1. ComplexHeatmap
  2. man
  3. anno_oncoprint_barplot.Rd
Browse code

add max_density argument

Zuguang Gu authored on 15/06/2022 10:42:56
Showing1 changed files
man/anno_oncoprint_barplot.Rd
History View file @c94e524
... ... 
@@ -36,4 +36,5 @@ Zuguang Gu <z.gu@dkfz.de>
36 36 
 \examples{
37 37 
 # There is no example
38 38 
 NULL
39 
+
39 40 
 }
Browse code

rename to anno_textbox()

Zuguang Gu authored on 15/06/2022 10:11:58
Showing1 changed files
man/anno_oncoprint_barplot.Rd
History View file @5cefa67
... ... 
@@ -36,5 +36,4 @@ Zuguang Gu <z.gu@dkfz.de>
36 36 
 \examples{
37 37 
 # There is no example
38 38 
 NULL
39 
-
40 39 
 }
Browse code

add new argument 'beside' in 'anno_barplot()'

Zuguang Gu authored on 28/09/2021 11:13:16
Showing1 changed files
man/anno_oncoprint_barplot.Rd
History View file @80d025e
... ... 
@@ -8,7 +8,7 @@ Barplot Annotation for oncoPrint
8 8 
 }
9 9 
 \usage{
10 10 
 anno_oncoprint_barplot(type = NULL, which = c("column", "row"),
11 
-    bar_width = 0.6, ylim = NULL, show_fraction = FALSE, axis = TRUE,
11 
+    bar_width = 0.6, beside = FALSE, ylim = NULL, show_fraction = FALSE, axis = TRUE,
12 12 
     axis_param = if(which == "column") default_axis_param("column") else list(side = "top", labels_rot = 0),
13 13 
     width = NULL, height = NULL, border = FALSE)
14 14 
 }
... ... 
@@ -17,6 +17,7 @@ anno_oncoprint_barplot(type = NULL, which = c("column", "row"),
17 17 
   \item{type}{A vector of the alteration types in the data. It can be a subset of all alteration types if you don't want to show them all.}
18 18 
   \item{which}{Is it a row annotation or a column annotation?}
19 19 
   \item{bar_width}{Width of the bars.}
20 
+  \item{beside}{Will bars be stacked or be positioned beside each other?}
20 21 
   \item{ylim}{Data range.}
21 22 
   \item{show_fraction}{Whether to show the numbers or the fractions?}
22 23 
   \item{axis}{Whether draw axis?}
Browse code

won't generate color matrix when type=='none'

Zuguang Gu authored on 15/12/2020 12:01:39
Showing1 changed files
man/anno_oncoprint_barplot.Rd
History View file @110a6d6
... ... 
@@ -35,4 +35,5 @@ Zuguang Gu <z.gu@dkfz.de>
35 35 
 \examples{
36 36 
 # There is no example
37 37 
 NULL
38 
+
38 39 
 }
Browse code

translate stats::heatmap() and gplots::heatmap.2()

Zuguang Gu authored on 13/12/2020 20:54:51
Showing1 changed files
man/anno_oncoprint_barplot.Rd
History View file @2f64420
... ... 
@@ -35,5 +35,4 @@ Zuguang Gu <z.gu@dkfz.de>
35 35 
 \examples{
36 36 
 # There is no example
37 37 
 NULL
38 
-
39 38 
 }
Browse code

pheatmap(): adjust the setting of color and breaks

simplifyEnrichment authored on 06/10/2020 12:07:17
Showing1 changed files
man/anno_oncoprint_barplot.Rd
History View file @b912615
... ... 
@@ -8,7 +8,7 @@ Barplot Annotation for oncoPrint
8 8 
 }
9 9 
 \usage{
10 10 
 anno_oncoprint_barplot(type = NULL, which = c("column", "row"),
11 
-    bar_width = 0.6, ylim = NULL, axis = TRUE,
11 
+    bar_width = 0.6, ylim = NULL, show_fraction = FALSE, axis = TRUE,
12 12 
     axis_param = if(which == "column") default_axis_param("column") else list(side = "top", labels_rot = 0),
13 13 
     width = NULL, height = NULL, border = FALSE)
14 14 
 }
... ... 
@@ -18,6 +18,7 @@ anno_oncoprint_barplot(type = NULL, which = c("column", "row"),
18 18 
   \item{which}{Is it a row annotation or a column annotation?}
19 19 
   \item{bar_width}{Width of the bars.}
20 20 
   \item{ylim}{Data range.}
21 
+  \item{show_fraction}{Whether to show the numbers or the fractions?}
21 22 
   \item{axis}{Whether draw axis?}
22 23 
   \item{axis_param}{Parameters for controlling axis.}
23 24 
   \item{width}{Width of the annotation.}
Browse code

update

Zuguang Gu authored on 20/10/2019 06:57:30
Showing1 changed files
man/anno_oncoprint_barplot.Rd
History View file @7abc442
... ... 
@@ -34,4 +34,5 @@ Zuguang Gu <z.gu@dkfz.de>
34 34 
 \examples{
35 35 
 # There is no example
36 36 
 NULL
37 
+
37 38 
 }
Browse code

generate documentations by pkgdown

Zuguang Gu authored on 18/10/2019 11:34:02
Showing1 changed files
man/anno_oncoprint_barplot.Rd
History View file @1cb7fea
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,37 @@
1 
+\name{anno_oncoprint_barplot}
2 
+\alias{anno_oncoprint_barplot}
3 
+\title{
4 
+Barplot Annotation for oncoPrint
5 
+}
6 
+\description{
7 
+Barplot Annotation for oncoPrint
8 
+}
9 
+\usage{
10 
+anno_oncoprint_barplot(type = NULL, which = c("column", "row"),
11 
+    bar_width = 0.6, ylim = NULL, axis = TRUE,
12 
+    axis_param = if(which == "column") default_axis_param("column") else list(side = "top", labels_rot = 0),
13 
+    width = NULL, height = NULL, border = FALSE)
14 
+}
15 
+\arguments{
16 
+
17 
+  \item{type}{A vector of the alteration types in the data. It can be a subset of all alteration types if you don't want to show them all.}
18 
+  \item{which}{Is it a row annotation or a column annotation?}
19 
+  \item{bar_width}{Width of the bars.}
20 
+  \item{ylim}{Data range.}
21 
+  \item{axis}{Whether draw axis?}
22 
+  \item{axis_param}{Parameters for controlling axis.}
23 
+  \item{width}{Width of the annotation.}
24 
+  \item{height}{Height of the annotation.}
25 
+  \item{border}{Whether draw the border?}
26 
+
27 
+}
28 
+\details{
29 
+This annotation function should always be used with \code{\link{oncoPrint}}.
30 
+}
31 
+\author{
32 
+Zuguang Gu <z.gu@dkfz.de>
33 
+}
34 
+\examples{
35 
+# There is no example
36 
+NULL
37 
+}