1. ComplexHeatmap
  2. man
  3. Heatmap-class.rd
Browse code

generate documentations by pkgdown

Zuguang Gu authored on 18/10/2019 11:34:02
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man/Heatmap-class.rd
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deleted file mode 100644
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@@ -1,34 +0,0 @@
1 
-\name{Heatmap-class}
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-\docType{class}
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-\alias{Heatmap-class}
4 
-\title{
5 
-Class for a Single Heatmap
6 
-}
7 
-\description{
8 
-Class for a Single Heatmap
9 
-}
10 
-\details{
11 
-The \code{\link{Heatmap-class}} is not responsible for heatmap legend and annotation legends. The \code{\link{draw,Heatmap-method}} method
12 
-constructs a \code{\link{HeatmapList-class}} object which only contains one single heatmap
13 
-and call \code{\link{draw,HeatmapList-method}} to make the complete heatmap.
14 
-}
15 
-\section{Methods}{
16 
-The \code{\link{Heatmap-class}} provides following methods:
17 
-
18 
-\itemize{
19 
-  \item \code{\link{Heatmap}}: constructor method.
20 
-  \item \code{\link{draw,Heatmap-method}}: draw a single heatmap.
21 
-  \item \code{\link{add_heatmap,Heatmap-method}} append heatmaps and annotations to a list of heatmaps.
22 
-  \item \code{\link{row_order,HeatmapList-method}}: get order of rows
23 
-  \item \code{\link{column_order,HeatmapList-method}}: get order of columns
24 
-  \item \code{\link{row_dend,HeatmapList-method}}: get row dendrograms
25 
-  \item \code{\link{column_dend,HeatmapList-method}}: get column dendrograms
26 
-}}
27 
-\author{
28 
-Zuguang Gu <z.gu@dkfz.de>
29 
-}
30 
-\examples{
31 
-# There is no example
32 
-NULL
33 
-
34 
-}
Browse code

add jitter argument to Heatmap()

Zuguang Gu authored on 28/09/2019 08:37:13
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man/Heatmap-class.rd
History View file @9e95ee3
... ... 
@@ -30,4 +30,5 @@ Zuguang Gu <z.gu@dkfz.de>
30 30 
 \examples{
31 31 
 # There is no example
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 NULL
33 
+
33 34 
 }
Browse code

use pkgdown to build the doc site

Zuguang Gu authored on 24/09/2019 21:01:04
Showing1 changed files
man/Heatmap-class.rd
History View file @21aea96
... ... 
@@ -30,5 +30,4 @@ Zuguang Gu <z.gu@dkfz.de>
30 30 
 \examples{
31 31 
 # There is no example
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 NULL
33 
-
34 33 
 }
Browse code

set cluster_slice to FALSE for character matrix

Zuguang Gu authored on 18/01/2019 10:43:26
Showing1 changed files
man/Heatmap-class.rd
History View file @69345c7
... ... 
@@ -30,4 +30,5 @@ Zuguang Gu <z.gu@dkfz.de>
30 30 
 \examples{
31 31 
 # There is no example
32 32 
 NULL
33 
+
33 34 
 }
Browse code

add NEWs

Zuguang Gu authored on 30/12/2018 08:12:22
Showing1 changed files
man/Heatmap-class.rd
History View file @948414f
... ... 
@@ -30,5 +30,4 @@ Zuguang Gu <z.gu@dkfz.de>
30 30 
 \examples{
31 31 
 # There is no example
32 32 
 NULL
33 
-
34 33 
 }
Browse code

documentation checked

Zuguang Gu authored on 23/10/2018 19:59:12
Showing1 changed files
man/Heatmap-class.rd
History View file @3c40a7c
... ... 
@@ -2,15 +2,15 @@
2 2 
 \docType{class}
3 3 
 \alias{Heatmap-class}
4 4 
 \title{
5 
-Class for a single heatmap
5 
+Class for a Single Heatmap
6 6 
 }
7 7 
 \description{
8 
-Class for a single heatmap
8 
+Class for a Single Heatmap
9 9 
 }
10 10 
 \details{
11 11 
 The \code{\link{Heatmap-class}} is not responsible for heatmap legend and annotation legends. The \code{\link{draw,Heatmap-method}} method
12 
-will construct a \code{\link{HeatmapList-class}} object which only contains one single heatmap
13 
-and call \code{\link{draw,HeatmapList-method}} to make a complete heatmap.
12 
+constructs a \code{\link{HeatmapList-class}} object which only contains one single heatmap
13 
+and call \code{\link{draw,HeatmapList-method}} to make the complete heatmap.
14 14 
 }
15 15 
 \section{Methods}{
16 16 
 The \code{\link{Heatmap-class}} provides following methods:
... ... 
@@ -18,7 +18,7 @@ The \code{\link{Heatmap-class}} provides following methods:
18 18 
 \itemize{
19 19 
   \item \code{\link{Heatmap}}: constructor method.
20 20 
   \item \code{\link{draw,Heatmap-method}}: draw a single heatmap.
21 
-  \item \code{\link{add_heatmap,Heatmap-method}} append heatmaps and row annotations to a list of heatmaps.
21 
+  \item \code{\link{add_heatmap,Heatmap-method}} append heatmaps and annotations to a list of heatmaps.
22 22 
   \item \code{\link{row_order,HeatmapList-method}}: get order of rows
23 23 
   \item \code{\link{column_order,HeatmapList-method}}: get order of columns
24 24 
   \item \code{\link{row_dend,HeatmapList-method}}: get row dendrograms
Browse code

fix some bugs

Zuguang Gu authored on 19/10/2018 19:08:59
Showing1 changed files
man/Heatmap-class.rd
History View file @864bd88
... ... 
@@ -30,4 +30,5 @@ Zuguang Gu <z.gu@dkfz.de>
30 30 
 \examples{
31 31 
 # There is no example
32 32 
 NULL
33 
+
33 34 
 }
Browse code

update

Zuguang Gu authored on 17/10/2018 06:09:36
Showing1 changed files
man/Heatmap-class.rd
History View file @d9834c5
... ... 
@@ -30,5 +30,4 @@ Zuguang Gu <z.gu@dkfz.de>
30 30 
 \examples{
31 31 
 # There is no example
32 32 
 NULL
33 
-
34 33 
 }
Browse code

R CMD check passed

Zuguang Gu authored on 12/10/2018 19:19:48
Showing1 changed files
man/Heatmap-class.rd
History View file @b8dacfc
... ... 
@@ -30,4 +30,5 @@ Zuguang Gu <z.gu@dkfz.de>
30 30 
 \examples{
31 31 
 # There is no example
32 32 
 NULL
33 
+
33 34 
 }
Browse code

update

jokergoo authored on 12/10/2018 15:28:37
Showing1 changed files
man/Heatmap-class.rd
History View file @1a56796
... ... 
@@ -8,47 +8,6 @@ Class for a single heatmap
8 8 
 Class for a single heatmap
9 9 
 }
10 10 
 \details{
11 
-The components for a single heamtap are placed into a 9 x 7 layout:
12 
-
13 
-  \preformatted{
14 
-         +------+ (1)
15 
-         +------+ (2)
16 
-         +------+ (3)
17 
-         +------+ (4)
18 
-   +-+-+-+------+-+-+-+
19 
-   |1|2|3| 4(5) |5|6|7|
20 
-   +-+-+-+------+-+-+-+
21 
-         +------+ (6)
22 
-         +------+ (7)
23 
-         +------+ (8)
24 
-         +------+ (9)  }
25 
-
26 
-From top to bottom in column 4, the regions are:
27 
-
28 
-\itemize{
29 
-  \item title which is put on the top of the heatmap, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
30 
-  \item column cluster on the top, graphics are drawn by \code{\link{draw_dend,Heatmap-method}}.
31 
-  \item column annotation on the top, graphics are drawn by \code{\link{draw_annotation,Heatmap-method}}.
32 
-  \item column names on the top, graphics are drawn by \code{\link{draw_dimnames,Heatmap-method}}.
33 
-  \item heatmap body, graphics are drawn by \code{\link{draw_heatmap_body,Heatmap-method}}.
34 
-  \item column names on the bottom, graphics are drawn by \code{\link{draw_dimnames,Heatmap-method}}.
35 
-  \item column annotation on the bottom, graphics are drawn by \code{\link{draw_annotation,Heatmap-method}}.
36 
-  \item column cluster on the bottom, graphics are drawn by \code{\link{draw_dend,Heatmap-method}}.
37 
-  \item title on the bottom, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
38 
-}
39 
-
40 
-From left to right in row 5, the regions are:
41 
-
42 
-\itemize{
43 
-  \item title which is put in the left of the heatmap, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
44 
-  \item row cluster on the left, graphics are drawn by \code{\link{draw_dend,Heatmap-method}}.
45 
-  \item row names on the left, graphics are drawn by \code{\link{draw_dimnames,Heatmap-method}}.
46 
-  \item heatmap body
47 
-  \item row names on the right, graphics are drawn by \code{\link{draw_dimnames,Heatmap-method}}.
48 
-  \item row cluster on the right, graphics are drawn by \code{\link{draw_dend,Heatmap-method}}.
49 
-  \item title on the right, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
50 
-}
51 
-
52 11 
 The \code{\link{Heatmap-class}} is not responsible for heatmap legend and annotation legends. The \code{\link{draw,Heatmap-method}} method
53 12 
 will construct a \code{\link{HeatmapList-class}} object which only contains one single heatmap
54 13 
 and call \code{\link{draw,HeatmapList-method}} to make a complete heatmap.
... ... 
@@ -71,5 +30,4 @@ Zuguang Gu <z.gu@dkfz.de>
71 30 
 \examples{
72 31 
 # There is no example
73 32 
 NULL
74 
-
75 33 
 }
Browse code

vignette check passed

Zuguang Gu authored on 20/09/2018 22:09:48
Showing1 changed files
man/Heatmap-class.rd
History View file @249fdfa
... ... 
@@ -71,4 +71,5 @@ Zuguang Gu <z.gu@dkfz.de>
71 71 
 \examples{
72 72 
 # There is no example
73 73 
 NULL
74 
+
74 75 
 }
Browse code

R CMD check passed

Zuguang Gu authored on 20/09/2018 12:48:08
Showing1 changed files
man/Heatmap-class.rd
History View file @ad35494
1 1 
old mode 100755
2 2 
new mode 100644
... ... 
@@ -69,7 +69,6 @@ The \code{\link{Heatmap-class}} provides following methods:
69 69 
 Zuguang Gu <z.gu@dkfz.de>
70 70 
 }
71 71 
 \examples{
72 
-# for examples, please go to `Heatmap` method page
72 
+# There is no example
73 73 
 NULL
74 
-
75 74 
 }
Browse code

revised documentations

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@114991 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 19/03/2016 17:59:18
Showing1 changed files
man/Heatmap-class.rd
History View file @378e502
... ... 
@@ -60,6 +60,10 @@ The \code{\link{Heatmap-class}} provides following methods:
60 60 
   \item \code{\link{Heatmap}}: constructor method.
61 61 
   \item \code{\link{draw,Heatmap-method}}: draw a single heatmap.
62 62 
   \item \code{\link{add_heatmap,Heatmap-method}} append heatmaps and row annotations to a list of heatmaps.
63 
+  \item \code{\link{row_order,HeatmapList-method}}: get order of rows
64 
+  \item \code{\link{column_order,HeatmapList-method}}: get order of columns
65 
+  \item \code{\link{row_dend,HeatmapList-method}}: get row dendrograms
66 
+  \item \code{\link{column_dend,HeatmapList-method}}: get column dendrograms
63 67 
 }}
64 68 
 \author{
65 69 
 Zuguang Gu <z.gu@dkfz.de>
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
Showing1 changed files
man/Heatmap-class.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
Showing1 changed files
man/Heatmap-class.rd
History View file @12e8549
... ... 
@@ -11,7 +11,7 @@ Class for a single heatmap
11 11 
 The components for a single heamtap are placed into a 9 x 7 layout:
12 12
13 13 
   \preformatted{
14 
-+------+ (1)
14 
+         +------+ (1)
15 15 
          +------+ (2)
16 16 
          +------+ (3)
17 17 
          +------+ (4)
... ... 
@@ -27,13 +27,13 @@ From top to bottom in column 4, the regions are:
27 27
28 28 
 \itemize{
29 29 
   \item title which is put on the top of the heatmap, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
30 
-  \item column cluster on the top, graphics are drawn by \code{\link{draw_hclust,Heatmap-method}}.
30 
+  \item column cluster on the top, graphics are drawn by \code{\link{draw_dend,Heatmap-method}}.
31 31 
   \item column annotation on the top, graphics are drawn by \code{\link{draw_annotation,Heatmap-method}}.
32 32 
   \item column names on the top, graphics are drawn by \code{\link{draw_dimnames,Heatmap-method}}.
33 33 
   \item heatmap body, graphics are drawn by \code{\link{draw_heatmap_body,Heatmap-method}}.
34 34 
   \item column names on the bottom, graphics are drawn by \code{\link{draw_dimnames,Heatmap-method}}.
35 35 
   \item column annotation on the bottom, graphics are drawn by \code{\link{draw_annotation,Heatmap-method}}.
36 
-  \item column cluster on the bottom, graphics are drawn by \code{\link{draw_hclust,Heatmap-method}}.
36 
+  \item column cluster on the bottom, graphics are drawn by \code{\link{draw_dend,Heatmap-method}}.
37 37 
   \item title on the bottom, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
38 38 
 }
39 39
... ... 
@@ -41,11 +41,11 @@ From left to right in row 5, the regions are:
41 41
42 42 
 \itemize{
43 43 
   \item title which is put in the left of the heatmap, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
44 
-  \item row cluster on the left, graphics are drawn by \code{\link{draw_hclust,Heatmap-method}}.
44 
+  \item row cluster on the left, graphics are drawn by \code{\link{draw_dend,Heatmap-method}}.
45 45 
   \item row names on the left, graphics are drawn by \code{\link{draw_dimnames,Heatmap-method}}.
46 46 
   \item heatmap body
47 47 
   \item row names on the right, graphics are drawn by \code{\link{draw_dimnames,Heatmap-method}}.
48 
-  \item row cluster on the right, graphics are drawn by \code{\link{draw_hclust,Heatmap-method}}.
48 
+  \item row cluster on the right, graphics are drawn by \code{\link{draw_dend,Heatmap-method}}.
49 49 
   \item title on the right, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
50 50 
 }
51 51
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
man/Heatmap-class.rd
History View file @7ab3fd2
... ... 
@@ -9,6 +9,7 @@ Class for a single heatmap
9 9 
 }
10 10 
 \details{
11 11 
 The components for a single heamtap are placed into a 9 x 7 layout:
12 
+
12 13 
   \preformatted{
13 14 
 +------+ (1)
14 15 
          +------+ (2)
... ... 
@@ -23,6 +24,7 @@ The components for a single heamtap are placed into a 9 x 7 layout:
23 24 
          +------+ (9)  }
24 25
25 26 
 From top to bottom in column 4, the regions are:
27 
+
26 28 
 \itemize{
27 29 
   \item title which is put on the top of the heatmap, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
28 30 
   \item column cluster on the top, graphics are drawn by \code{\link{draw_hclust,Heatmap-method}}.
... ... 
@@ -36,6 +38,7 @@ From top to bottom in column 4, the regions are:
36 38 
 }
37 39
38 40 
 From left to right in row 5, the regions are:
41 
+
39 42 
 \itemize{
40 43 
   \item title which is put in the left of the heatmap, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
41 44 
   \item row cluster on the left, graphics are drawn by \code{\link{draw_hclust,Heatmap-method}}.
... ... 
@@ -52,6 +55,7 @@ and call \code{\link{draw,HeatmapList-method}} to make a complete heatmap.
52 55 
 }
53 56 
 \section{Methods}{
54 57 
 The \code{\link{Heatmap-class}} provides following methods:
58 
+
55 59 
 \itemize{
56 60 
   \item \code{\link{Heatmap}}: constructor method.
57 61 
   \item \code{\link{draw,Heatmap-method}}: draw a single heatmap.
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 1de356e1d1343725223e03ff696f931d80b2842b

Merge branch 'master' of https://github.com/jokergoo/mheatmap


Commit id: 478962957a34b7a5e87c8336989bae3df54f9559

change default colors



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107356 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 12/08/2015 22:03:22
Showing1 changed files
man/Heatmap-class.rd
History View file @ba8a507
... ... 
@@ -20,8 +20,7 @@ The components for a single heamtap are placed into a 9 x 7 layout:
20 20 
          +------+ (6)
21 21 
          +------+ (7)
22 22 
          +------+ (8)
23 
-         +------+ (9)
24 
-  }
23 
+         +------+ (9)  }
25 24
26 25 
 From top to bottom in column 4, the regions are:
27 26 
 \itemize{
... ... 
@@ -57,13 +56,12 @@ The \code{\link{Heatmap-class}} provides following methods:
57 56 
   \item \code{\link{Heatmap}}: constructor method.
58 57 
   \item \code{\link{draw,Heatmap-method}}: draw a single heatmap.
59 58 
   \item \code{\link{add_heatmap,Heatmap-method}} append heatmaps and row annotations to a list of heatmaps.
60 
-}
61 
-
62 
-}
59 
+}}
63 60 
 \author{
64 61 
 Zuguang Gu <z.gu@dkfz.de>
65 62 
 }
66 63 
 \examples{
67 64 
 # for examples, please go to `Heatmap` method page
68 65 
 NULL
66 
+
69 67 
 }
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
Showing1 changed files
man/Heatmap-class.rd
History View file @f597719
... ... 
@@ -3,17 +3,14 @@
3 3 
 \alias{Heatmap-class}
4 4 
 \title{
5 5 
 Class for a single heatmap
6 
-
7 6 
 }
8 7 
 \description{
9 8 
 Class for a single heatmap
10 
-
11 9 
 }
12 10 
 \details{
13 11 
 The components for a single heamtap are placed into a 9 x 7 layout:
14 
-
15 12 
   \preformatted{
16 
-         +------+ (1)
13 
++------+ (1)
17 14 
          +------+ (2)
18 15 
          +------+ (3)
19 16 
          +------+ (4)
... ... 
@@ -27,7 +24,6 @@ The components for a single heamtap are placed into a 9 x 7 layout:
27 24 
   }
28 25
29 26 
 From top to bottom in column 4, the regions are:
30 
-
31 27 
 \itemize{
32 28 
   \item title which is put on the top of the heatmap, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
33 29 
   \item column cluster on the top, graphics are drawn by \code{\link{draw_hclust,Heatmap-method}}.
... ... 
@@ -41,7 +37,6 @@ From top to bottom in column 4, the regions are:
41 37 
 }
42 38
43 39 
 From left to right in row 5, the regions are:
44 
-
45 40 
 \itemize{
46 41 
   \item title which is put in the left of the heatmap, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
47 42 
   \item row cluster on the left, graphics are drawn by \code{\link{draw_hclust,Heatmap-method}}.
... ... 
@@ -55,11 +50,9 @@ From left to right in row 5, the regions are:
55 50 
 The \code{\link{Heatmap-class}} is not responsible for heatmap legend and annotation legends. The \code{\link{draw,Heatmap-method}} method
56 51 
 will construct a \code{\link{HeatmapList-class}} object which only contains one single heatmap
57 52 
 and call \code{\link{draw,HeatmapList-method}} to make a complete heatmap.
58 
-
59 53 
 }
60 54 
 \section{Methods}{
61 55 
 The \code{\link{Heatmap-class}} provides following methods:
62 
-
63 56 
 \itemize{
64 57 
   \item \code{\link{Heatmap}}: constructor method.
65 58 
   \item \code{\link{draw,Heatmap-method}}: draw a single heatmap.
... ... 
@@ -69,20 +62,8 @@ The \code{\link{Heatmap-class}} provides following methods:
69 62 
 }
70 63 
 \author{
71 64 
 Zuguang Gu <z.gu@dkfz.de>
72 
-
73 65 
 }
74 66 
 \examples{
75 
-
76 
-
77 
-
78 
-
79 
-
80 
-
81 
-
82 
-
83 
-
84 
-
85 
-
86 
-
87 67 
 # for examples, please go to `Heatmap` method page
88 
-NULL}
68 
+NULL
69 
+}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 262e3960558c1f61b986f5be7a2ffd4599f704fa

comprehensive modifications



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107311 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 10/08/2015 22:17:54
Showing1 changed files
man/Heatmap-class.rd
History View file @5ab2cb8
... ... 
@@ -79,5 +79,10 @@ Zuguang Gu <z.gu@dkfz.de>
79 79
80 80
81 81
82 
+
83 
+
84 
+
85 
+
86 
+
82 87 
 # for examples, please go to `Heatmap` method page
83 88 
 NULL}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 73171be89c157222e8e71e85daa8a37ce509a4e2

add border argument in anno_* family functions



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107201 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 06/08/2015 17:46:06
Showing1 changed files
man/Heatmap-class.rd
History View file @aee203e
... ... 
@@ -78,5 +78,6 @@ Zuguang Gu <z.gu@dkfz.de>
78 78
79 79
80 80
81 
+
81 82 
 # for examples, please go to `Heatmap` method page
82 83 
 NULL}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 3429d28233ef2cbeafcd05307042d7c7aa54a2a2

add decorate* family functions



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107197 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 06/08/2015 16:40:59
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man/Heatmap-class.rd
History View file @7f268ee
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@@ -74,5 +74,9 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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+
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+
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+
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+
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 # for examples, please go to `Heatmap` method page
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 NULL}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: d5adc92bdbf27b45a6a4b5c7e29d2e4fe8380194

allow reordering



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107130 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 04/08/2015 20:24:37
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man/Heatmap-class.rd
History View file @dc0f5a9
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@@ -72,5 +72,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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+
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 # for examples, please go to `Heatmap` method page
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 NULL}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 174dbdcbcad3be858d664784793f1b2424acc2c0

remove plot.HeatmapList and print.HeatmapList



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@106530 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 18/07/2015 18:14:29
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man/Heatmap-class.rd
History View file @b08d7ba
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@@ -72,6 +72,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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-
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 # for examples, please go to `Heatmap` method page
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 NULL}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 4cbce102eabb1633fc8980b1374795bfb44507df

Merge branch 'master' of https://github.com/jokergoo/ComplexHeatmap


Commit id: a15bbec76c85c15bc27273ce15f5118ea087132f

refreshed documentatinos


Commit id: b1fe0a94aa09a4a47e5a02383ce662580f057bdc

ColorMapping object has default value for name slot



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@106487 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 16/07/2015 15:21:23
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man/Heatmap-class.rd
History View file @3bb5581
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@@ -72,5 +72,6 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # for examples, please go to `Heatmap` method page
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 NULL}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: ff9ffa810ca9f16a253861d97301062962dbe38b

titles support expression now



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@106147 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 13/07/2015 21:26:16
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man/Heatmap-class.rd
History View file @0725063
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@@ -72,7 +72,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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-
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-
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 # for examples, please go to `Heatmap` method page
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 NULL}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: e811f8100ef035ff75c16312b3e5112cc82d4a49

continuous legend is supported



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@106027 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 13/07/2015 10:21:55
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man/Heatmap-class.rd
History View file @2224e09
... ... 
@@ -72,5 +72,7 @@ Zuguang Gu <z.gu@dkfz.de>
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73 73 
 }
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 \examples{
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+
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+
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 # for examples, please go to `Heatmap` method page
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 NULL}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 2786dac4ddaa97c69cc24e29e121ed1a1624cdf4

Merge branch 'master' of https://github.com/jokergoo/mheatmap


Commit id: a61c101325601aa0d4d3ba81e10c33d4a8b34c63

rows can be split if providing a clustering object



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105855 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 06/07/2015 22:31:19
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man/Heatmap-class.rd
History View file @07961c6
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@@ -72,9 +72,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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-
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-
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 # for examples, please go to `Heatmap` method page
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-NULL
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-
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-}
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+NULL}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 9d7fc297a370b44dd3bfb12696ed9eac33aed48a

refreshed documentations



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105365 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 23/06/2015 10:24:06
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man/Heatmap-class.rd
History View file @10b246c
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@@ -73,6 +73,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # for examples, please go to `Heatmap` method page
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 NULL
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Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 1d5cea822fed8ed91d7ead49f520f719b3fecfd9

refreshed documentations



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105355 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 23/06/2015 08:33:59
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man/Heatmap-class.rd
History View file @7f6dddf
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@@ -72,5 +72,8 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # for examples, please go to `Heatmap` method page
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-NULL}
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+NULL
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+
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+}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 1682e4aed696b8fa901530ebc6b9d67ad2a013ad

refresh documentations and NAMESPACE



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105345 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 22/06/2015 21:57:04
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man/Heatmap-class.rd
History View file @6f1307c
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@@ -2,17 +2,15 @@
2 2 
 \docType{class}
3 3 
 \alias{Heatmap-class}
4 4 
 \title{
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-Class for a single heatmap
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-
5 
+Class for a single heatmap
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8 7 
 }
9 8 
 \description{
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-Class for a single heatmap
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-
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+Class for a single heatmap
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13 11 
 }
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 \details{
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-The components for a single heamtap are placed into a 9 x 7 layout:
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+The components for a single heamtap are placed into a 9 x 7 layout:
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   \preformatted{
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          +------+ (1)
... ... 
@@ -28,7 +26,7 @@ The components for a single heamtap are placed into a 9 x 7 layout:
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          +------+ (9)
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   }
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-From top to bottom in column 4, the regions are:
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+From top to bottom in column 4, the regions are:
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 \itemize{
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   \item title which is put on the top of the heatmap, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
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@@ -42,7 +40,7 @@ From top to bottom in column 4, the regions are:
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   \item title on the bottom, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
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 }
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-From left to right in row 5, the regions are:
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+From left to right in row 5, the regions are:
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 \itemize{
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   \item title which is put in the left of the heatmap, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
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@@ -54,12 +52,13 @@ From left to right in row 5, the regions are:
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   \item title on the right, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
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 }
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-The \code{\link{Heatmap-class}} is not responsible for heatmap legend and annotation legends. The \code{\link{draw,Heatmap-method}} method will construct a \code{\link{HeatmapList-class}} object which only contains one single heatmap and call \code{\link{draw,HeatmapList-method}} to make a complete heatmap.
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-
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+The \code{\link{Heatmap-class}} is not responsible for heatmap legend and annotation legends. The \code{\link{draw,Heatmap-method}} method
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+will construct a \code{\link{HeatmapList-class}} object which only contains one single heatmap
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+and call \code{\link{draw,HeatmapList-method}} to make a complete heatmap.
59 58
60 59 
 }
61 60 
 \section{Methods}{
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-The \code{\link{Heatmap-class}} provides following methods:
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+The \code{\link{Heatmap-class}} provides following methods:
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 \itemize{
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   \item \code{\link{Heatmap}}: constructor method.
... ... 
@@ -67,14 +66,11 @@ The \code{\link{Heatmap-class}} provides following methods:
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   \item \code{\link{add_heatmap,Heatmap-method}} append heatmaps and row annotations to a list of heatmaps.
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 }
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-
71 69 
 }
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 \author{
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-Zuguang Gu <z.gu@dkfz.de>
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-
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+Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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 # for examples, please go to `Heatmap` method page
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-NULL
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-}
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+NULL}
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
man/Heatmap-class.rd
History View file @4818ea9
... ... 
@@ -2,15 +2,17 @@
2 2 
 \docType{class}
3 3 
 \alias{Heatmap-class}
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 \title{
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-Class for a single heatmap
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+Class for a single heatmap
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+
6 7
7 8 
 }
8 9 
 \description{
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-Class for a single heatmap
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+Class for a single heatmap
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+
10 12
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 }
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 \details{
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-The components for a single heamtap are placed into a 9 x 7 layout:
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+The components for a single heamtap are placed into a 9 x 7 layout:
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   \preformatted{
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          +------+ (1)
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@@ -26,7 +28,7 @@ The components for a single heamtap are placed into a 9 x 7 layout:
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          +------+ (9)
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   }
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29 
-From top to bottom in column 4, the regions are:
31 
+From top to bottom in column 4, the regions are:
30 32
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 \itemize{
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   \item title which is put on the top of the heatmap, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
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@@ -40,7 +42,7 @@ From top to bottom in column 4, the regions are:
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   \item title on the bottom, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
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 }
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-From left to right in row 5, the regions are:
45 
+From left to right in row 5, the regions are:
44 46
45 47 
 \itemize{
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   \item title which is put in the left of the heatmap, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
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@@ -52,13 +54,12 @@ From left to right in row 5, the regions are:
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   \item title on the right, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
53 55 
 }
54 56
55 
-The \code{\link{Heatmap-class}} is not responsible for heatmap legend and annotation legends. The \code{\link{draw,Heatmap-method}} method
56 
-will construct a \code{\link{HeatmapList-class}} object which only contains one single heatmap
57 
-and call \code{\link{draw,HeatmapList-method}} to make a complete heatmap.
57 
+The \code{\link{Heatmap-class}} is not responsible for heatmap legend and annotation legends. The \code{\link{draw,Heatmap-method}} method will construct a \code{\link{HeatmapList-class}} object which only contains one single heatmap and call \code{\link{draw,HeatmapList-method}} to make a complete heatmap.
58 
+
58 59
59 60 
 }
60 61 
 \section{Methods}{
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-The \code{\link{Heatmap-class}} provides following methods:
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+The \code{\link{Heatmap-class}} provides following methods:
62 63
63 64 
 \itemize{
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   \item \code{\link{Heatmap}}: constructor method.
... ... 
@@ -66,11 +67,14 @@ The \code{\link{Heatmap-class}} provides following methods:
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   \item \code{\link{add_heatmap,Heatmap-method}} append heatmaps and row annotations to a list of heatmaps.
67 68 
 }
68 69
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+
69 71 
 }
70 72 
 \author{
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-Zuguang Gu <z.gu@dkfz.de>
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+Zuguang Gu <z.gu@dkfz.de>
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+
72 75
73 76 
 }
74 77 
 \examples{
75 78 
 # for examples, please go to `Heatmap` method page
76 
-NULL}
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+NULL
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+}
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/Heatmap-class.rd
History View file @f0eb7a9
... ... 
@@ -2,17 +2,15 @@
2 2 
 \docType{class}
3 3 
 \alias{Heatmap-class}
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 \title{
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-Class for a single heatmap
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-
5 
+Class for a single heatmap
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8 7 
 }
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 \description{
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-Class for a single heatmap
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-
9 
+Class for a single heatmap
12 10
13 11 
 }
14 12 
 \details{
15 
-The components for a single heamtap are placed into a 9 x 7 layout:
13 
+The components for a single heamtap are placed into a 9 x 7 layout:
16 14
17 15 
   \preformatted{
18 16 
          +------+ (1)
... ... 
@@ -28,7 +26,7 @@ The components for a single heamtap are placed into a 9 x 7 layout:
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          +------+ (9)
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   }
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-From top to bottom in column 4, the regions are:
29 
+From top to bottom in column 4, the regions are:
32 30
33 31 
 \itemize{
34 32 
   \item title which is put on the top of the heatmap, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
... ... 
@@ -42,7 +40,7 @@ From top to bottom in column 4, the regions are:
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   \item title on the bottom, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
43 41 
 }
44 42
45 
-From left to right in row 5, the regions are:
43 
+From left to right in row 5, the regions are:
46 44
47 45 
 \itemize{
48 46 
   \item title which is put in the left of the heatmap, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
... ... 
@@ -54,12 +52,13 @@ From left to right in row 5, the regions are:
54 52 
   \item title on the right, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
55 53 
 }
56 54
57 
-The \code{\link{Heatmap-class}} is not responsible for heatmap legend and annotation legends. The \code{\link{draw,Heatmap-method}} method will construct a \code{\link{HeatmapList-class}} object which only contains one single heatmap and call \code{\link{draw,HeatmapList-method}} to make a complete heatmap.
58 
-
55 
+The \code{\link{Heatmap-class}} is not responsible for heatmap legend and annotation legends. The \code{\link{draw,Heatmap-method}} method
56 
+will construct a \code{\link{HeatmapList-class}} object which only contains one single heatmap
57 
+and call \code{\link{draw,HeatmapList-method}} to make a complete heatmap.
59 58
60 59 
 }
61 60 
 \section{Methods}{
62 
-The \code{\link{Heatmap-class}} provides following methods:
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+The \code{\link{Heatmap-class}} provides following methods:
63 62
64 63 
 \itemize{
65 64 
   \item \code{\link{Heatmap}}: constructor method.
... ... 
@@ -67,14 +66,11 @@ The \code{\link{Heatmap-class}} provides following methods:
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   \item \code{\link{add_heatmap,Heatmap-method}} append heatmaps and row annotations to a list of heatmaps.
68 67 
 }
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-
71 69 
 }
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 \author{
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-Zuguang Gu <z.gu@dkfz.de>
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-
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+Zuguang Gu <z.gu@dkfz.de>
75 72
76 73 
 }
77 74 
 \examples{
78 75 
 # for examples, please go to `Heatmap` method page
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-NULL
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-}
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+NULL}
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
man/Heatmap-class.rd
History View file @d1da987
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,80 @@
1 
+\name{Heatmap-class}
2 
+\docType{class}
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+\alias{Heatmap-class}
4 
+\title{
5 
+Class for a single heatmap
6 
+
7 
+
8 
+}
9 
+\description{
10 
+Class for a single heatmap
11 
+
12 
+
13 
+}
14 
+\details{
15 
+The components for a single heamtap are placed into a 9 x 7 layout:
16 
+
17 
+  \preformatted{
18 
+         +------+ (1)
19 
+         +------+ (2)
20 
+         +------+ (3)
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+         +------+ (4)
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+   +-+-+-+------+-+-+-+
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+   |1|2|3| 4(5) |5|6|7|
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+   +-+-+-+------+-+-+-+
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+         +------+ (6)
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+         +------+ (7)
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+         +------+ (8)
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+         +------+ (9)
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+  }
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+
31 
+From top to bottom in column 4, the regions are:
32 
+
33 
+\itemize{
34 
+  \item title which is put on the top of the heatmap, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
35 
+  \item column cluster on the top, graphics are drawn by \code{\link{draw_hclust,Heatmap-method}}.
36 
+  \item column annotation on the top, graphics are drawn by \code{\link{draw_annotation,Heatmap-method}}.
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+  \item column names on the top, graphics are drawn by \code{\link{draw_dimnames,Heatmap-method}}.
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+  \item heatmap body, graphics are drawn by \code{\link{draw_heatmap_body,Heatmap-method}}.
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+  \item column names on the bottom, graphics are drawn by \code{\link{draw_dimnames,Heatmap-method}}.
40 
+  \item column annotation on the bottom, graphics are drawn by \code{\link{draw_annotation,Heatmap-method}}.
41 
+  \item column cluster on the bottom, graphics are drawn by \code{\link{draw_hclust,Heatmap-method}}.
42 
+  \item title on the bottom, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
43 
+}
44 
+
45 
+From left to right in row 5, the regions are:
46 
+
47 
+\itemize{
48 
+  \item title which is put in the left of the heatmap, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
49 
+  \item row cluster on the left, graphics are drawn by \code{\link{draw_hclust,Heatmap-method}}.
50 
+  \item row names on the left, graphics are drawn by \code{\link{draw_dimnames,Heatmap-method}}.
51 
+  \item heatmap body
52 
+  \item row names on the right, graphics are drawn by \code{\link{draw_dimnames,Heatmap-method}}.
53 
+  \item row cluster on the right, graphics are drawn by \code{\link{draw_hclust,Heatmap-method}}.
54 
+  \item title on the right, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
55 
+}
56 
+
57 
+The \code{\link{Heatmap-class}} is not responsible for heatmap legend and annotation legends. The \code{\link{draw,Heatmap-method}} method will construct a \code{\link{HeatmapList-class}} object which only contains one single heatmap and call \code{\link{draw,HeatmapList-method}} to make a complete heatmap.
58 
+
59 
+
60 
+}
61 
+\section{Methods}{
62 
+The \code{\link{Heatmap-class}} provides following methods:
63 
+
64 
+\itemize{
65 
+  \item \code{\link{Heatmap}}: constructor method.
66 
+  \item \code{\link{draw,Heatmap-method}}: draw a single heatmap.
67 
+  \item \code{\link{add_heatmap,Heatmap-method}} append heatmaps and row annotations to a list of heatmaps.
68 
+}
69 
+
70 
+
71 
+}
72 
+\author{
73 
+Zuguang Gu <z.gu@dkfz.de>
74 
+
75 
+
76 
+}
77 
+\examples{
78 
+# for examples, please go to `Heatmap` method page
79 
+NULL
80 
+}