Browse code

generate documentations by pkgdown

Zuguang Gu authored on 18/10/2019 11:34:02
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@@ -1,46 +0,0 @@
1
-\name{anno_barplot}
2
-\alias{anno_barplot}
3
-\title{
4
-Barplot Annotation
5
-}
6
-\description{
7
-Barplot Annotation
8
-}
9
-\usage{
10
-anno_barplot(x, baseline = 0, which = c("column", "row"), border = TRUE, bar_width = 0.6,
11
-    gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, axis = TRUE,
12
-    axis_param = default_axis_param(which),
13
-    width = NULL, height = NULL, ...)
14
-}
15
-\arguments{
16
-
17
-  \item{x}{The value vector. The value can be a vector or a matrix. The length of the vector or the number of rows of the matrix is taken as the number of the observations of the annotation. If \code{x} is a vector, the barplots will be represented as stacked barplots.}
18
-  \item{baseline}{baseline of bars. The value should be "min" or "max", or a numeric value. It is enforced to be zero for stacked barplots.}
19
-  \item{which}{Whether it is a column annotation or a row annotation?}
20
-  \item{border}{Wether draw borders of the annotation region?}
21
-  \item{bar_width}{Relative width of the bars. The value should be smaller than one.}
22
-  \item{gp}{Graphic parameters for points. The length of each graphic parameter can be 1, length of \code{x} if \code{x} is a vector, or number of columns of \code{x} is \code{x} is a matrix.}
23
-  \item{ylim}{Data ranges. By default it is \code{range(x)} if \code{x} is a vector, or \code{range(rowSums(x))} if \code{x} is a matrix.}
24
-  \item{extend}{The extension to both side of \code{ylim}. The value is a percent value corresponding to \code{ylim[2] - ylim[1]}.}
25
-  \item{axis}{Whether to add axis?}
26
-  \item{axis_param}{parameters for controlling axis. See \code{\link{default_axis_param}} for all possible settings and default parameters.}
27
-  \item{width}{Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.}
28
-  \item{height}{Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.}
29
-  \item{...}{Other arguments.}
30
-
31
-}
32
-\value{
33
-An annotation function which can be used in \code{\link{HeatmapAnnotation}}.
34
-}
35
-\seealso{
36
-\url{https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#barplot_annotation}
37
-}
38
-\examples{
39
-anno = anno_barplot(1:10)
40
-draw(anno, test = "a vector")
41
-
42
-m = matrix(runif(4*10), nc = 4)
43
-m = t(apply(m, 1, function(x) x/sum(x)))
44
-anno = anno_barplot(m, gp = gpar(fill = 2:5), bar_width = 1, height = unit(6, "cm"))
45
-draw(anno, test = "proportion matrix")
46
-}
Browse code

check arguments from old versions

jokergoo authored on 02/11/2018 11:11:30
Showing1 changed files
... ...
@@ -10,7 +10,7 @@ Barplot Annotation
10 10
 anno_barplot(x, baseline = 0, which = c("column", "row"), border = TRUE, bar_width = 0.6,
11 11
     gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, axis = TRUE,
12 12
     axis_param = default_axis_param(which),
13
-    width = NULL, height = NULL)
13
+    width = NULL, height = NULL, ...)
14 14
 }
15 15
 \arguments{
16 16
 
... ...
@@ -26,6 +26,7 @@ anno_barplot(x, baseline = 0, which = c("column", "row"), border = TRUE, bar_wid
26 26
   \item{axis_param}{parameters for controlling axis. See \code{\link{default_axis_param}} for all possible settings and default parameters.}
27 27
   \item{width}{Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.}
28 28
   \item{height}{Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.}
29
+  \item{...}{Other arguments.}
29 30
 
30 31
 }
31 32
 \value{
Browse code

documentation checked

Zuguang Gu authored on 23/10/2018 19:59:12
Showing1 changed files
... ...
@@ -31,6 +31,9 @@ anno_barplot(x, baseline = 0, which = c("column", "row"), border = TRUE, bar_wid
31 31
 \value{
32 32
 An annotation function which can be used in \code{\link{HeatmapAnnotation}}.
33 33
 }
34
+\seealso{
35
+\url{https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#barplot_annotation}
36
+}
34 37
 \examples{
35 38
 anno = anno_barplot(1:10)
36 39
 draw(anno, test = "a vector")
Browse code

update

jokergoo authored on 12/10/2018 15:28:37
Showing1 changed files
... ...
@@ -24,8 +24,8 @@ anno_barplot(x, baseline = 0, which = c("column", "row"), border = TRUE, bar_wid
24 24
   \item{extend}{The extension to both side of \code{ylim}. The value is a percent value corresponding to \code{ylim[2] - ylim[1]}.}
25 25
   \item{axis}{Whether to add axis?}
26 26
   \item{axis_param}{parameters for controlling axis. See \code{\link{default_axis_param}} for all possible settings and default parameters.}
27
-  \item{width}{Width of the annotation.}
28
-  \item{height}{Height of the annotation.}
27
+  \item{width}{Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.}
28
+  \item{height}{Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.}
29 29
 
30 30
 }
31 31
 \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
... ...
@@ -1,43 +1,42 @@
1 1
 \name{anno_barplot}
2 2
 \alias{anno_barplot}
3 3
 \title{
4
-Using barplot as annotation
4
+Barplot Annotation
5 5
 }
6 6
 \description{
7
-Using barplot as annotation
7
+Barplot Annotation
8 8
 }
9 9
 \usage{
10
-anno_barplot(x, baseline = "min", which = c("column", "row"), border = TRUE, bar_width = 0.6,
11
-    gp = gpar(fill = "#CCCCCC"), ylim = NULL, axis = FALSE, axis_side = NULL,
12
-    axis_gp = gpar(fontsize = 8), axis_direction = c("normal", "reverse"), ...)
10
+anno_barplot(x, baseline = 0, which = c("column", "row"), border = TRUE, bar_width = 0.6,
11
+    gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, axis = TRUE,
12
+    axis_param = default_axis_param(which),
13
+    width = NULL, height = NULL)
13 14
 }
14 15
 \arguments{
15 16
 
16
-  \item{x}{a vector of numeric values. If the value is a matrix, columns of the matrix will be represented as stacked barplots. Note for stacked barplots, each row in the matrix should only contain values with same sign (either all positive or all negative).}
17
-  \item{baseline}{baseline for bars. The value should be "min" or "max", or a numeric value. It is enforced to be zero for stacked barplots.}
18
-  \item{which}{is the annotation a column annotation or a row annotation?}
19
-  \item{border}{whether show border of the annotation compoment}
20
-  \item{bar_width}{relative width of the bars, should less than one}
21
-  \item{gp}{graphic parameters. If it is the stacked barplots, the length of the graphic parameter should  be same as the number of stacks.}
22
-  \item{ylim}{data ranges.}
23
-  \item{axis}{whether add axis}
24
-  \item{axis_side}{if it is placed as column annotation, value can only be "left" or "right". If it is placed as row annotation, value can only be "bottom" or "top".}
25
-  \item{axis_gp}{graphic parameters for axis}
26
-  \item{axis_direction}{if the annotation is row annotation, should the axis be from left to right (default) or follow the reversed direction?}
27
-  \item{...}{for future use.}
17
+  \item{x}{The value vector. The value can be a vector or a matrix. The length of the vector or the number of rows of the matrix is taken as the number of the observations of the annotation. If \code{x} is a vector, the barplots will be represented as stacked barplots.}
18
+  \item{baseline}{baseline of bars. The value should be "min" or "max", or a numeric value. It is enforced to be zero for stacked barplots.}
19
+  \item{which}{Whether it is a column annotation or a row annotation?}
20
+  \item{border}{Wether draw borders of the annotation region?}
21
+  \item{bar_width}{Relative width of the bars. The value should be smaller than one.}
22
+  \item{gp}{Graphic parameters for points. The length of each graphic parameter can be 1, length of \code{x} if \code{x} is a vector, or number of columns of \code{x} is \code{x} is a matrix.}
23
+  \item{ylim}{Data ranges. By default it is \code{range(x)} if \code{x} is a vector, or \code{range(rowSums(x))} if \code{x} is a matrix.}
24
+  \item{extend}{The extension to both side of \code{ylim}. The value is a percent value corresponding to \code{ylim[2] - ylim[1]}.}
25
+  \item{axis}{Whether to add axis?}
26
+  \item{axis_param}{parameters for controlling axis. See \code{\link{default_axis_param}} for all possible settings and default parameters.}
27
+  \item{width}{Width of the annotation.}
28
+  \item{height}{Height of the annotation.}
28 29
 
29 30
 }
30 31
 \value{
31
-A graphic function which can be set in \code{\link{HeatmapAnnotation}} constructor method.
32
-}
33
-\author{
34
-Zuguang Gu <z.gu@dkfz.de>
32
+An annotation function which can be used in \code{\link{HeatmapAnnotation}}.
35 33
 }
36 34
 \examples{
37
-f = anno_barplot(rnorm(10))
38
-grid.newpage(); f(1:10)
39
-
40
-f = anno_barplot(rnorm(10), which = "row")
41
-grid.newpage(); f(1:10)
35
+anno = anno_barplot(1:10)
36
+draw(anno, test = "a vector")
42 37
 
38
+m = matrix(runif(4*10), nc = 4)
39
+m = t(apply(m, 1, function(x) x/sum(x)))
40
+anno = anno_barplot(m, gp = gpar(fill = 2:5), bar_width = 1, height = unit(6, "cm"))
41
+draw(anno, test = "proportion matrix")
43 42
 }
Browse code

barplots annotation supports stacked barplots

Zuguang Gu authored on 14/10/2016 11:34:33
Showing1 changed files
... ...
@@ -13,12 +13,12 @@ anno_barplot(x, baseline = "min", which = c("column", "row"), border = TRUE, bar
13 13
 }
14 14
 \arguments{
15 15
 
16
-  \item{x}{a vector of numeric values.}
17
-  \item{baseline}{baseline for bars. The value should be "min" or "max", or a numeric value.}
16
+  \item{x}{a vector of numeric values. If the value is a matrix, columns of the matrix will be represented as stacked barplots. Note for stacked barplots, each row in the matrix should only contain values with same sign (either all positive or all negative).}
17
+  \item{baseline}{baseline for bars. The value should be "min" or "max", or a numeric value. It is enforced to be zero for stacked barplots.}
18 18
   \item{which}{is the annotation a column annotation or a row annotation?}
19 19
   \item{border}{whether show border of the annotation compoment}
20 20
   \item{bar_width}{relative width of the bars, should less than one}
21
-  \item{gp}{graphic parameters.}
21
+  \item{gp}{graphic parameters. If it is the stacked barplots, the length of the graphic parameter should  be same as the number of stacks.}
22 22
   \item{ylim}{data ranges.}
23 23
   \item{axis}{whether add axis}
24 24
   \item{axis_side}{if it is placed as column annotation, value can only be "left" or "right". If it is placed as row annotation, value can only be "bottom" or "top".}
Browse code

name assigned to vp with data ranges

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@111675 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 20/12/2015 21:18:10
Showing1 changed files
... ...
@@ -8,7 +8,7 @@ Using barplot as annotation
8 8
 }
9 9
 \usage{
10 10
 anno_barplot(x, baseline = "min", which = c("column", "row"), border = TRUE, bar_width = 0.6,
11
-    gp = gpar(fill = "#CCCCCC"), lim = NULL, axis = FALSE, axis_side = NULL,
11
+    gp = gpar(fill = "#CCCCCC"), ylim = NULL, axis = FALSE, axis_side = NULL,
12 12
     axis_gp = gpar(fontsize = 8), axis_direction = c("normal", "reverse"), ...)
13 13
 }
14 14
 \arguments{
... ...
@@ -19,7 +19,7 @@ anno_barplot(x, baseline = "min", which = c("column", "row"), border = TRUE, bar
19 19
   \item{border}{whether show border of the annotation compoment}
20 20
   \item{bar_width}{relative width of the bars, should less than one}
21 21
   \item{gp}{graphic parameters.}
22
-  \item{lim}{data ranges.}
22
+  \item{ylim}{data ranges.}
23 23
   \item{axis}{whether add axis}
24 24
   \item{axis_side}{if it is placed as column annotation, value can only be "left" or "right". If it is placed as row annotation, value can only be "bottom" or "top".}
25 25
   \item{axis_gp}{graphic parameters for axis}
Browse code

Merge branch 'master' into devel

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
Showing1 changed files
... ...
@@ -21,7 +21,7 @@ anno_barplot(x, baseline = "min", which = c("column", "row"), border = TRUE, bar
21 21
   \item{gp}{graphic parameters.}
22 22
   \item{lim}{data ranges.}
23 23
   \item{axis}{whether add axis}
24
-  \item{axis_side}{if it is placed as column annotation, value can only be "left" or "right".If it is placed as row annotation, value can only be "bottom" or "top".}
24
+  \item{axis_side}{if it is placed as column annotation, value can only be "left" or "right". If it is placed as row annotation, value can only be "bottom" or "top".}
25 25
   \item{axis_gp}{graphic parameters for axis}
26 26
   \item{axis_direction}{if the annotation is row annotation, should the axis be from left to right (default) or follow the reversed direction?}
27 27
   \item{...}{for future use.}
Browse code

Merge branch 'master' into devel

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@109144 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 03/10/2015 10:32:07
Showing1 changed files
... ...
@@ -8,7 +8,7 @@ Using barplot as annotation
8 8
 }
9 9
 \usage{
10 10
 anno_barplot(x, baseline = "min", which = c("column", "row"), border = TRUE, bar_width = 0.6,
11
-    gp = gpar(fill = "#CCCCCC"), axis = FALSE, axis_side = NULL,
11
+    gp = gpar(fill = "#CCCCCC"), lim = NULL, axis = FALSE, axis_side = NULL,
12 12
     axis_gp = gpar(fontsize = 8), axis_direction = c("normal", "reverse"), ...)
13 13
 }
14 14
 \arguments{
... ...
@@ -19,6 +19,7 @@ anno_barplot(x, baseline = "min", which = c("column", "row"), border = TRUE, bar
19 19
   \item{border}{whether show border of the annotation compoment}
20 20
   \item{bar_width}{relative width of the bars, should less than one}
21 21
   \item{gp}{graphic parameters.}
22
+  \item{lim}{data ranges.}
22 23
   \item{axis}{whether add axis}
23 24
   \item{axis_side}{if it is placed as column annotation, value can only be "left" or "right".If it is placed as row annotation, value can only be "bottom" or "top".}
24 25
   \item{axis_gp}{graphic parameters for axis}
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

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
... ...
@@ -9,7 +9,8 @@ Using barplot as annotation
9 9
 \usage{
10 10
 anno_barplot(x, baseline = "min", which = c("column", "row"), border = TRUE, bar_width = 0.6,
11 11
     gp = gpar(fill = "#CCCCCC"), axis = FALSE, axis_side = NULL,
12
-    axis_gp = gpar(fontsize = 8), axis_direction = c("normal", "reverse"), ...)}
12
+    axis_gp = gpar(fontsize = 8), axis_direction = c("normal", "reverse"), ...)
13
+}
13 14
 \arguments{
14 15
 
15 16
   \item{x}{a vector of numeric values.}
... ...
@@ -23,6 +24,7 @@ anno_barplot(x, baseline = "min", which = c("column", "row"), border = TRUE, bar
23 24
   \item{axis_gp}{graphic parameters for axis}
24 25
   \item{axis_direction}{if the annotation is row annotation, should the axis be from left to right (default) or follow the reversed direction?}
25 26
   \item{...}{for future use.}
27
+
26 28
 }
27 29
 \value{
28 30
 A graphic function which can be set in \code{\link{HeatmapAnnotation}} constructor method.
... ...
@@ -36,4 +38,5 @@ grid.newpage(); f(1:10)
36 38
 
37 39
 f = anno_barplot(rnorm(10), which = "row")
38 40
 grid.newpage(); f(1:10)
41
+
39 42
 }
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{anno_barplot}
3 3
 \title{
4 4
 Using barplot as annotation
5
-
6 5
 }
7 6
 \description{
8 7
 Using barplot as annotation
9
-
10 8
 }
11 9
 \usage{
12 10
 anno_barplot(x, baseline = "min", which = c("column", "row"), border = TRUE, bar_width = 0.6,
... ...
@@ -28,27 +26,14 @@ anno_barplot(x, baseline = "min", which = c("column", "row"), border = TRUE, bar
28 26
 }
29 27
 \value{
30 28
 A graphic function which can be set in \code{\link{HeatmapAnnotation}} constructor method.
31
-
32 29
 }
33 30
 \author{
34 31
 Zuguang Gu <z.gu@dkfz.de>
35
-
36 32
 }
37 33
 \examples{
38
-
39
-
40
-
41
-
42
-
43
-
44
-
45
-
46
-
47
-
48
-
49
-
50 34
 f = anno_barplot(rnorm(10))
51 35
 grid.newpage(); f(1:10)
52 36
 
53 37
 f = anno_barplot(rnorm(10), which = "row")
54
-grid.newpage(); f(1:10)}
38
+grid.newpage(); f(1:10)
39
+}
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
... ...
@@ -9,12 +9,13 @@ Using barplot as annotation
9 9
 
10 10
 }
11 11
 \usage{
12
-anno_barplot(x, which = c("column", "row"), border = TRUE, bar_width = 0.6,
12
+anno_barplot(x, baseline = "min", which = c("column", "row"), border = TRUE, bar_width = 0.6,
13 13
     gp = gpar(fill = "#CCCCCC"), axis = FALSE, axis_side = NULL,
14
-    axis_gp = gpar(fontsize = 8), ...)}
14
+    axis_gp = gpar(fontsize = 8), axis_direction = c("normal", "reverse"), ...)}
15 15
 \arguments{
16 16
 
17 17
   \item{x}{a vector of numeric values.}
18
+  \item{baseline}{baseline for bars. The value should be "min" or "max", or a numeric value.}
18 19
   \item{which}{is the annotation a column annotation or a row annotation?}
19 20
   \item{border}{whether show border of the annotation compoment}
20 21
   \item{bar_width}{relative width of the bars, should less than one}
... ...
@@ -22,6 +23,7 @@ anno_barplot(x, which = c("column", "row"), border = TRUE, bar_width = 0.6,
22 23
   \item{axis}{whether add axis}
23 24
   \item{axis_side}{if it is placed as column annotation, value can only be "left" or "right".If it is placed as row annotation, value can only be "bottom" or "top".}
24 25
   \item{axis_gp}{graphic parameters for axis}
26
+  \item{axis_direction}{if the annotation is row annotation, should the axis be from left to right (default) or follow the reversed direction?}
25 27
   \item{...}{for future use.}
26 28
 }
27 29
 \value{
... ...
@@ -40,6 +42,11 @@ Zuguang Gu <z.gu@dkfz.de>
40 42
 
41 43
 
42 44
 
45
+
46
+
47
+
48
+
49
+
43 50
 f = anno_barplot(rnorm(10))
44 51
 grid.newpage(); f(1:10)
45 52
 
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
... ...
@@ -9,13 +9,15 @@ Using barplot as annotation
9 9
 
10 10
 }
11 11
 \usage{
12
-anno_barplot(x, which = c("column", "row"),
12
+anno_barplot(x, which = c("column", "row"), border = TRUE, bar_width = 0.6,
13 13
     gp = gpar(fill = "#CCCCCC"), axis = FALSE, axis_side = NULL,
14 14
     axis_gp = gpar(fontsize = 8), ...)}
15 15
 \arguments{
16 16
 
17 17
   \item{x}{a vector of numeric values.}
18 18
   \item{which}{is the annotation a column annotation or a row annotation?}
19
+  \item{border}{whether show border of the annotation compoment}
20
+  \item{bar_width}{relative width of the bars, should less than one}
19 21
   \item{gp}{graphic parameters.}
20 22
   \item{axis}{whether add axis}
21 23
   \item{axis_side}{if it is placed as column annotation, value can only be "left" or "right".If it is placed as row annotation, value can only be "bottom" or "top".}
... ...
@@ -37,6 +39,7 @@ Zuguang Gu <z.gu@dkfz.de>
37 39
 
38 40
 
39 41
 
42
+
40 43
 f = anno_barplot(rnorm(10))
41 44
 grid.newpage(); f(1:10)
42 45
 
Browse code

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Commit id: 3429d28233ef2cbeafcd05307042d7c7aa54a2a2

add decorate* family functions



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

z.gu authored on 06/08/2015 16:40:59
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@@ -33,6 +33,10 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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+
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+
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+
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+
36 40
 f = anno_barplot(rnorm(10))
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 grid.newpage(); f(1:10)
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Commit id: d5adc92bdbf27b45a6a4b5c7e29d2e4fe8380194

allow reordering



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

z.gu authored on 04/08/2015 20:24:37
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@@ -31,6 +31,8 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
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 }
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 \examples{
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+
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+
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 f = anno_barplot(rnorm(10))
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 grid.newpage(); f(1:10)
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Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 174dbdcbcad3be858d664784793f1b2424acc2c0

remove plot.HeatmapList and print.HeatmapList



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

z.gu authored on 18/07/2015 18:14:29
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@@ -14,11 +14,11 @@ anno_barplot(x, which = c("column", "row"),
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     axis_gp = gpar(fontsize = 8), ...)}
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 \arguments{
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-  \item{x}{a vector of values.}
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+  \item{x}{a vector of numeric values.}
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   \item{which}{is the annotation a column annotation or a row annotation?}
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   \item{gp}{graphic parameters.}
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   \item{axis}{whether add axis}
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-  \item{axis_side}{value in "left", "right", "bottom" and "top"}
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+  \item{axis_side}{if it is placed as column annotation, value can only be "left" or "right".If it is placed as row annotation, value can only be "bottom" or "top".}
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   \item{axis_gp}{graphic parameters for axis}
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   \item{...}{for future use.}
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 }
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@@ -31,7 +31,6 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
32 32
 }
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 \examples{
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-
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 f = anno_barplot(rnorm(10))
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 grid.newpage(); f(1:10)
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Browse code

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Commit id: 4cbce102eabb1633fc8980b1374795bfb44507df

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


Commit id: a15bbec76c85c15bc27273ce15f5118ea087132f

refreshed documentatinos


Commit id: b1fe0a94aa09a4a47e5a02383ce662580f057bdc

ColorMapping object has default value for name slot



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

z.gu authored on 16/07/2015 15:21:23
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@@ -31,6 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
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 }
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 \examples{
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+
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 f = anno_barplot(rnorm(10))
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 grid.newpage(); f(1:10)
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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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@@ -31,8 +31,6 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
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 }
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 \examples{
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-
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-
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 f = anno_barplot(rnorm(10))
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 grid.newpage(); f(1:10)
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Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: e811f8100ef035ff75c16312b3e5112cc82d4a49

continuous legend is supported



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

z.gu authored on 13/07/2015 10:21:55
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@@ -31,6 +31,8 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
32 32
 }
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 \examples{
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+
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+
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 f = anno_barplot(rnorm(10))
35 37
 grid.newpage(); f(1:10)
36 38
 
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 2786dac4ddaa97c69cc24e29e121ed1a1624cdf4

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


Commit id: a61c101325601aa0d4d3ba81e10c33d4a8b34c63

rows can be split if providing a clustering object



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

z.gu authored on 06/07/2015 22:31:19
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@@ -31,12 +31,8 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
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 }
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 \examples{
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-
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-
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 f = anno_barplot(rnorm(10))
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 grid.newpage(); f(1:10)
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 f = anno_barplot(rnorm(10), which = "row")
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-grid.newpage(); f(1:10)
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-
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-}
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+grid.newpage(); f(1:10)}
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Commit id: 9d7fc297a370b44dd3bfb12696ed9eac33aed48a

refreshed documentations



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

z.gu authored on 23/06/2015 10:24:06
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@@ -32,6 +32,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 f = anno_barplot(rnorm(10))
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 grid.newpage(); f(1:10)
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Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 1d5cea822fed8ed91d7ead49f520f719b3fecfd9

refreshed documentations



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

z.gu authored on 23/06/2015 08:33:59
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@@ -31,8 +31,11 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 
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 }
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 \examples{
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+
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 f = anno_barplot(rnorm(10))
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 grid.newpage(); f(1:10)
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 f = anno_barplot(rnorm(10), which = "row")
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-grid.newpage(); f(1:10)}
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+grid.newpage(); f(1:10)
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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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@@ -1,20 +1,17 @@
1 1
 \name{anno_barplot}
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 \alias{anno_barplot}
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 \title{
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-Using barplot as annotation  
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-
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+Using barplot as annotation
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 }
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 \description{
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-Using barplot as annotation  
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-
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+Using barplot as annotation
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 }
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 \usage{
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 anno_barplot(x, which = c("column", "row"),
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     gp = gpar(fill = "#CCCCCC"), axis = FALSE, axis_side = NULL,
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-    axis_gp = gpar(fontsize = 8), ...)
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-}
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+    axis_gp = gpar(fontsize = 8), ...)}
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 \arguments{
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   \item{x}{a vector of values.}
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@@ -24,16 +21,13 @@ anno_barplot(x, which = c("column", "row"),
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   \item{axis_side}{value in "left", "right", "bottom" and "top"}
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   \item{axis_gp}{graphic parameters for axis}
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   \item{...}{for future use.}
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-
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 }
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 \value{
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-A graphic function which can be set in \code{\link{HeatmapAnnotation}} constructor method.  
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-
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+A graphic function which can be set in \code{\link{HeatmapAnnotation}} constructor method.
32 27
 
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 }
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 \author{
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-Zuguang Gu <z.gu@dkfz.de>  
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-
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+Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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@@ -41,5 +35,4 @@ f = anno_barplot(rnorm(10))
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 grid.newpage(); f(1:10)
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 f = anno_barplot(rnorm(10), which = "row")
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-grid.newpage(); f(1:10)
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-}
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+grid.newpage(); f(1:10)}
Browse code

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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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@@ -1,17 +1,20 @@
1 1
 \name{anno_barplot}
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 \alias{anno_barplot}
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 \title{
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-Using barplot as annotation
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+Using barplot as annotation  
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+
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 }
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 \description{
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-Using barplot as annotation
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+Using barplot as annotation  
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+
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 }
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 \usage{
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 anno_barplot(x, which = c("column", "row"),
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     gp = gpar(fill = "#CCCCCC"), axis = FALSE, axis_side = NULL,
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-    axis_gp = gpar(fontsize = 8), ...)}
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+    axis_gp = gpar(fontsize = 8), ...)
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+}
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 \arguments{
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   \item{x}{a vector of values.}
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@@ -21,13 +24,16 @@ anno_barplot(x, which = c("column", "row"),
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   \item{axis_side}{value in "left", "right", "bottom" and "top"}
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   \item{axis_gp}{graphic parameters for axis}
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   \item{...}{for future use.}
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+
24 28
 }
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 \value{
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-A graphic function which can be set in \code{\link{HeatmapAnnotation}} constructor method.
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+A graphic function which can be set in \code{\link{HeatmapAnnotation}} constructor method.  
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+
27 32
 
28 33
 }
29 34
 \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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+
31 37
 
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 }
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 \examples{
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@@ -35,4 +41,5 @@ f = anno_barplot(rnorm(10))
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 grid.newpage(); f(1:10)
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 f = anno_barplot(rnorm(10), which = "row")
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-grid.newpage(); f(1:10)}
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+grid.newpage(); f(1:10)
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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
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@@ -1,20 +1,17 @@
1 1
 \name{anno_barplot}
2 2
 \alias{anno_barplot}
3 3
 \title{
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-Using barplot as annotation  
5
-
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+Using barplot as annotation
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 }
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 \description{
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-Using barplot as annotation  
10
-
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+Using barplot as annotation
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12 10
 }
13 11
 \usage{
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 anno_barplot(x, which = c("column", "row"),
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     gp = gpar(fill = "#CCCCCC"), axis = FALSE, axis_side = NULL,
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-    axis_gp = gpar(fontsize = 8), ...)
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-}
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+    axis_gp = gpar(fontsize = 8), ...)}
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 \arguments{
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   \item{x}{a vector of values.}
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@@ -24,16 +21,13 @@ anno_barplot(x, which = c("column", "row"),
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   \item{axis_side}{value in "left", "right", "bottom" and "top"}
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   \item{axis_gp}{graphic parameters for axis}
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   \item{...}{for future use.}
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-
28 24
 }
29 25
 \value{
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-A graphic function which can be set in \code{\link{HeatmapAnnotation}} constructor method.  
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-
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+A graphic function which can be set in \code{\link{HeatmapAnnotation}} constructor method.
32 27
 
33 28
 }
34 29
 \author{
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-Zuguang Gu <z.gu@dkfz.de>  
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-
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+Zuguang Gu <z.gu@dkfz.de>
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38 32
 }
39 33
 \examples{
... ...
@@ -41,5 +35,4 @@ f = anno_barplot(rnorm(10))
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 grid.newpage(); f(1:10)
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43 37
 f = anno_barplot(rnorm(10), which = "row")
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-grid.newpage(); f(1:10)
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-}
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+grid.newpage(); f(1:10)}
Browse code

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Commit id: 72c5e9c3243eaf6a26e529a2a16fa77af40a1291

axes are supported in annotations



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@104323 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 28/05/2015 14:20:38
Showing1 changed files
... ...
@@ -12,13 +12,17 @@ Using barplot as annotation
12 12
 }
13 13
 \usage{
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 anno_barplot(x, which = c("column", "row"),
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-    gp = gpar(fill = "#CCCCCC"), ...)
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+    gp = gpar(fill = "#CCCCCC"), axis = FALSE, axis_side = NULL,
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+    axis_gp = gpar(fontsize = 8), ...)
16 17
 }
17 18
 \arguments{
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   \item{x}{a vector of values.}
20 21
   \item{which}{is the annotation a column annotation or a row annotation?}
21 22
   \item{gp}{graphic parameters.}
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+  \item{axis}{whether add axis}
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+  \item{axis_side}{value in "left", "right", "bottom" and "top"}
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+  \item{axis_gp}{graphic parameters for axis}
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   \item{...}{for future use.}
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24 28
 }
Browse code

add package to repository

ComplexHeatmap/ podkat/ RBM/


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@101658 bc3139a8-67e5-0310-9ffc-ced21a209358

s.arora authored on 31/03/2015 18:31:58
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1 1
new file mode 100644
... ...
@@ -0,0 +1,41 @@
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+\name{anno_barplot}
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+\alias{anno_barplot}
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+\title{
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+Using barplot as annotation  
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+
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+
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+}
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+\description{
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+Using barplot as annotation  
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+
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+
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+}
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+\usage{
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+anno_barplot(x, which = c("column", "row"),
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+    gp = gpar(fill = "#CCCCCC"), ...)
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+}
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+\arguments{
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+
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+  \item{x}{a vector of values.}
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+  \item{which}{is the annotation a column annotation or a row annotation?}
21
+  \item{gp}{graphic parameters.}
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+  \item{...}{for future use.}
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+
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+}
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+\value{
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+A graphic function which can be set in \code{\link{HeatmapAnnotation}} constructor method.  
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+
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+
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+}
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+\author{
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+Zuguang Gu <z.gu@dkfz.de>  
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+
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+
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+}
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+\examples{
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+f = anno_barplot(rnorm(10))
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+grid.newpage(); f(1:10)
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+
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+f = anno_barplot(rnorm(10), which = "row")
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+grid.newpage(); f(1:10)
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+}