Zuguang Gu authored on 18/10/2019 11:34:02 | 1 | 1 |
deleted file mode 100644 |
| ... | ... |
@@ -1,33 +0,0 @@ |
| 1 |
-\name{draw-SingleAnnotation-method}
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| 2 |
-\alias{draw,SingleAnnotation-method}
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| 3 |
-\title{
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|
| 4 |
-Draw the Single Annotation |
|
| 5 |
-} |
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| 6 |
-\description{
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|
| 7 |
-Draw the Single Annotation |
|
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-} |
|
| 9 |
-\usage{
|
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| 10 |
-\S4method{draw}{SingleAnnotation}(object, index, k = 1, n = 1, test = FALSE,
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|
| 11 |
- anno_mark_param = list()) |
|
| 12 |
-} |
|
| 13 |
-\arguments{
|
|
| 14 |
- |
|
| 15 |
- \item{object}{A \code{\link{SingleAnnotation-class}} object.}
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| 16 |
- \item{index}{A vector of indices.}
|
|
| 17 |
- \item{k}{The index of the slice.}
|
|
| 18 |
- \item{n}{Total number of slices. \code{k} and \code{n} are used to adjust annotation names. E.g. if \code{k} is 2 and \code{n} is 3, the annotation names are not drawn.}
|
|
| 19 |
- \item{test}{Is it in test mode? The value can be logical or a text which is plotted as the title of plot.}
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| 20 |
- \item{anno_mark_param}{It contains specific parameters for drawing \code{\link{anno_mark}}.}
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| 21 |
- |
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| 22 |
-} |
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| 23 |
-\value{
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| 24 |
-No value is returned. |
|
| 25 |
-} |
|
| 26 |
-\author{
|
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| 27 |
-Zuguang Gu <z.gu@dkfz.de> |
|
| 28 |
-} |
|
| 29 |
-\examples{
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-# There is no example |
|
| 31 |
-NULL |
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| 32 |
- |
|
| 33 |
-} |
Zuguang Gu authored on 28/09/2019 08:37:13
Zuguang Gu authored on 24/09/2019 21:01:04
Zuguang Gu authored on 18/01/2019 10:43:26
Zuguang Gu authored on 30/12/2018 08:12:22
Zuguang Gu authored on 07/12/2018 14:41:15 | ... | ... |
@@ -7,7 +7,8 @@ Draw the Single Annotation |
| 7 | 7 |
Draw the Single Annotation |
| 8 | 8 |
} |
| 9 | 9 |
\usage{
|
| 10 |
-\S4method{draw}{SingleAnnotation}(object, index, k = 1, n = 1, test = FALSE)
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+\S4method{draw}{SingleAnnotation}(object, index, k = 1, n = 1, test = FALSE,
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+ anno_mark_param = list()) |
|
| 11 | 12 |
} |
| 12 | 13 |
\arguments{
|
| 13 | 14 |
|
| ... | ... |
@@ -16,6 +17,7 @@ Draw the Single Annotation |
| 16 | 17 |
\item{k}{The index of the slice.}
|
| 17 | 18 |
\item{n}{Total number of slices. \code{k} and \code{n} are used to adjust annotation names. E.g. if \code{k} is 2 and \code{n} is 3, the annotation names are not drawn.}
|
| 18 | 19 |
\item{test}{Is it in test mode? The value can be logical or a text which is plotted as the title of plot.}
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| 20 |
+ \item{anno_mark_param}{It contains specific parameters for drawing \code{\link{anno_mark}}.}
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|
| 19 | 21 |
|
| 20 | 22 |
} |
| 21 | 23 |
\value{
|
Zuguang Gu authored on 19/10/2018 19:08:59
Zuguang Gu authored on 17/10/2018 06:09:36
Zuguang Gu authored on 12/10/2018 19:19:48
jokergoo authored on 12/10/2018 15:28:37
Zuguang Gu authored on 20/09/2018 22:09:48
Zuguang Gu authored on 20/09/2018 12:48:08 | 1 | 1 |
old mode 100755 |
| 2 | 2 |
new mode 100644 |
| ... | ... |
@@ -1,26 +1,22 @@ |
| 1 | 1 |
\name{draw-SingleAnnotation-method}
|
| 2 | 2 |
\alias{draw,SingleAnnotation-method}
|
| 3 | 3 |
\title{
|
| 4 |
-Draw the single annotation |
|
| 4 |
+Draw the Single Annotation |
|
| 5 | 5 |
} |
| 6 | 6 |
\description{
|
| 7 |
-Draw the single annotation |
|
| 7 |
+Draw the Single Annotation |
|
| 8 | 8 |
} |
| 9 | 9 |
\usage{
|
| 10 |
-\S4method{draw}{SingleAnnotation}(object, index, k = NULL, n = NULL)
|
|
| 10 |
+\S4method{draw}{SingleAnnotation}(object, index, k = 1, n = 1, test = FALSE)
|
|
| 11 | 11 |
} |
| 12 | 12 |
\arguments{
|
| 13 | 13 |
|
| 14 |
- \item{object}{a \code{\link{SingleAnnotation-class}} object.}
|
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| 15 |
- \item{index}{a vector of orders}
|
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| 16 |
- \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the names of the viewport which contains the annotation graphics.}
|
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| 17 |
- \item{n}{total number of row slices}
|
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+ \item{object}{A \code{\link{SingleAnnotation-class}} object.}
|
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+ \item{index}{A vector of indices.}
|
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+ \item{k}{The index of the slice.}
|
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+ \item{n}{Total number of slices. \code{k} and \code{n} are used to adjust annotation names. E.g. if \code{k} is 2 and \code{n} is 3, the annotation names are not drawn.}
|
|
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+ \item{test}{Is it in test mode? The value can be logical or a text which is plotted as the title of plot.}
|
|
| 18 | 19 |
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-} |
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-\details{
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-A viewport is created. |
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- |
|
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-The graphics would be different depending the annotation is a row annotation or a column annotation. |
|
| 24 | 20 |
} |
| 25 | 21 |
\value{
|
| 26 | 22 |
No value is returned. |
| ... | ... |
@@ -29,27 +25,6 @@ No value is returned. |
| 29 | 25 |
Zuguang Gu <z.gu@dkfz.de> |
| 30 | 26 |
} |
| 31 | 27 |
\examples{
|
| 32 |
-anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
|
|
| 33 |
-grid.newpage(); draw(anno, 1:5) |
|
| 34 |
-grid.newpage(); draw(anno, c(1, 4, 3, 5, 2)) |
|
| 35 |
- |
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| 36 |
-anno = SingleAnnotation(value = c("a", "a", "a", "b", "b", "b"),
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- col = c("a" = "red", "b" = "blue"))
|
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| 38 |
-grid.newpage(); draw(anno, 1:5) |
|
| 39 |
-grid.newpage(); draw(anno, c(1, 4, 3, 5, 2)) |
|
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- |
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-anno = SingleAnnotation(value = c("a", "a", "a", "b", "b", "b"),
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- col = c("a" = "red", "b" = "blue"), which = "row")
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-grid.newpage(); draw(anno, 1:5) |
|
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- |
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-anno = SingleAnnotation(value = 1:10) |
|
| 46 |
-grid.newpage(); draw(anno, 1:10) |
|
| 47 |
- |
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| 48 |
-require(circlize) |
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-anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red")))
|
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| 50 |
-grid.newpage(); draw(anno, 1:10) |
|
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- |
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-anno = SingleAnnotation(fun = anno_points(1:10)) |
|
| 53 |
-grid.newpage(); draw(anno, 1:10) |
|
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- |
|
| 28 |
+# There is no example |
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| 29 |
+NULL |
|
| 55 | 30 |
} |
Zuguang Gu authored on 17/10/2017 20:55:32 | ... | ... |
@@ -13,11 +13,7 @@ Draw the single annotation |
| 13 | 13 |
|
| 14 | 14 |
\item{object}{a \code{\link{SingleAnnotation-class}} object.}
|
| 15 | 15 |
\item{index}{a vector of orders}
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| 16 |
-<<<<<<< HEAD |
|
| 17 | 16 |
\item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the names of the viewport which contains the annotation graphics.}
|
| 18 |
-======= |
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| 19 |
- \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewport which contains the annotation graphics.}
|
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| 20 |
->>>>>>> bioc/master |
|
| 21 | 17 |
\item{n}{total number of row slices}
|
| 22 | 18 |
|
| 23 | 19 |
} |
Zuguang Gu authored on 17/10/2017 19:44:53
Zuguang Gu authored on 20/08/2017 05:56:30 | ... | ... |
@@ -13,7 +13,7 @@ Draw the single annotation |
| 13 | 13 |
|
| 14 | 14 |
\item{object}{a \code{\link{SingleAnnotation-class}} object.}
|
| 15 | 15 |
\item{index}{a vector of orders}
|
| 16 |
- \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewport which contains the annotation graphics.}
|
|
| 16 |
+ \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the names of the viewport which contains the annotation graphics.}
|
|
| 17 | 17 |
\item{n}{total number of row slices}
|
| 18 | 18 |
|
| 19 | 19 |
} |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@110567 bc3139a8-67e5-0310-9ffc-ced21a209358
Zuguang Gu authored on 12/11/2015 10:07:49 | ... | ... |
@@ -13,7 +13,7 @@ Draw the single annotation |
| 13 | 13 |
|
| 14 | 14 |
\item{object}{a \code{\link{SingleAnnotation-class}} object.}
|
| 15 | 15 |
\item{index}{a vector of orders}
|
| 16 |
- \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewportwhich contains the annotation graphics.}
|
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| 16 |
+ \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewport which contains the annotation graphics.}
|
|
| 17 | 17 |
\item{n}{total number of row slices}
|
| 18 | 18 |
|
| 19 | 19 |
} |
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@110567 bc3139a8-67e5-0310-9ffc-ced21a209358
z.gu authored on 12/11/2015 10:07:49 | ... | ... |
@@ -13,7 +13,7 @@ Draw the single annotation |
| 13 | 13 |
|
| 14 | 14 |
\item{object}{a \code{\link{SingleAnnotation-class}} object.}
|
| 15 | 15 |
\item{index}{a vector of orders}
|
| 16 |
- \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewportwhich contains the annotation graphics.}
|
|
| 16 |
+ \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewport which contains the annotation graphics.}
|
|
| 17 | 17 |
\item{n}{total number of row slices}
|
| 18 | 18 |
|
| 19 | 19 |
} |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@108253 bc3139a8-67e5-0310-9ffc-ced21a209358
Zuguang Gu authored on 07/09/2015 20:39:32 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 Commit id: db263179df8a28bd25eb5afcf64aa9c37b2fdd32
refresh docs
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107358 bc3139a8-67e5-0310-9ffc-ced21a209358
Zuguang Gu authored on 12/08/2015 22:49:59 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 Commit id: 1de356e1d1343725223e03ff696f931d80b2842b
Merge branch 'master' of https://github.com/jokergoo/mheatmap
Commit id: 478962957a34b7a5e87c8336989bae3df54f9559
change default colors
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107356 bc3139a8-67e5-0310-9ffc-ced21a209358
Zuguang Gu authored on 12/08/2015 22:03:22 | ... | ... |
@@ -7,13 +7,15 @@ Draw the single annotation |
| 7 | 7 |
Draw the single annotation |
| 8 | 8 |
} |
| 9 | 9 |
\usage{
|
| 10 |
-\S4method{draw}{SingleAnnotation}(object, index, k = NULL, n = NULL)}
|
|
| 10 |
+\S4method{draw}{SingleAnnotation}(object, index, k = NULL, n = NULL)
|
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| 11 |
+} |
|
| 11 | 12 |
\arguments{
|
| 12 | 13 |
|
| 13 | 14 |
\item{object}{a \code{\link{SingleAnnotation-class}} object.}
|
| 14 | 15 |
\item{index}{a vector of orders}
|
| 15 | 16 |
\item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewportwhich contains the annotation graphics.}
|
| 16 | 17 |
\item{n}{total number of row slices}
|
| 18 |
+ |
|
| 17 | 19 |
} |
| 18 | 20 |
\details{
|
| 19 | 21 |
A viewport is created. |
| ... | ... |
@@ -48,4 +50,5 @@ grid.newpage(); draw(anno, 1:10) |
| 48 | 50 |
|
| 49 | 51 |
anno = SingleAnnotation(fun = anno_points(1:10)) |
| 50 | 52 |
grid.newpage(); draw(anno, 1:10) |
| 53 |
+ |
|
| 51 | 54 |
} |
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 | ... | ... |
@@ -7,13 +7,15 @@ Draw the single annotation |
| 7 | 7 |
Draw the single annotation |
| 8 | 8 |
} |
| 9 | 9 |
\usage{
|
| 10 |
-\S4method{draw}{SingleAnnotation}(object, index, k = NULL, n = NULL)}
|
|
| 10 |
+\S4method{draw}{SingleAnnotation}(object, index, k = NULL, n = NULL)
|
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+} |
|
| 11 | 12 |
\arguments{
|
| 12 | 13 |
|
| 13 | 14 |
\item{object}{a \code{\link{SingleAnnotation-class}} object.}
|
| 14 | 15 |
\item{index}{a vector of orders}
|
| 15 | 16 |
\item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewportwhich contains the annotation graphics.}
|
| 16 | 17 |
\item{n}{total number of row slices}
|
| 18 |
+ |
|
| 17 | 19 |
} |
| 18 | 20 |
\details{
|
| 19 | 21 |
A viewport is created. |
| ... | ... |
@@ -48,4 +50,5 @@ grid.newpage(); draw(anno, 1:10) |
| 48 | 50 |
|
| 49 | 51 |
anno = SingleAnnotation(fun = anno_points(1:10)) |
| 50 | 52 |
grid.newpage(); draw(anno, 1:10) |
| 53 |
+ |
|
| 51 | 54 |
} |
Commit id: f1b195419490dad46029cf7b681508ed21ba8c60
refreshed documentations
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107316 bc3139a8-67e5-0310-9ffc-ced21a209358
Zuguang Gu authored on 11/08/2015 10:42:08 | ... | ... |
@@ -2,11 +2,9 @@ |
| 2 | 2 |
\alias{draw,SingleAnnotation-method}
|
| 3 | 3 |
\title{
|
| 4 | 4 |
Draw the single annotation |
| 5 |
- |
|
| 6 | 5 |
} |
| 7 | 6 |
\description{
|
| 8 | 7 |
Draw the single annotation |
| 9 |
- |
|
| 10 | 8 |
} |
| 11 | 9 |
\usage{
|
| 12 | 10 |
\S4method{draw}{SingleAnnotation}(object, index, k = NULL, n = NULL)}
|
| ... | ... |
@@ -19,31 +17,15 @@ Draw the single annotation |
| 19 | 17 |
} |
| 20 | 18 |
\details{
|
| 21 | 19 |
A viewport is created. |
| 22 |
- |
|
| 23 | 20 |
The graphics would be different depending the annotation is a row annotation or a column annotation. |
| 24 |
- |
|
| 25 | 21 |
} |
| 26 | 22 |
\value{
|
| 27 | 23 |
No value is returned. |
| 28 |
- |
|
| 29 | 24 |
} |
| 30 | 25 |
\author{
|
| 31 | 26 |
Zuguang Gu <z.gu@dkfz.de> |
| 32 |
- |
|
| 33 | 27 |
} |
| 34 | 28 |
\examples{
|
| 35 |
- |
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| 36 |
- |
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| 37 |
- |
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| 38 |
- |
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- |
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- |
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- |
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- |
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- |
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- |
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- |
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- |
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| 47 | 29 |
anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
|
| 48 | 30 |
grid.newpage(); draw(anno, 1:5) |
| 49 | 31 |
grid.newpage(); draw(anno, c(1, 4, 3, 5, 2)) |
| ... | ... |
@@ -65,4 +47,5 @@ anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red"
|
| 65 | 47 |
grid.newpage(); draw(anno, 1:10) |
| 66 | 48 |
|
| 67 | 49 |
anno = SingleAnnotation(fun = anno_points(1:10)) |
| 68 |
-grid.newpage(); draw(anno, 1:10)} |
|
| 50 |
+grid.newpage(); draw(anno, 1:10) |
|
| 51 |
+} |
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 | ... | ... |
@@ -2,11 +2,9 @@ |
| 2 | 2 |
\alias{draw,SingleAnnotation-method}
|
| 3 | 3 |
\title{
|
| 4 | 4 |
Draw the single annotation |
| 5 |
- |
|
| 6 | 5 |
} |
| 7 | 6 |
\description{
|
| 8 | 7 |
Draw the single annotation |
| 9 |
- |
|
| 10 | 8 |
} |
| 11 | 9 |
\usage{
|
| 12 | 10 |
\S4method{draw}{SingleAnnotation}(object, index, k = NULL, n = NULL)}
|
| ... | ... |
@@ -19,31 +17,15 @@ Draw the single annotation |
| 19 | 17 |
} |
| 20 | 18 |
\details{
|
| 21 | 19 |
A viewport is created. |
| 22 |
- |
|
| 23 | 20 |
The graphics would be different depending the annotation is a row annotation or a column annotation. |
| 24 |
- |
|
| 25 | 21 |
} |
| 26 | 22 |
\value{
|
| 27 | 23 |
No value is returned. |
| 28 |
- |
|
| 29 | 24 |
} |
| 30 | 25 |
\author{
|
| 31 | 26 |
Zuguang Gu <z.gu@dkfz.de> |
| 32 |
- |
|
| 33 | 27 |
} |
| 34 | 28 |
\examples{
|
| 35 |
- |
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| 36 |
- |
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| 37 |
- |
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| 38 |
- |
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| 39 |
- |
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| 40 |
- |
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| 41 |
- |
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| 42 |
- |
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| 43 |
- |
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| 44 |
- |
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| 45 |
- |
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| 46 |
- |
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| 47 | 29 |
anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
|
| 48 | 30 |
grid.newpage(); draw(anno, 1:5) |
| 49 | 31 |
grid.newpage(); draw(anno, c(1, 4, 3, 5, 2)) |
| ... | ... |
@@ -65,4 +47,5 @@ anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red"
|
| 65 | 47 |
grid.newpage(); draw(anno, 1:10) |
| 66 | 48 |
|
| 67 | 49 |
anno = SingleAnnotation(fun = anno_points(1:10)) |
| 68 |
-grid.newpage(); draw(anno, 1:10)} |
|
| 50 |
+grid.newpage(); draw(anno, 1:10) |
|
| 51 |
+} |
Commit id: 262e3960558c1f61b986f5be7a2ffd4599f704fa
comprehensive modifications
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107311 bc3139a8-67e5-0310-9ffc-ced21a209358
Zuguang Gu authored on 10/08/2015 22:17:54 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 Commit id: 73171be89c157222e8e71e85daa8a37ce509a4e2
add border argument in anno_* family functions
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107201 bc3139a8-67e5-0310-9ffc-ced21a209358
Zuguang Gu authored on 06/08/2015 17:46:06 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 Commit id: 3429d28233ef2cbeafcd05307042d7c7aa54a2a2
add decorate* family functions
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107197 bc3139a8-67e5-0310-9ffc-ced21a209358
Zuguang Gu authored on 06/08/2015 16:40:59 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 Commit id: d5adc92bdbf27b45a6a4b5c7e29d2e4fe8380194
allow reordering
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107130 bc3139a8-67e5-0310-9ffc-ced21a209358
Zuguang Gu authored on 04/08/2015 20:24:37 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 Commit id: 722ae931d95ad2242857b94a1383ad39650a6012
refresh documentations
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@106977 bc3139a8-67e5-0310-9ffc-ced21a209358
Zuguang Gu authored on 01/08/2015 18:51:11 | ... | ... |
@@ -9,12 +9,13 @@ Draw the single annotation |
| 9 | 9 |
|
| 10 | 10 |
} |
| 11 | 11 |
\usage{
|
| 12 |
-\S4method{draw}{SingleAnnotation}(object, index, k = NULL)}
|
|
| 12 |
+\S4method{draw}{SingleAnnotation}(object, index, k = NULL, n = NULL)}
|
|
| 13 | 13 |
\arguments{
|
| 14 | 14 |
|
| 15 | 15 |
\item{object}{a \code{\link{SingleAnnotation-class}} object.}
|
| 16 | 16 |
\item{index}{a vector of orders}
|
| 17 | 17 |
\item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewportwhich contains the annotation graphics.}
|
| 18 |
+ \item{n}{total number of row slices}
|
|
| 18 | 19 |
} |
| 19 | 20 |
\details{
|
| 20 | 21 |
A viewport is created. |
Commit id: 722ae931d95ad2242857b94a1383ad39650a6012
refresh documentations
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@106977 bc3139a8-67e5-0310-9ffc-ced21a209358
z.gu authored on 01/08/2015 18:51:11 | ... | ... |
@@ -9,12 +9,13 @@ Draw the single annotation |
| 9 | 9 |
|
| 10 | 10 |
} |
| 11 | 11 |
\usage{
|
| 12 |
-\S4method{draw}{SingleAnnotation}(object, index, k = NULL)}
|
|
| 12 |
+\S4method{draw}{SingleAnnotation}(object, index, k = NULL, n = NULL)}
|
|
| 13 | 13 |
\arguments{
|
| 14 | 14 |
|
| 15 | 15 |
\item{object}{a \code{\link{SingleAnnotation-class}} object.}
|
| 16 | 16 |
\item{index}{a vector of orders}
|
| 17 | 17 |
\item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewportwhich contains the annotation graphics.}
|
| 18 |
+ \item{n}{total number of row slices}
|
|
| 18 | 19 |
} |
| 19 | 20 |
\details{
|
| 20 | 21 |
A viewport is created. |
Commit id: 174dbdcbcad3be858d664784793f1b2424acc2c0
remove plot.HeatmapList and print.HeatmapList
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@106530 bc3139a8-67e5-0310-9ffc-ced21a209358
Zuguang Gu authored on 18/07/2015 18:14:29 | ... | ... |
@@ -14,7 +14,7 @@ Draw the single annotation |
| 14 | 14 |
|
| 15 | 15 |
\item{object}{a \code{\link{SingleAnnotation-class}} object.}
|
| 16 | 16 |
\item{index}{a vector of orders}
|
| 17 |
- \item{k}{if row annotation is splitted, the value identifies which row slice.}
|
|
| 17 |
+ \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewportwhich contains the annotation graphics.}
|
|
| 18 | 18 |
} |
| 19 | 19 |
\details{
|
| 20 | 20 |
A viewport is created. |
| ... | ... |
@@ -31,7 +31,6 @@ Zuguang Gu <z.gu@dkfz.de> |
| 31 | 31 |
|
| 32 | 32 |
} |
| 33 | 33 |
\examples{
|
| 34 |
- |
|
| 35 | 34 |
anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
|
| 36 | 35 |
grid.newpage(); draw(anno, 1:5) |
| 37 | 36 |
grid.newpage(); draw(anno, c(1, 4, 3, 5, 2)) |
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 | ... | ... |
@@ -14,7 +14,7 @@ Draw the single annotation |
| 14 | 14 |
|
| 15 | 15 |
\item{object}{a \code{\link{SingleAnnotation-class}} object.}
|
| 16 | 16 |
\item{index}{a vector of orders}
|
| 17 |
- \item{k}{if row annotation is splitted, the value identifies which row slice.}
|
|
| 17 |
+ \item{k}{if row annotation is splitted, the value identifies which row slice. It is only used for the naems of the viewportwhich contains the annotation graphics.}
|
|
| 18 | 18 |
} |
| 19 | 19 |
\details{
|
| 20 | 20 |
A viewport is created. |
| ... | ... |
@@ -31,7 +31,6 @@ Zuguang Gu <z.gu@dkfz.de> |
| 31 | 31 |
|
| 32 | 32 |
} |
| 33 | 33 |
\examples{
|
| 34 |
- |
|
| 35 | 34 |
anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
|
| 36 | 35 |
grid.newpage(); draw(anno, 1:5) |
| 37 | 36 |
grid.newpage(); draw(anno, c(1, 4, 3, 5, 2)) |
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: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@106487 bc3139a8-67e5-0310-9ffc-ced21a209358
Zuguang Gu authored on 16/07/2015 15:21:23 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 Commit id: ff9ffa810ca9f16a253861d97301062962dbe38b
titles support expression now
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@106147 bc3139a8-67e5-0310-9ffc-ced21a209358
Zuguang Gu authored on 13/07/2015 21:26:16 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 Commit id: e811f8100ef035ff75c16312b3e5112cc82d4a49
continuous legend is supported
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@106027 bc3139a8-67e5-0310-9ffc-ced21a209358
Zuguang Gu authored on 13/07/2015 10:21:55 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 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: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105855 bc3139a8-67e5-0310-9ffc-ced21a209358
Zuguang Gu authored on 06/07/2015 22:31:19 | ... | ... |
@@ -31,8 +31,6 @@ Zuguang Gu <z.gu@dkfz.de> |
| 31 | 31 |
|
| 32 | 32 |
} |
| 33 | 33 |
\examples{
|
| 34 |
- |
|
| 35 |
- |
|
| 36 | 34 |
anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
|
| 37 | 35 |
grid.newpage(); draw(anno, 1:5) |
| 38 | 36 |
grid.newpage(); draw(anno, c(1, 4, 3, 5, 2)) |
| ... | ... |
@@ -54,6 +52,4 @@ anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red"
|
| 54 | 52 |
grid.newpage(); draw(anno, 1:10) |
| 55 | 53 |
|
| 56 | 54 |
anno = SingleAnnotation(fun = anno_points(1:10)) |
| 57 |
-grid.newpage(); draw(anno, 1:10) |
|
| 58 |
- |
|
| 59 |
-} |
|
| 55 |
+grid.newpage(); draw(anno, 1:10)} |
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 | ... | ... |
@@ -31,8 +31,6 @@ Zuguang Gu <z.gu@dkfz.de> |
| 31 | 31 |
|
| 32 | 32 |
} |
| 33 | 33 |
\examples{
|
| 34 |
- |
|
| 35 |
- |
|
| 36 | 34 |
anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
|
| 37 | 35 |
grid.newpage(); draw(anno, 1:5) |
| 38 | 36 |
grid.newpage(); draw(anno, c(1, 4, 3, 5, 2)) |
| ... | ... |
@@ -54,6 +52,4 @@ anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red"
|
| 54 | 52 |
grid.newpage(); draw(anno, 1:10) |
| 55 | 53 |
|
| 56 | 54 |
anno = SingleAnnotation(fun = anno_points(1:10)) |
| 57 |
-grid.newpage(); draw(anno, 1:10) |
|
| 58 |
- |
|
| 59 |
-} |
|
| 55 |
+grid.newpage(); draw(anno, 1:10)} |
Commit id: 9d7fc297a370b44dd3bfb12696ed9eac33aed48a
refreshed documentations
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105365 bc3139a8-67e5-0310-9ffc-ced21a209358
Zuguang Gu authored on 23/06/2015 10:24:06 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 Commit id: 1d5cea822fed8ed91d7ead49f520f719b3fecfd9
refreshed documentations
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105355 bc3139a8-67e5-0310-9ffc-ced21a209358
Zuguang Gu authored on 23/06/2015 08:33:59 | ... | ... |
@@ -31,6 +31,7 @@ Zuguang Gu <z.gu@dkfz.de> |
| 31 | 31 |
|
| 32 | 32 |
} |
| 33 | 33 |
\examples{
|
| 34 |
+ |
|
| 34 | 35 |
anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
|
| 35 | 36 |
grid.newpage(); draw(anno, 1:5) |
| 36 | 37 |
grid.newpage(); draw(anno, c(1, 4, 3, 5, 2)) |
| ... | ... |
@@ -52,4 +53,6 @@ anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red"
|
| 52 | 53 |
grid.newpage(); draw(anno, 1:10) |
| 53 | 54 |
|
| 54 | 55 |
anno = SingleAnnotation(fun = anno_points(1:10)) |
| 55 |
-grid.newpage(); draw(anno, 1:10)} |
|
| 56 |
+grid.newpage(); draw(anno, 1:10) |
|
| 57 |
+ |
|
| 58 |
+} |
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 | ... | ... |
@@ -31,6 +31,7 @@ Zuguang Gu <z.gu@dkfz.de> |
| 31 | 31 |
|
| 32 | 32 |
} |
| 33 | 33 |
\examples{
|
| 34 |
+ |
|
| 34 | 35 |
anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
|
| 35 | 36 |
grid.newpage(); draw(anno, 1:5) |
| 36 | 37 |
grid.newpage(); draw(anno, c(1, 4, 3, 5, 2)) |
| ... | ... |
@@ -52,4 +53,6 @@ anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red"
|
| 52 | 53 |
grid.newpage(); draw(anno, 1:10) |
| 53 | 54 |
|
| 54 | 55 |
anno = SingleAnnotation(fun = anno_points(1:10)) |
| 55 |
-grid.newpage(); draw(anno, 1:10)} |
|
| 56 |
+grid.newpage(); draw(anno, 1:10) |
|
| 57 |
+ |
|
| 58 |
+} |
Commit id: 1682e4aed696b8fa901530ebc6b9d67ad2a013ad
refresh documentations and NAMESPACE
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105345 bc3139a8-67e5-0310-9ffc-ced21a209358
Zuguang Gu authored on 22/06/2015 21:57:04 | ... | ... |
@@ -1,40 +1,33 @@ |
| 1 | 1 |
\name{draw-SingleAnnotation-method}
|
| 2 | 2 |
\alias{draw,SingleAnnotation-method}
|
| 3 | 3 |
\title{
|
| 4 |
-Draw the single annotation |
|
| 5 |
- |
|
| 4 |
+Draw the single annotation |
|
| 6 | 5 |
|
| 7 | 6 |
} |
| 8 | 7 |
\description{
|
| 9 |
-Draw the single annotation |
|
| 10 |
- |
|
| 8 |
+Draw the single annotation |
|
| 11 | 9 |
|
| 12 | 10 |
} |
| 13 | 11 |
\usage{
|
| 14 |
-\S4method{draw}{SingleAnnotation}(object, index, k = NULL)
|
|
| 15 |
-} |
|
| 12 |
+\S4method{draw}{SingleAnnotation}(object, index, k = NULL)}
|
|
| 16 | 13 |
\arguments{
|
| 17 | 14 |
|
| 18 | 15 |
\item{object}{a \code{\link{SingleAnnotation-class}} object.}
|
| 19 | 16 |
\item{index}{a vector of orders}
|
| 20 | 17 |
\item{k}{if row annotation is splitted, the value identifies which row slice.}
|
| 21 |
- |
|
| 22 | 18 |
} |
| 23 | 19 |
\details{
|
| 24 |
-A viewport is created. |
|
| 25 |
- |
|
| 26 |
-The graphics would be different depending the annotation is a row annotation or a column annotation. |
|
| 20 |
+A viewport is created. |
|
| 27 | 21 |
|
| 22 |
+The graphics would be different depending the annotation is a row annotation or a column annotation. |
|
| 28 | 23 |
|
| 29 | 24 |
} |
| 30 | 25 |
\value{
|
| 31 |
-No value is returned. |
|
| 32 |
- |
|
| 26 |
+No value is returned. |
|
| 33 | 27 |
|
| 34 | 28 |
} |
| 35 | 29 |
\author{
|
| 36 |
-Zuguang Gu <z.gu@dkfz.de> |
|
| 37 |
- |
|
| 30 |
+Zuguang Gu <z.gu@dkfz.de> |
|
| 38 | 31 |
|
| 39 | 32 |
} |
| 40 | 33 |
\examples{
|
| ... | ... |
@@ -59,5 +52,4 @@ anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red"
|
| 59 | 52 |
grid.newpage(); draw(anno, 1:10) |
| 60 | 53 |
|
| 61 | 54 |
anno = SingleAnnotation(fun = anno_points(1:10)) |
| 62 |
-grid.newpage(); draw(anno, 1:10) |
|
| 63 |
-} |
|
| 55 |
+grid.newpage(); draw(anno, 1:10)} |
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 | ... | ... |
@@ -1,40 +1,33 @@ |
| 1 | 1 |
\name{draw-SingleAnnotation-method}
|
| 2 | 2 |
\alias{draw,SingleAnnotation-method}
|
| 3 | 3 |
\title{
|
| 4 |
-Draw the single annotation |
|
| 5 |
- |
|
| 4 |
+Draw the single annotation |
|
| 6 | 5 |
|
| 7 | 6 |
} |
| 8 | 7 |
\description{
|
| 9 |
-Draw the single annotation |
|
| 10 |
- |
|
| 8 |
+Draw the single annotation |
|
| 11 | 9 |
|
| 12 | 10 |
} |
| 13 | 11 |
\usage{
|
| 14 |
-\S4method{draw}{SingleAnnotation}(object, index, k = NULL)
|
|
| 15 |
-} |
|
| 12 |
+\S4method{draw}{SingleAnnotation}(object, index, k = NULL)}
|
|
| 16 | 13 |
\arguments{
|
| 17 | 14 |
|
| 18 | 15 |
\item{object}{a \code{\link{SingleAnnotation-class}} object.}
|
| 19 | 16 |
\item{index}{a vector of orders}
|
| 20 | 17 |
\item{k}{if row annotation is splitted, the value identifies which row slice.}
|
| 21 |
- |
|
| 22 | 18 |
} |
| 23 | 19 |
\details{
|
| 24 |
-A viewport is created. |
|
| 25 |
- |
|
| 26 |
-The graphics would be different depending the annotation is a row annotation or a column annotation. |
|
| 20 |
+A viewport is created. |
|
| 27 | 21 |
|
| 22 |
+The graphics would be different depending the annotation is a row annotation or a column annotation. |
|
| 28 | 23 |
|
| 29 | 24 |
} |
| 30 | 25 |
\value{
|
| 31 |
-No value is returned. |
|
| 32 |
- |
|
| 26 |
+No value is returned. |
|
| 33 | 27 |
|
| 34 | 28 |
} |
| 35 | 29 |
\author{
|
| 36 |
-Zuguang Gu <z.gu@dkfz.de> |
|
| 37 |
- |
|
| 30 |
+Zuguang Gu <z.gu@dkfz.de> |
|
| 38 | 31 |
|
| 39 | 32 |
} |
| 40 | 33 |
\examples{
|
| ... | ... |
@@ -59,5 +52,4 @@ anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red"
|
| 59 | 52 |
grid.newpage(); draw(anno, 1:10) |
| 60 | 53 |
|
| 61 | 54 |
anno = SingleAnnotation(fun = anno_points(1:10)) |
| 62 |
-grid.newpage(); draw(anno, 1:10) |
|
| 63 |
-} |
|
| 55 |
+grid.newpage(); draw(anno, 1:10)} |
Commit id: ff6ad79beeef75c709dc08588bb942ad86de9761
rotation for heatmap title supported
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105315 bc3139a8-67e5-0310-9ffc-ced21a209358
Zuguang Gu authored on 22/06/2015 15:09:06 | ... | ... |
@@ -1,33 +1,40 @@ |
| 1 | 1 |
\name{draw-SingleAnnotation-method}
|
| 2 | 2 |
\alias{draw,SingleAnnotation-method}
|
| 3 | 3 |
\title{
|
| 4 |
-Draw the single annotation |
|
| 4 |
+Draw the single annotation |
|
| 5 |
+ |
|
| 5 | 6 |
|
| 6 | 7 |
} |
| 7 | 8 |
\description{
|
| 8 |
-Draw the single annotation |
|
| 9 |
+Draw the single annotation |
|
| 10 |
+ |
|
| 9 | 11 |
|
| 10 | 12 |
} |
| 11 | 13 |
\usage{
|
| 12 |
-\S4method{draw}{SingleAnnotation}(object, index, k = NULL)}
|
|
| 14 |
+\S4method{draw}{SingleAnnotation}(object, index, k = NULL)
|
|
| 15 |
+} |
|
| 13 | 16 |
\arguments{
|
| 14 | 17 |
|
| 15 | 18 |
\item{object}{a \code{\link{SingleAnnotation-class}} object.}
|
| 16 | 19 |
\item{index}{a vector of orders}
|
| 17 | 20 |
\item{k}{if row annotation is splitted, the value identifies which row slice.}
|
| 21 |
+ |
|
| 18 | 22 |
} |
| 19 | 23 |
\details{
|
| 20 |
-A viewport is created. |
|
| 24 |
+A viewport is created. |
|
| 25 |
+ |
|
| 26 |
+The graphics would be different depending the annotation is a row annotation or a column annotation. |
|
| 21 | 27 |
|
| 22 |
-The graphics would be different depending the annotation is a row annotation or a column annotation. |
|
| 23 | 28 |
|
| 24 | 29 |
} |
| 25 | 30 |
\value{
|
| 26 |
-No value is returned. |
|
| 31 |
+No value is returned. |
|
| 32 |
+ |
|
| 27 | 33 |
|
| 28 | 34 |
} |
| 29 | 35 |
\author{
|
| 30 |
-Zuguang Gu <z.gu@dkfz.de> |
|
| 36 |
+Zuguang Gu <z.gu@dkfz.de> |
|
| 37 |
+ |
|
| 31 | 38 |
|
| 32 | 39 |
} |
| 33 | 40 |
\examples{
|
| ... | ... |
@@ -52,4 +59,5 @@ anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red"
|
| 52 | 59 |
grid.newpage(); draw(anno, 1:10) |
| 53 | 60 |
|
| 54 | 61 |
anno = SingleAnnotation(fun = anno_points(1:10)) |
| 55 |
-grid.newpage(); draw(anno, 1:10)} |
|
| 62 |
+grid.newpage(); draw(anno, 1:10) |
|
| 63 |
+} |
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 | ... | ... |
@@ -1,33 +1,40 @@ |
| 1 | 1 |
\name{draw-SingleAnnotation-method}
|
| 2 | 2 |
\alias{draw,SingleAnnotation-method}
|
| 3 | 3 |
\title{
|
| 4 |
-Draw the single annotation |
|
| 4 |
+Draw the single annotation |
|
| 5 |
+ |
|
| 5 | 6 |
|
| 6 | 7 |
} |
| 7 | 8 |
\description{
|
| 8 |
-Draw the single annotation |
|
| 9 |
+Draw the single annotation |
|
| 10 |
+ |
|
| 9 | 11 |
|
| 10 | 12 |
} |
| 11 | 13 |
\usage{
|
| 12 |
-\S4method{draw}{SingleAnnotation}(object, index, k = NULL)}
|
|
| 14 |
+\S4method{draw}{SingleAnnotation}(object, index, k = NULL)
|
|
| 15 |
+} |
|
| 13 | 16 |
\arguments{
|
| 14 | 17 |
|
| 15 | 18 |
\item{object}{a \code{\link{SingleAnnotation-class}} object.}
|
| 16 | 19 |
\item{index}{a vector of orders}
|
| 17 | 20 |
\item{k}{if row annotation is splitted, the value identifies which row slice.}
|
| 21 |
+ |
|
| 18 | 22 |
} |
| 19 | 23 |
\details{
|
| 20 |
-A viewport is created. |
|
| 24 |
+A viewport is created. |
|
| 25 |
+ |
|
| 26 |
+The graphics would be different depending the annotation is a row annotation or a column annotation. |
|
| 21 | 27 |
|
| 22 |
-The graphics would be different depending the annotation is a row annotation or a column annotation. |
|
| 23 | 28 |
|
| 24 | 29 |
} |
| 25 | 30 |
\value{
|
| 26 |
-No value is returned. |
|
| 31 |
+No value is returned. |
|
| 32 |
+ |
|
| 27 | 33 |
|
| 28 | 34 |
} |
| 29 | 35 |
\author{
|
| 30 |
-Zuguang Gu <z.gu@dkfz.de> |
|
| 36 |
+Zuguang Gu <z.gu@dkfz.de> |
|
| 37 |
+ |
|
| 31 | 38 |
|
| 32 | 39 |
} |
| 33 | 40 |
\examples{
|
| ... | ... |
@@ -52,4 +59,5 @@ anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red"
|
| 52 | 59 |
grid.newpage(); draw(anno, 1:10) |
| 53 | 60 |
|
| 54 | 61 |
anno = SingleAnnotation(fun = anno_points(1:10)) |
| 55 |
-grid.newpage(); draw(anno, 1:10)} |
|
| 62 |
+grid.newpage(); draw(anno, 1:10) |
|
| 63 |
+} |
Commit id: 6cf15a1b2514d9c86295206a55c9d5efadc00f70
check row orders
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105276 bc3139a8-67e5-0310-9ffc-ced21a209358
Zuguang Gu authored on 21/06/2015 17:44:09 | ... | ... |
@@ -1,40 +1,33 @@ |
| 1 | 1 |
\name{draw-SingleAnnotation-method}
|
| 2 | 2 |
\alias{draw,SingleAnnotation-method}
|
| 3 | 3 |
\title{
|
| 4 |
-Draw the single annotation |
|
| 5 |
- |
|
| 4 |
+Draw the single annotation |
|
| 6 | 5 |
|
| 7 | 6 |
} |
| 8 | 7 |
\description{
|
| 9 |
-Draw the single annotation |
|
| 10 |
- |
|
| 8 |
+Draw the single annotation |
|
| 11 | 9 |
|
| 12 | 10 |
} |
| 13 | 11 |
\usage{
|
| 14 |
-\S4method{draw}{SingleAnnotation}(object, index, k = NULL)
|
|
| 15 |
-} |
|
| 12 |
+\S4method{draw}{SingleAnnotation}(object, index, k = NULL)}
|
|
| 16 | 13 |
\arguments{
|
| 17 | 14 |
|
| 18 | 15 |
\item{object}{a \code{\link{SingleAnnotation-class}} object.}
|
| 19 | 16 |
\item{index}{a vector of orders}
|
| 20 | 17 |
\item{k}{if row annotation is splitted, the value identifies which row slice.}
|
| 21 |
- |
|
| 22 | 18 |
} |
| 23 | 19 |
\details{
|
| 24 |
-A viewport is created. |
|
| 25 |
- |
|
| 26 |
-The graphics would be different depending the annotation is a row annotation or a column annotation. |
|
| 20 |
+A viewport is created. |
|
| 27 | 21 |
|
| 22 |
+The graphics would be different depending the annotation is a row annotation or a column annotation. |
|
| 28 | 23 |
|
| 29 | 24 |
} |
| 30 | 25 |
\value{
|
| 31 |
-No value is returned. |
|
| 32 |
- |
|
| 26 |
+No value is returned. |
|
| 33 | 27 |
|
| 34 | 28 |
} |
| 35 | 29 |
\author{
|
| 36 |
-Zuguang Gu <z.gu@dkfz.de> |
|
| 37 |
- |
|
| 30 |
+Zuguang Gu <z.gu@dkfz.de> |
|
| 38 | 31 |
|
| 39 | 32 |
} |
| 40 | 33 |
\examples{
|
| ... | ... |
@@ -59,5 +52,4 @@ anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red"
|
| 59 | 52 |
grid.newpage(); draw(anno, 1:10) |
| 60 | 53 |
|
| 61 | 54 |
anno = SingleAnnotation(fun = anno_points(1:10)) |
| 62 |
-grid.newpage(); draw(anno, 1:10) |
|
| 63 |
-} |
|
| 55 |
+grid.newpage(); draw(anno, 1:10)} |
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 | ... | ... |
@@ -1,40 +1,33 @@ |
| 1 | 1 |
\name{draw-SingleAnnotation-method}
|
| 2 | 2 |
\alias{draw,SingleAnnotation-method}
|
| 3 | 3 |
\title{
|
| 4 |
-Draw the single annotation |
|
| 5 |
- |
|
| 4 |
+Draw the single annotation |
|
| 6 | 5 |
|
| 7 | 6 |
} |
| 8 | 7 |
\description{
|
| 9 |
-Draw the single annotation |
|
| 10 |
- |
|
| 8 |
+Draw the single annotation |
|
| 11 | 9 |
|
| 12 | 10 |
} |
| 13 | 11 |
\usage{
|
| 14 |
-\S4method{draw}{SingleAnnotation}(object, index, k = NULL)
|
|
| 15 |
-} |
|
| 12 |
+\S4method{draw}{SingleAnnotation}(object, index, k = NULL)}
|
|
| 16 | 13 |
\arguments{
|
| 17 | 14 |
|
| 18 | 15 |
\item{object}{a \code{\link{SingleAnnotation-class}} object.}
|
| 19 | 16 |
\item{index}{a vector of orders}
|
| 20 | 17 |
\item{k}{if row annotation is splitted, the value identifies which row slice.}
|
| 21 |
- |
|
| 22 | 18 |
} |
| 23 | 19 |
\details{
|
| 24 |
-A viewport is created. |
|
| 25 |
- |
|
| 26 |
-The graphics would be different depending the annotation is a row annotation or a column annotation. |
|
| 20 |
+A viewport is created. |
|
| 27 | 21 |
|
| 22 |
+The graphics would be different depending the annotation is a row annotation or a column annotation. |
|
| 28 | 23 |
|
| 29 | 24 |
} |
| 30 | 25 |
\value{
|
| 31 |
-No value is returned. |
|
| 32 |
- |
|
| 26 |
+No value is returned. |
|
| 33 | 27 |
|
| 34 | 28 |
} |
| 35 | 29 |
\author{
|
| 36 |
-Zuguang Gu <z.gu@dkfz.de> |
|
| 37 |
- |
|
| 30 |
+Zuguang Gu <z.gu@dkfz.de> |
|
| 38 | 31 |
|
| 39 | 32 |
} |
| 40 | 33 |
\examples{
|
| ... | ... |
@@ -59,5 +52,4 @@ anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red"
|
| 59 | 52 |
grid.newpage(); draw(anno, 1:10) |
| 60 | 53 |
|
| 61 | 54 |
anno = SingleAnnotation(fun = anno_points(1:10)) |
| 62 |
-grid.newpage(); draw(anno, 1:10) |
|
| 63 |
-} |
|
| 55 |
+grid.newpage(); draw(anno, 1:10)} |
Commit id: 4769a51610e162e0f84b7fc1bb7bb69deb61c3e6
adjust component name and size
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105094 bc3139a8-67e5-0310-9ffc-ced21a209358
Zuguang Gu authored on 17/06/2015 20:03:45 | ... | ... |
@@ -11,12 +11,13 @@ Draw the single annotation |
| 11 | 11 |
|
| 12 | 12 |
} |
| 13 | 13 |
\usage{
|
| 14 |
-\S4method{draw}{SingleAnnotation}(object, index)
|
|
| 14 |
+\S4method{draw}{SingleAnnotation}(object, index, k = NULL)
|
|
| 15 | 15 |
} |
| 16 | 16 |
\arguments{
|
| 17 | 17 |
|
| 18 | 18 |
\item{object}{a \code{\link{SingleAnnotation-class}} object.}
|
| 19 | 19 |
\item{index}{a vector of orders}
|
| 20 |
+ \item{k}{if row annotation is splitted, the value identifies which row slice.}
|
|
| 20 | 21 |
|
| 21 | 22 |
} |
| 22 | 23 |
\details{
|
Commit id: 4769a51610e162e0f84b7fc1bb7bb69deb61c3e6
adjust component name and size
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105094 bc3139a8-67e5-0310-9ffc-ced21a209358
z.gu authored on 17/06/2015 20:03:45 | ... | ... |
@@ -11,12 +11,13 @@ Draw the single annotation |
| 11 | 11 |
|
| 12 | 12 |
} |
| 13 | 13 |
\usage{
|
| 14 |
-\S4method{draw}{SingleAnnotation}(object, index)
|
|
| 14 |
+\S4method{draw}{SingleAnnotation}(object, index, k = NULL)
|
|
| 15 | 15 |
} |
| 16 | 16 |
\arguments{
|
| 17 | 17 |
|
| 18 | 18 |
\item{object}{a \code{\link{SingleAnnotation-class}} object.}
|
| 19 | 19 |
\item{index}{a vector of orders}
|
| 20 |
+ \item{k}{if row annotation is splitted, the value identifies which row slice.}
|
|
| 20 | 21 |
|
| 21 | 22 |
} |
| 22 | 23 |
\details{
|
ComplexHeatmap/ podkat/ RBM/
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@101658 bc3139a8-67e5-0310-9ffc-ced21a209358
Sonali Arora authored on 31/03/2015 18:31:58 | 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,62 @@ |
| 1 |
+\name{draw-SingleAnnotation-method}
|
|
| 2 |
+\alias{draw,SingleAnnotation-method}
|
|
| 3 |
+\title{
|
|
| 4 |
+Draw the single annotation |
|
| 5 |
+ |
|
| 6 |
+ |
|
| 7 |
+} |
|
| 8 |
+\description{
|
|
| 9 |
+Draw the single annotation |
|
| 10 |
+ |
|
| 11 |
+ |
|
| 12 |
+} |
|
| 13 |
+\usage{
|
|
| 14 |
+\S4method{draw}{SingleAnnotation}(object, index)
|
|
| 15 |
+} |
|
| 16 |
+\arguments{
|
|
| 17 |
+ |
|
| 18 |
+ \item{object}{a \code{\link{SingleAnnotation-class}} object.}
|
|
| 19 |
+ \item{index}{a vector of orders}
|
|
| 20 |
+ |
|
| 21 |
+} |
|
| 22 |
+\details{
|
|
| 23 |
+A viewport is created. |
|
| 24 |
+ |
|
| 25 |
+The graphics would be different depending the annotation is a row annotation or a column annotation. |
|
| 26 |
+ |
|
| 27 |
+ |
|
| 28 |
+} |
|
| 29 |
+\value{
|
|
| 30 |
+No value is returned. |
|
| 31 |
+ |
|
| 32 |
+ |
|
| 33 |
+} |
|
| 34 |
+\author{
|
|
| 35 |
+Zuguang Gu <z.gu@dkfz.de> |
|
| 36 |
+ |
|
| 37 |
+ |
|
| 38 |
+} |
|
| 39 |
+\examples{
|
|
| 40 |
+anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
|
|
| 41 |
+grid.newpage(); draw(anno, 1:5) |
|
| 42 |
+grid.newpage(); draw(anno, c(1, 4, 3, 5, 2)) |
|
| 43 |
+ |
|
| 44 |
+anno = SingleAnnotation(value = c("a", "a", "a", "b", "b", "b"),
|
|
| 45 |
+ col = c("a" = "red", "b" = "blue"))
|
|
| 46 |
+grid.newpage(); draw(anno, 1:5) |
|
| 47 |
+grid.newpage(); draw(anno, c(1, 4, 3, 5, 2)) |
|
| 48 |
+ |
|
| 49 |
+anno = SingleAnnotation(value = c("a", "a", "a", "b", "b", "b"),
|
|
| 50 |
+ col = c("a" = "red", "b" = "blue"), which = "row")
|
|
| 51 |
+grid.newpage(); draw(anno, 1:5) |
|
| 52 |
+ |
|
| 53 |
+anno = SingleAnnotation(value = 1:10) |
|
| 54 |
+grid.newpage(); draw(anno, 1:10) |
|
| 55 |
+ |
|
| 56 |
+require(circlize) |
|
| 57 |
+anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red")))
|
|
| 58 |
+grid.newpage(); draw(anno, 1:10) |
|
| 59 |
+ |
|
| 60 |
+anno = SingleAnnotation(fun = anno_points(1:10)) |
|
| 61 |
+grid.newpage(); draw(anno, 1:10) |
|
| 62 |
+} |
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 | 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,62 @@ |
| 1 |
+\name{draw-SingleAnnotation-method}
|
|
| 2 |
+\alias{draw,SingleAnnotation-method}
|
|
| 3 |
+\title{
|
|
| 4 |
+Draw the single annotation |
|
| 5 |
+ |
|
| 6 |
+ |
|
| 7 |
+} |
|
| 8 |
+\description{
|
|
| 9 |
+Draw the single annotation |
|
| 10 |
+ |
|
| 11 |
+ |
|
| 12 |
+} |
|
| 13 |
+\usage{
|
|
| 14 |
+\S4method{draw}{SingleAnnotation}(object, index)
|
|
| 15 |
+} |
|
| 16 |
+\arguments{
|
|
| 17 |
+ |
|
| 18 |
+ \item{object}{a \code{\link{SingleAnnotation-class}} object.}
|
|
| 19 |
+ \item{index}{a vector of orders}
|
|
| 20 |
+ |
|
| 21 |
+} |
|
| 22 |
+\details{
|
|
| 23 |
+A viewport is created. |
|
| 24 |
+ |
|
| 25 |
+The graphics would be different depending the annotation is a row annotation or a column annotation. |
|
| 26 |
+ |
|
| 27 |
+ |
|
| 28 |
+} |
|
| 29 |
+\value{
|
|
| 30 |
+No value is returned. |
|
| 31 |
+ |
|
| 32 |
+ |
|
| 33 |
+} |
|
| 34 |
+\author{
|
|
| 35 |
+Zuguang Gu <z.gu@dkfz.de> |
|
| 36 |
+ |
|
| 37 |
+ |
|
| 38 |
+} |
|
| 39 |
+\examples{
|
|
| 40 |
+anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
|
|
| 41 |
+grid.newpage(); draw(anno, 1:5) |
|
| 42 |
+grid.newpage(); draw(anno, c(1, 4, 3, 5, 2)) |
|
| 43 |
+ |
|
| 44 |
+anno = SingleAnnotation(value = c("a", "a", "a", "b", "b", "b"),
|
|
| 45 |
+ col = c("a" = "red", "b" = "blue"))
|
|
| 46 |
+grid.newpage(); draw(anno, 1:5) |
|
| 47 |
+grid.newpage(); draw(anno, c(1, 4, 3, 5, 2)) |
|
| 48 |
+ |
|
| 49 |
+anno = SingleAnnotation(value = c("a", "a", "a", "b", "b", "b"),
|
|
| 50 |
+ col = c("a" = "red", "b" = "blue"), which = "row")
|
|
| 51 |
+grid.newpage(); draw(anno, 1:5) |
|
| 52 |
+ |
|
| 53 |
+anno = SingleAnnotation(value = 1:10) |
|
| 54 |
+grid.newpage(); draw(anno, 1:10) |
|
| 55 |
+ |
|
| 56 |
+require(circlize) |
|
| 57 |
+anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red")))
|
|
| 58 |
+grid.newpage(); draw(anno, 1:10) |
|
| 59 |
+ |
|
| 60 |
+anno = SingleAnnotation(fun = anno_points(1:10)) |
|
| 61 |
+grid.newpage(); draw(anno, 1:10) |
|
| 62 |
+} |