Browse code

generate documentations by pkgdown

Zuguang Gu authored on 18/10/2019 11:34:02
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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}
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-\title{
5
-Class for a Single Heatmap
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-}
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
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-NULL
33
-
34
-}
Browse code

add jitter argument to Heatmap()

Zuguang Gu authored on 28/09/2019 08:37:13
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@@ -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

use pkgdown to build the doc site

Zuguang Gu authored on 24/09/2019 21:01:04
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@@ -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
 }
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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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@@ -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
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@@ -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
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@@ -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
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@@ -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
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@@ -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
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@@ -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
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@@ -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)
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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)
22
-         +------+ (7)
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-         +------+ (8)
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-         +------+ (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
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@@ -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
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
... ...
@@ -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
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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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... ...
@@ -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
... ...
@@ -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
... ...
@@ -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
... ...
@@ -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
... ...
@@ -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
... ...
@@ -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
Showing1 changed files
... ...
@@ -74,5 +74,9 @@ Zuguang Gu <z.gu@dkfz.de>
74 74
 \examples{
75 75
 
76 76
 
77
+
78
+
79
+
80
+
77 81
 # for examples, please go to `Heatmap` method page
78 82
 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
Showing1 changed files
... ...
@@ -72,5 +72,7 @@ Zuguang Gu <z.gu@dkfz.de>
72 72
 
73 73
 }
74 74
 \examples{
75
+
76
+
75 77
 # for examples, please go to `Heatmap` method page
76 78
 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
Showing1 changed files
... ...
@@ -72,6 +72,5 @@ Zuguang Gu <z.gu@dkfz.de>
72 72
 
73 73
 }
74 74
 \examples{
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-
76 75
 # for examples, please go to `Heatmap` method page
77 76
 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
Showing1 changed files
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@@ -72,5 +72,6 @@ Zuguang Gu <z.gu@dkfz.de>
72 72
 
73 73
 }
74 74
 \examples{
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+
75 76
 # for examples, please go to `Heatmap` method page
76 77
 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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@@ -72,7 +72,5 @@ Zuguang Gu <z.gu@dkfz.de>
72 72
 
73 73
 }
74 74
 \examples{
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-
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-
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 # for examples, please go to `Heatmap` method page
78 76
 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
Showing1 changed files
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@@ -72,5 +72,7 @@ Zuguang Gu <z.gu@dkfz.de>
72 72
 
73 73
 }
74 74
 \examples{
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+
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+
75 77
 # for examples, please go to `Heatmap` method page
76 78
 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
Showing1 changed files
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@@ -72,9 +72,5 @@ Zuguang Gu <z.gu@dkfz.de>
72 72
 
73 73
 }
74 74
 \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
Showing1 changed files
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@@ -73,6 +73,7 @@ Zuguang Gu <z.gu@dkfz.de>
73 73
 }
74 74
 \examples{
75 75
 
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+
76 77
 # for examples, please go to `Heatmap` method page
77 78
 NULL
78 79
 
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
Showing1 changed files
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@@ -72,5 +72,8 @@ Zuguang Gu <z.gu@dkfz.de>
72 72
 
73 73
 }
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 \examples{
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+
75 76
 # 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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@@ -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
7 6
 
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
 }
14 12
 \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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@@ -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:
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33 31
 \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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 }
44 42
 
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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:
46 44
 
47 45
 \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}}.
... ...
@@ -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}}.
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}{
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-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
 }
69 68
 
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-
71 69
 }
72 70
 \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

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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@@ -2,15 +2,17 @@
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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+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
 
11 13
 }
12 14
 \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:  
14 16
 
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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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-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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31 33
 \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:
40 42
   \item title on the bottom, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
41 43
 }
42 44
 
43
-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:
52 54
   \item title on the right, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
53 55
 }
54 56
 
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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
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{
64 65
   \item \code{\link{Heatmap}}: constructor method.
... ...
@@ -66,11 +67,14 @@ The \code{\link{Heatmap-class}} provides following methods:
66 67
   \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
... ...
@@ -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
7 6
 
8 7
 }
9 8
 \description{
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-Class for a single heatmap  
11
-
9
+Class for a single heatmap
12 10
 
13 11
 }
14 12
 \details{
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-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:
28 26
          +------+ (9)
29 27
   }
30 28
 
31
-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:
42 40
   \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}{
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-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:
67 66
   \item \code{\link{add_heatmap,Heatmap-method}} append heatmaps and row annotations to a list of heatmaps.
68 67
 }
69 68
 
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-
71 69
 }
72 70
 \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
79
-NULL
80
-}
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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
1 1
new file mode 100644
... ...
@@ -0,0 +1,80 @@
1
+\name{Heatmap-class}
2
+\docType{class}
3
+\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)
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+         +------+ (2)
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+         +------+ (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}}.
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+  \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}}.
39
+  \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}}.
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+  \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
+}