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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@@ -1,45 +0,0 @@
1
-\name{decorate_heatmap_body}
2
-\alias{decorate_heatmap_body}
3
-\title{
4
-Decorate Heatmap Bodies
5
-}
6
-\description{
7
-Decorate Heatmap Bodies
8
-}
9
-\usage{
10
-decorate_heatmap_body(heatmap, code,
11
-    slice = 1, row_slice = slice, column_slice = 1,
12
-    envir = new.env(parent = parent.frame()))
13
-}
14
-\arguments{
15
-
16
-  \item{heatmap}{Name of the heatmap which is set as \code{name} argument in \code{\link{Heatmap}} function.}
17
-  \item{code}{Code that adds graphics in the selected heatmap body.}
18
-  \item{slice}{Index of the row slice in the heatmap.}
19
-  \item{row_slice}{Index of the row slice in the heatmap.}
20
-  \item{column_slice}{Index of the column slice in the heatmap.}
21
-  \item{envir}{Where to look for variables inside \code{code}.}
22
-
23
-}
24
-\details{
25
-There is a viewport for each slice in each heatmap.
26
-This function contructs the name of the viewport,
27
-goes to the viewport by \code{\link[grid:viewports]{seekViewport}}, runs the code
28
-to that viewport and finally goes back to the original viewport.
29
-}
30
-\value{
31
-This function returns no value.
32
-}
33
-\seealso{
34
-\url{https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-decoration.html}
35
-}
36
-\author{
37
-Zuguang Gu <z.gu@dkfz.de>
38
-}
39
-\examples{
40
-set.seed(123)
41
-Heatmap(matrix(rnorm(100), 10), name = "mat")
42
-decorate_heatmap_body("mat", {
43
-    grid.circle(gp = gpar(fill = "#FF000080"))
44
-})
45
-}
Browse code

fix warnings in Rd files

Zuguang Gu authored on 28/11/2018 09:32:19
Showing1 changed files
... ...
@@ -24,7 +24,7 @@ decorate_heatmap_body(heatmap, code,
24 24
 \details{
25 25
 There is a viewport for each slice in each heatmap.
26 26
 This function contructs the name of the viewport,
27
-goes to the viewport by \code{\link[grid]{seekViewport}}, runs the code
27
+goes to the viewport by \code{\link[grid:viewports]{seekViewport}}, runs the code
28 28
 to that viewport and finally goes back to the original viewport.
29 29
 }
30 30
 \value{
Browse code

documentation checked

Zuguang Gu authored on 23/10/2018 19:59:12
Showing1 changed files
... ...
@@ -1,10 +1,10 @@
1 1
 \name{decorate_heatmap_body}
2 2
 \alias{decorate_heatmap_body}
3 3
 \title{
4
-Decorate the heatmap body
4
+Decorate Heatmap Bodies
5 5
 }
6 6
 \description{
7
-Decorate the heatmap body
7
+Decorate Heatmap Bodies
8 8
 }
9 9
 \usage{
10 10
 decorate_heatmap_body(heatmap, code,
... ...
@@ -13,23 +13,26 @@ decorate_heatmap_body(heatmap, code,
13 13
 }
14 14
 \arguments{
15 15
 
16
-  \item{heatmap}{name of the heatmap which is set as \code{name} argument in \code{\link{Heatmap}} function.}
17
-  \item{code}{code that adds graphics in the selected heatmap body.}
18
-  \item{slice}{index of row slices in the heatmap.}
19
-  \item{row_slice}{index of row slices in the heatmap.}
20
-  \item{column_slice}{index of column slices in the heatmap.}
21
-  \item{envir}{where to look for variables inside \code{code}}
16
+  \item{heatmap}{Name of the heatmap which is set as \code{name} argument in \code{\link{Heatmap}} function.}
17
+  \item{code}{Code that adds graphics in the selected heatmap body.}
18
+  \item{slice}{Index of the row slice in the heatmap.}
19
+  \item{row_slice}{Index of the row slice in the heatmap.}
20
+  \item{column_slice}{Index of the column slice in the heatmap.}
21
+  \item{envir}{Where to look for variables inside \code{code}.}
22 22
 
23 23
 }
24 24
 \details{
25
-There is a viewport for each row slice and each column slice in each heatmap.
25
+There is a viewport for each slice in each heatmap.
26 26
 This function contructs the name of the viewport,
27
-goes to the viewport by \code{\link[grid]{seekViewport}} and applies code
28
-to that viewport.
27
+goes to the viewport by \code{\link[grid]{seekViewport}}, runs the code
28
+to that viewport and finally goes back to the original viewport.
29 29
 }
30 30
 \value{
31 31
 This function returns no value.
32 32
 }
33
+\seealso{
34
+\url{https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-decoration.html}
35
+}
33 36
 \author{
34 37
 Zuguang Gu <z.gu@dkfz.de>
35 38
 }
Browse code

update

jokergoo authored on 12/10/2018 15:28:37
Showing1 changed files
... ...
@@ -13,11 +13,11 @@ decorate_heatmap_body(heatmap, code,
13 13
 }
14 14
 \arguments{
15 15
 
16
-  \item{heatmap}{name of the heatmap which is set as \code{name} argument in \code{\link{Heatmap}} function}
17
-  \item{code}{code that adds graphics in the selected heatmap body}
18
-  \item{slice}{index of row slices in the heatmap}
19
-  \item{row_slice}{index of row slices in the heatmap}
20
-  \item{column_slice}{index of column slices in the heatmap}
16
+  \item{heatmap}{name of the heatmap which is set as \code{name} argument in \code{\link{Heatmap}} function.}
17
+  \item{code}{code that adds graphics in the selected heatmap body.}
18
+  \item{slice}{index of row slices in the heatmap.}
19
+  \item{row_slice}{index of row slices in the heatmap.}
20
+  \item{column_slice}{index of column slices in the heatmap.}
21 21
   \item{envir}{where to look for variables inside \code{code}}
22 22
 
23 23
 }
... ...
@@ -26,22 +26,6 @@ There is a viewport for each row slice and each column slice in each heatmap.
26 26
 This function contructs the name of the viewport,
27 27
 goes to the viewport by \code{\link[grid]{seekViewport}} and applies code
28 28
 to that viewport.
29
-
30
-If you know the number of rows and columns for that row slice, it is
31
-simple to calculate the position of every small grid in the row slice.
32
-E.g., the position for the grid in i^th row and j^th column is:
33
-
34
-  \preformatted{
35
-    # assume nc is the number of columns 
36
-    # and nr is the number of rows in that row slice
37
-    unit((i-0.5)/nc, "npc")
38
-    unit((j-0.5)/nr, "npc")
39
-
40
-    # the width is
41
-    unit(1/nc, "npc")
42
-
43
-    # the height is
44
-    unit(1/nr, "npc")  }
45 29
 }
46 30
 \value{
47 31
 This function returns no value.
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
... ...
@@ -7,18 +7,22 @@ Decorate the heatmap body
7 7
 Decorate the heatmap body
8 8
 }
9 9
 \usage{
10
-decorate_heatmap_body(heatmap, code, slice = 1, envir = new.env(parent = parent.frame()))
10
+decorate_heatmap_body(heatmap, code,
11
+    slice = 1, row_slice = slice, column_slice = 1,
12
+    envir = new.env(parent = parent.frame()))
11 13
 }
12 14
 \arguments{
13 15
 
14
-  \item{heatmap}{name of the heatmap which is set as \code{name} option in \code{\link{Heatmap}} function}
16
+  \item{heatmap}{name of the heatmap which is set as \code{name} argument in \code{\link{Heatmap}} function}
15 17
   \item{code}{code that adds graphics in the selected heatmap body}
16
-  \item{slice}{index of row slices in the heatmap if it is split by rows}
18
+  \item{slice}{index of row slices in the heatmap}
19
+  \item{row_slice}{index of row slices in the heatmap}
20
+  \item{column_slice}{index of column slices in the heatmap}
17 21
   \item{envir}{where to look for variables inside \code{code}}
18 22
 
19 23
 }
20 24
 \details{
21
-There is a viewport for each row slice in each heatmap.
25
+There is a viewport for each row slice and each column slice in each heatmap.
22 26
 This function contructs the name of the viewport,
23 27
 goes to the viewport by \code{\link[grid]{seekViewport}} and applies code
24 28
 to that viewport.
Browse code

decorate_*() adds envir

Zuguang Gu authored on 29/01/2017 20:43:42
Showing1 changed files
... ...
@@ -7,13 +7,14 @@ Decorate the heatmap body
7 7
 Decorate the heatmap body
8 8
 }
9 9
 \usage{
10
-decorate_heatmap_body(heatmap, code, slice = 1)
10
+decorate_heatmap_body(heatmap, code, slice = 1, envir = new.env(parent = parent.frame()))
11 11
 }
12 12
 \arguments{
13 13
 
14 14
   \item{heatmap}{name of the heatmap which is set as \code{name} option in \code{\link{Heatmap}} function}
15 15
   \item{code}{code that adds graphics in the selected heatmap body}
16 16
   \item{slice}{index of row slices in the heatmap if it is split by rows}
17
+  \item{envir}{where to look for variables inside \code{code}}
17 18
 
18 19
 }
19 20
 \details{
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
... ...
@@ -22,7 +22,7 @@ This function contructs the name of the viewport,
22 22
 goes to the viewport by \code{\link[grid]{seekViewport}} and applies code
23 23
 to that viewport.
24 24
 
25
-Since you know the number of rows and columns for that row slice, it is
25
+If you know the number of rows and columns for that row slice, it is
26 26
 simple to calculate the position of every small grid in the row slice.
27 27
 E.g., the position for the grid in i^th row and j^th column is:
28 28
 
Browse code

anoying rebase

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@111684 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 20/12/2015 21:42:51
Showing1 changed files
... ...
@@ -11,9 +11,9 @@ decorate_heatmap_body(heatmap, code, slice = 1)
11 11
 }
12 12
 \arguments{
13 13
 
14
-  \item{heatmap}{name of the heatmap}
14
+  \item{heatmap}{name of the heatmap which is set as \code{name} option in \code{\link{Heatmap}} function}
15 15
   \item{code}{code that adds graphics in the selected heatmap body}
16
-  \item{slice}{index of row slices in the heatmap}
16
+  \item{slice}{index of row slices in the heatmap if it is split by rows}
17 17
 
18 18
 }
19 19
 \details{
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
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
... ...
@@ -7,19 +7,39 @@ Decorate the heatmap body
7 7
 Decorate the heatmap body
8 8
 }
9 9
 \usage{
10
-decorate_heatmap_body(heatmap, code = {}, slice = 1)
10
+decorate_heatmap_body(heatmap, code, slice = 1)
11 11
 }
12 12
 \arguments{
13 13
 
14 14
   \item{heatmap}{name of the heatmap}
15
-  \item{code}{code that is executed in the heatmap body}
15
+  \item{code}{code that adds graphics in the selected heatmap body}
16 16
   \item{slice}{index of row slices in the heatmap}
17 17
 
18 18
 }
19 19
 \details{
20
-This simple function actually contructs the name of the viewport,
20
+There is a viewport for each row slice in each heatmap.
21
+This function contructs the name of the viewport,
21 22
 goes to the viewport by \code{\link[grid]{seekViewport}} and applies code
22 23
 to that viewport.
24
+
25
+Since you know the number of rows and columns for that row slice, it is
26
+simple to calculate the position of every small grid in the row slice.
27
+E.g., the position for the grid in i^th row and j^th column is:
28
+
29
+  \preformatted{
30
+    # assume nc is the number of columns 
31
+    # and nr is the number of rows in that row slice
32
+    unit((i-0.5)/nc, "npc")
33
+    unit((j-0.5)/nr, "npc")
34
+
35
+    # the width is
36
+    unit(1/nc, "npc")
37
+
38
+    # the height is
39
+    unit(1/nr, "npc")  }
40
+}
41
+\value{
42
+This function returns no value.
23 43
 }
24 44
 \author{
25 45
 Zuguang Gu <z.gu@dkfz.de>
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
... ...
@@ -7,12 +7,14 @@ Decorate the heatmap body
7 7
 Decorate the heatmap body
8 8
 }
9 9
 \usage{
10
-decorate_heatmap_body(heatmap, code = {}, slice = 1)}
10
+decorate_heatmap_body(heatmap, code = {}, slice = 1)
11
+}
11 12
 \arguments{
12 13
 
13 14
   \item{heatmap}{name of the heatmap}
14 15
   \item{code}{code that is executed in the heatmap body}
15 16
   \item{slice}{index of row slices in the heatmap}
17
+
16 18
 }
17 19
 \details{
18 20
 This simple function actually contructs the name of the viewport,
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
... ...
@@ -2,11 +2,9 @@
2 2
 \alias{decorate_heatmap_body}
3 3
 \title{
4 4
 Decorate the heatmap body
5
-
6 5
 }
7 6
 \description{
8 7
 Decorate the heatmap body
9
-
10 8
 }
11 9
 \usage{
12 10
 decorate_heatmap_body(heatmap, code = {}, slice = 1)}
... ...
@@ -20,11 +18,9 @@ decorate_heatmap_body(heatmap, code = {}, slice = 1)}
20 18
 This simple function actually contructs the name of the viewport,
21 19
 goes to the viewport by \code{\link[grid]{seekViewport}} and applies code
22 20
 to that viewport.
23
-
24 21
 }
25 22
 \author{
26 23
 Zuguang Gu <z.gu@dkfz.de>
27
-
28 24
 }
29 25
 \examples{
30 26
 set.seed(123)
... ...
@@ -32,5 +28,4 @@ Heatmap(matrix(rnorm(100), 10), name = "mat")
32 28
 decorate_heatmap_body("mat", {
33 29
     grid.circle(gp = gpar(fill = "#FF000080"))
34 30
 })
35
-
36 31
 }
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
1 1
new file mode 100644
... ...
@@ -0,0 +1,36 @@
1
+\name{decorate_heatmap_body}
2
+\alias{decorate_heatmap_body}
3
+\title{
4
+Decorate the heatmap body
5
+
6
+}
7
+\description{
8
+Decorate the heatmap body
9
+
10
+}
11
+\usage{
12
+decorate_heatmap_body(heatmap, code = {}, slice = 1)}
13
+\arguments{
14
+
15
+  \item{heatmap}{name of the heatmap}
16
+  \item{code}{code that is executed in the heatmap body}
17
+  \item{slice}{index of row slices in the heatmap}
18
+}
19
+\details{
20
+This simple function actually contructs the name of the viewport,
21
+goes to the viewport by \code{\link[grid]{seekViewport}} and applies code
22
+to that viewport.
23
+
24
+}
25
+\author{
26
+Zuguang Gu <z.gu@dkfz.de>
27
+
28
+}
29
+\examples{
30
+set.seed(123)
31
+Heatmap(matrix(rnorm(100), 10), name = "mat")
32
+decorate_heatmap_body("mat", {
33
+    grid.circle(gp = gpar(fill = "#FF000080"))
34
+})
35
+
36
+}