1. ComplexHeatmap
  2. man
  3. ComplexHeatmap-package.rd
Browse code

generate documentations by pkgdown

Zuguang Gu authored on 18/10/2019 11:34:02
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man/ComplexHeatmap-package.rd
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1 
-\name{ComplexHeatmap-package}
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-\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 
-}
Browse code

add jitter argument to Heatmap()

Zuguang Gu authored on 28/09/2019 08:37:13
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man/ComplexHeatmap-package.rd
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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 
 }
Browse code

use pkgdown to build the doc site

Zuguang Gu authored on 24/09/2019 21:01:04
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man/ComplexHeatmap-package.rd
History View file @21aea96
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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
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 NULL
43 
-
44 43 
 }
Browse code

set cluster_slice to FALSE for character matrix

Zuguang Gu authored on 18/01/2019 10:43:26
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man/ComplexHeatmap-package.rd
History View file @69345c7
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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 
 }
Browse code

add NEWs

Zuguang Gu authored on 30/12/2018 08:12:22
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man/ComplexHeatmap-package.rd
History View file @948414f
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@@ -40,5 +40,4 @@ The complete reference of ComplexHeatmap package is available at \url{http://jok
40 40 
 \examples{
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 # There is no example
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 NULL
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-
44 43 
 }
Browse code

documentation checked

Zuguang Gu authored on 23/10/2018 19:59:12
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man/ComplexHeatmap-package.rd
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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
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man/ComplexHeatmap-package.rd
History View file @864bd88
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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 
 }
Browse code

update

Zuguang Gu authored on 17/10/2018 06:09:36
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man/ComplexHeatmap-package.rd
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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 
 }
Browse code

R CMD check passed

Zuguang Gu authored on 12/10/2018 19:19:48
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man/ComplexHeatmap-package.rd
History View file @b8dacfc
... ... 
@@ -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 
 }
Browse code

update

jokergoo authored on 12/10/2018 15:28:37
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man/ComplexHeatmap-package.rd
History View file @1a56796
... ... 
@@ -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
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man/ComplexHeatmap-package.rd
History View file @249fdfa
... ... 
@@ -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
man/ComplexHeatmap-package.rd
History View file @ad35494
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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man/ComplexHeatmap-package.rd
History View file @8e55abf
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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man/ComplexHeatmap-package.rd
History View file @12e8549
... ... 
@@ -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
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man/ComplexHeatmap-package.rd
History View file @7ab3fd2
... ... 
@@ -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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man/ComplexHeatmap-package.rd
History View file @f597719
... ... 
@@ -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
man/ComplexHeatmap-package.rd
History View file @2c7a208
... ... 
@@ -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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man/ComplexHeatmap-package.rd
History View file @6f1307c
... ... 
@@ -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

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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man/ComplexHeatmap-package.rd
History View file @4818ea9
... ... 
@@ -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
man/ComplexHeatmap-package.rd
History View file @f0eb7a9
... ... 
@@ -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
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man/ComplexHeatmap-package.rd
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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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+Making complex heatmap
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+
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+
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+}
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+\description{
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+Making complex heatmap
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+
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+
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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 multiple heatmaps as well as self-defining annotation graphics.
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+
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+The package is implemented in an object oriented way.  Components of heatmap lists are abstracted into several classes.
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+
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+\itemize{
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+  \item \code{\link{Heatmap-class}}: a single heatmap containing heatmap body, row/column names, titles, dendrograms and column annotations.
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+  \item \code{\link{HeatmapList-class}}: a list of heatmaps and row annotations.
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+  \item \code{\link{HeatmapAnnotation-class}}: a list of row annotations or column annotations.
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+}
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+
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+There are also several internal classes:
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+
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+\itemize{
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+  \item \code{\link{SingleAnnotation-class}}: a single row annotation or column annotation.
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+  \item \code{\link{ColorMapping-class}}: mapping from values to colors.
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+}
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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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+}