2 2  \docType{package} 3 3  \alias{ComplexHeatmap-package} 4 4  \title{ 5 -Making complex heatmap 5 +Make complex heatmaps 6 6  } 7 7  \description{ 8 -Making complex heatmap 8 +Make complex heatmaps 9 9  } 10 10  \details{ 11 11  This package aims to provide a simple and flexible way to arrange 12 -multiple heatmaps as well as self-defining annotation graphics. 12 +multiple heatmaps as well as flexible annotation graphics. 13 13   14 14  The package is implemented in an object-oriented way.  15 15  Components of heatmap lists are abstracted into several classes. 16 16   17 17  \itemize{ 18 18  \item \code{\link{Heatmap-class}}: a single heatmap containing heatmap body, row/column names, titles, dendrograms and column annotations. 19 - \item \code{\link{HeatmapList-class}}: a list of heatmaps and row annotations. 20 - \item \code{\link{HeatmapAnnotation-class}}: a list of row annotations or column annotations. 19 + \item \code{\link{HeatmapList-class}}: a list of heatmaps and row/column annotations. 20 + \item \code{\link{HeatmapAnnotation-class}}: a list of row/column annotations. 21 21  } 22 22   23 23  There are also several internal classes: ... ... @@ -31,10 +31,9 @@ There are also several internal classes: 31 31  For plotting one single heatmap, please go to the documentation page of \code{\link{Heatmap}}. 32 32  For plotting multiple heatmaps, please go to \code{\link{HeatmapList-class}}, \code{+.AdditiveUnit} and \code{\%v\%.AdditiveUnit}. 33 33   34 -The vignette provides detailed explanation of how to use this package. 34 +You can refer to the ComplexHeatmap Complete Reference for all the information of this package (). 35 35  } 36 36  \examples{ 37 37  # There is no example 38 38  NULL 39 - 40 39  }

#### vignette check passed

Zuguang Gu authored on 20/09/2018 22:09:48
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 ... ... @@ -36,4 +36,5 @@ The vignette provides detailed explanation of how to use this package. 36 36  \examples{ 37 37  # There is no example 38 38  NULL 39 + 39 40  }

#### 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 ... ... @@ -25,15 +25,15 @@ There are also several internal classes: 25 25  \itemize{ 26 26  \item \code{\link{SingleAnnotation-class}}: a single row annotation or column annotation. 27 27  \item \code{\link{ColorMapping-class}}: mapping from values to colors. 28 + \item \code{\link{AnnotationFunction-class}}: construct an annotation function which allows subsetting. 28 29  } 29 30   30 31  For plotting one single heatmap, please go to the documentation page of \code{\link{Heatmap}}. 31 -For plotting multiple heatmaps, please go to \code{\link{HeatmapList-class}} and \code{+.AdditiveUnit}. 32 +For plotting multiple heatmaps, please go to \code{\link{HeatmapList-class}}, \code{+.AdditiveUnit} and \code{\%v\%.AdditiveUnit}. 32 33   33 34  The vignette provides detailed explanation of how to use this package. 34 35  } 35 36  \examples{ 36 37  # There is no example 37 38  NULL 38 - 39 39  }

#### 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

#### resolve conflict from master branch

z.gu authored on 03/09/2015 20:32:44
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 ... ... @@ -32,3 +32,8 @@ For plotting multiple heatmaps, please go to \code{\link{HeatmapList-class}} and 32 32   33 33  The vignette provides detailed explanation of how to use this package. 34 34  } 35 +\examples{ 36 +# There is no example 37 +NULL 38 + 39 +}

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

Commit id: db263179df8a28bd25eb5afcf64aa9c37b2fdd32

refresh docs

z.gu authored on 12/08/2015 22:49:59
Showing1 changed files
 ... ... @@ -10,8 +10,10 @@ Making complex heatmap 10 10  \details{ 11 11  This package aims to provide a simple and flexible way to arrange 12 12  multiple heatmaps as well as self-defining annotation graphics. 13 + 13 14  The package is implemented in an object-oriented way.  14 15  Components of heatmap lists are abstracted into several classes. 16 + 15 17  \itemize{ 16 18  \item \code{\link{Heatmap-class}}: a single heatmap containing heatmap body, row/column names, titles, dendrograms and column annotations. 17 19  \item \code{\link{HeatmapList-class}}: a list of heatmaps and row annotations. ... ... @@ -19,6 +21,7 @@ Components of heatmap lists are abstracted into several classes. 19 21  } 20 22   21 23  There are also several internal classes: 24 + 22 25  \itemize{ 23 26  \item \code{\link{SingleAnnotation-class}}: a single row annotation or column annotation. 24 27  \item \code{\link{ColorMapping-class}}: mapping from values to colors. ... ... @@ -26,5 +29,6 @@ There are also several internal classes: 26 29   27 30  For plotting one single heatmap, please go to the documentation page of \code{\link{Heatmap}}. 28 31  For plotting multiple heatmaps, please go to \code{\link{HeatmapList-class}} and \code{+.AdditiveUnit}. 32 + 29 33  The vignette provides detailed explanation of how to use this package. 30 34  }

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

refreshed documentations

z.gu authored on 11/08/2015 10:42:08
Showing1 changed files
 ... ... @@ -3,19 +3,15 @@ 3 3  \alias{ComplexHeatmap-package} 4 4  \title{ 5 5  Making complex heatmap 6 - 7 6  } 8 7  \description{ 9 8  Making complex heatmap 10 - 11 9  } 12 10  \details{ 13 11  This package aims to provide a simple and flexible way to arrange 14 12  multiple heatmaps as well as self-defining annotation graphics. 15 - 16 13  The package is implemented in an object-oriented way.  17 14  Components of heatmap lists are abstracted into several classes. 18 - 19 15  \itemize{ 20 16  \item \code{\link{Heatmap-class}}: a single heatmap containing heatmap body, row/column names, titles, dendrograms and column annotations. 21 17  \item \code{\link{HeatmapList-class}}: a list of heatmaps and row annotations. ... ... @@ -23,7 +19,6 @@ Components of heatmap lists are abstracted into several classes. 23 19  } 24 20   25 21  There are also several internal classes: 26 - 27 22  \itemize{ 28 23  \item \code{\link{SingleAnnotation-class}}: a single row annotation or column annotation. 29 24  \item \code{\link{ColorMapping-class}}: mapping from values to colors. ... ... @@ -31,7 +26,5 @@ There are also several internal classes: 31 26   32 27  For plotting one single heatmap, please go to the documentation page of \code{\link{Heatmap}}. 33 28  For plotting multiple heatmaps, please go to \code{\link{HeatmapList-class}} and \code{+.AdditiveUnit}. 34 - 35 29  The vignette provides detailed explanation of how to use this package. 36 - 37 30  }

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

Commit id: dbcd94f09a509b142af23817e40c5b7b9e434c26

improved text in vignettes

z.gu authored on 07/07/2015 18:03:11
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 ... ... @@ -13,7 +13,7 @@ Making complex heatmap 13 13  This package aims to provide a simple and flexible way to arrange 14 14  multiple heatmaps as well as self-defining annotation graphics. 15 15   16 -The package is implemented in an object oriented way.  16 +The package is implemented in an object-oriented way.  17 17  Components of heatmap lists are abstracted into several classes. 18 18   19 19  \itemize{

#### 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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 ... ... @@ -2,19 +2,19 @@ 2 2  \docType{package} 3 3  \alias{ComplexHeatmap-package} 4 4  \title{ 5 -Making complex heatmap  6 - 5 +Making complex heatmap 7 6   8 7  } 9 8  \description{ 10 -Making complex heatmap  11 - 9 +Making complex heatmap 12 10   13 11  } 14 12  \details{ 15 -This package aims to provide a simple and flexible way to arrange multiple heatmaps as well as self-defining annotation graphics.  13 +This package aims to provide a simple and flexible way to arrange 14 +multiple heatmaps as well as self-defining annotation graphics. 16 15   17 -The package is implemented in an object oriented way. Components of heatmap lists are abstracted into several classes.  16 +The package is implemented in an object oriented way.  17 +Components of heatmap lists are abstracted into several classes. 18 18   19 19  \itemize{ 20 20  \item \code{\link{Heatmap-class}}: a single heatmap containing heatmap body, row/column names, titles, dendrograms and column annotations. ... ... @@ -22,16 +22,16 @@ The package is implemented in an object oriented way. Components of heatmap lis 22 22  \item \code{\link{HeatmapAnnotation-class}}: a list of row annotations or column annotations. 23 23  } 24 24   25 -There are also several internal classes:  25 +There are also several internal classes: 26 26   27 27  \itemize{ 28 28  \item \code{\link{SingleAnnotation-class}}: a single row annotation or column annotation. 29 29  \item \code{\link{ColorMapping-class}}: mapping from values to colors. 30 30  } 31 31   32 -For plotting one single heatmap, please go to the documentation page of \code{\link{Heatmap}}. For plotting multiple heatmaps, please go to \code{\link{HeatmapList-class}} and \code{+.AdditiveUnit}.  33 - 34 -The vignette provides detailed explanation of how to use this package.  32 +For plotting one single heatmap, please go to the documentation page of \code{\link{Heatmap}}. 33 +For plotting multiple heatmaps, please go to \code{\link{HeatmapList-class}} and \code{+.AdditiveUnit}. 35 34   35 +The vignette provides detailed explanation of how to use this package. 36 36   37 37  }

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

rotation for heatmap title supported

z.gu authored on 22/06/2015 15:09:06
Showing1 changed files
 ... ... @@ -2,19 +2,19 @@ 2 2  \docType{package} 3 3  \alias{ComplexHeatmap-package} 4 4  \title{ 5 -Making complex heatmap 5 +Making complex heatmap  6 + 6 7   7 8  } 8 9  \description{ 9 -Making complex heatmap 10 +Making complex heatmap  11 + 10 12   11 13  } 12 14  \details{ 13 -This package aims to provide a simple and flexible way to arrange 14 -multiple heatmaps as well as self-defining annotation graphics. 15 +This package aims to provide a simple and flexible way to arrange multiple heatmaps as well as self-defining annotation graphics.  15 16   16 -The package is implemented in an object oriented way.  17 -Components of heatmap lists are abstracted into several classes. 17 +The package is implemented in an object oriented way. Components of heatmap lists are abstracted into several classes.  18 18   19 19  \itemize{ 20 20  \item \code{\link{Heatmap-class}}: a single heatmap containing heatmap body, row/column names, titles, dendrograms and column annotations. ... ... @@ -22,16 +22,16 @@ Components of heatmap lists are abstracted into several classes. 22 22  \item \code{\link{HeatmapAnnotation-class}}: a list of row annotations or column annotations. 23 23  } 24 24   25 -There are also several internal classes: 25 +There are also several internal classes:  26 26   27 27  \itemize{ 28 28  \item \code{\link{SingleAnnotation-class}}: a single row annotation or column annotation. 29 29  \item \code{\link{ColorMapping-class}}: mapping from values to colors. 30 30  } 31 31   32 -For plotting one single heatmap, please go to the documentation page of \code{\link{Heatmap}}. 33 -For plotting multiple heatmaps, please go to \code{\link{HeatmapList-class}} and \code{+.AdditiveUnit}. 32 +For plotting one single heatmap, please go to the documentation page of \code{\link{Heatmap}}. For plotting multiple heatmaps, please go to \code{\link{HeatmapList-class}} and \code{+.AdditiveUnit}.  33 + 34 +The vignette provides detailed explanation of how to use this package.  34 35   35 -The vignette provides detailed explanation of how to use this package. 36 36   37 37  }

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

check row orders

z.gu authored on 21/06/2015 17:44:09
Showing1 changed files
 ... ... @@ -2,19 +2,19 @@ 2 2  \docType{package} 3 3  \alias{ComplexHeatmap-package} 4 4  \title{ 5 -Making complex heatmap  6 - 5 +Making complex heatmap 7 6   8 7  } 9 8  \description{ 10 -Making complex heatmap  11 - 9 +Making complex heatmap 12 10   13 11  } 14 12  \details{ 15 -This package aims to provide a simple and flexible way to arrange multiple heatmaps as well as self-defining annotation graphics.  13 +This package aims to provide a simple and flexible way to arrange 14 +multiple heatmaps as well as self-defining annotation graphics. 16 15   17 -The package is implemented in an object oriented way. Components of heatmap lists are abstracted into several classes.  16 +The package is implemented in an object oriented way.  17 +Components of heatmap lists are abstracted into several classes. 18 18   19 19  \itemize{ 20 20  \item \code{\link{Heatmap-class}}: a single heatmap containing heatmap body, row/column names, titles, dendrograms and column annotations. ... ... @@ -22,16 +22,16 @@ The package is implemented in an object oriented way. Components of heatmap lis 22 22  \item \code{\link{HeatmapAnnotation-class}}: a list of row annotations or column annotations. 23 23  } 24 24   25 -There are also several internal classes:  25 +There are also several internal classes: 26 26   27 27  \itemize{ 28 28  \item \code{\link{SingleAnnotation-class}}: a single row annotation or column annotation. 29 29  \item \code{\link{ColorMapping-class}}: mapping from values to colors. 30 30  } 31 31   32 -For plotting one single heatmap, please go to the documentation page of \code{\link{Heatmap}}. For plotting multiple heatmaps, please go to \code{\link{HeatmapList-class}} and \code{+.AdditiveUnit}.  33 - 34 -The vignette provides detailed explanation of how to use this package.  32 +For plotting one single heatmap, please go to the documentation page of \code{\link{Heatmap}}. 33 +For plotting multiple heatmaps, please go to \code{\link{HeatmapList-class}} and \code{+.AdditiveUnit}. 35 34   35 +The vignette provides detailed explanation of how to use this package. 36 36   37 37  }

 1 1 new file mode 100644 ... ... @@ -0,0 +1,37 @@ 1 +\name{ComplexHeatmap-package} 2 +\docType{package} 3 +\alias{ComplexHeatmap-package} 4 +\title{ 5 +Making complex heatmap  6 + 7 + 8 +} 9 +\description{ 10 +Making complex heatmap  11 + 12 + 13 +} 14 +\details{ 15 +This package aims to provide a simple and flexible way to arrange multiple heatmaps as well as self-defining annotation graphics.  16 + 17 +The package is implemented in an object oriented way. Components of heatmap lists are abstracted into several classes.  18 + 19 +\itemize{ 20 + \item \code{\link{Heatmap-class}}: a single heatmap containing heatmap body, row/column names, titles, dendrograms and column annotations. 21 + \item \code{\link{HeatmapList-class}}: a list of heatmaps and row annotations. 22 + \item \code{\link{HeatmapAnnotation-class}}: a list of row annotations or column annotations. 23 +} 24 + 25 +There are also several internal classes:  26 + 27 +\itemize{ 28 + \item \code{\link{SingleAnnotation-class}}: a single row annotation or column annotation. 29 + \item \code{\link{ColorMapping-class}}: mapping from values to colors. 30 +} 31 + 32 +For plotting one single heatmap, please go to the documentation page of \code{\link{Heatmap}}. For plotting multiple heatmaps, please go to \code{\link{HeatmapList-class}} and \code{+.AdditiveUnit}.  33 + 34 +The vignette provides detailed explanation of how to use this package.  35 + 36 + 37 +}