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generate documentations by pkgdown

Zuguang Gu authored on 18/10/2019 11:34:02
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-\name{ComplexHeatmap-package}
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-\docType{package}
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-\alias{ComplexHeatmap-package}
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-\title{
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-Make complex heatmaps
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-}
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-\description{
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-Make complex heatmaps
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-}
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-\details{
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-This package aims to provide a simple and flexible way to arrange
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-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{
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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 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
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 NULL
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+
43 44
 }
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use pkgdown to build the doc site

Zuguang Gu authored on 24/09/2019 21:01:04
Showing1 changed files
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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
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-
44 43
 }
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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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@@ -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
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+
43 44
 }
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add NEWs

Zuguang Gu authored on 30/12/2018 08:12:22
Showing1 changed files
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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
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-
44 43
 }
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documentation checked

Zuguang Gu authored on 23/10/2018 19:59:12
Showing1 changed files
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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
Browse code

fix some bugs

Zuguang Gu authored on 19/10/2018 19:08:59
Showing1 changed files
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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
 }
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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
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 NULL
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-
40 39
 }
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R CMD check passed

Zuguang Gu authored on 12/10/2018 19:19:48
Showing1 changed files
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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
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 NULL
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+
39 40
 }
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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
 }
Browse code

vignette check passed

Zuguang Gu authored on 20/09/2018 22:09:48
Showing1 changed files
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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
 }
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
... ...
@@ -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
 }
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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@@ -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
+}
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
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@@ -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
 }
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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@@ -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
 }
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: dbcd94f09a509b142af23817e40c5b7b9e434c26

improved text in vignettes



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105881 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 07/07/2015 18:03:11
Showing1 changed files
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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{
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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@@ -2,19 +2,19 @@
2 2
 \docType{package}
3 3
 \alias{ComplexHeatmap-package}
4 4
 \title{
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-Making complex heatmap  
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-
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
 }
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
... ...
@@ -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
 }
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
... ...
@@ -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
 }
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 +1,37 @@
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
+}
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+
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+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}.  
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+
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+The vignette provides detailed explanation of how to use this package.  
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+
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+
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+}