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add max_density argument

Zuguang Gu authored on 15/06/2022 10:42:56
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@@ -36,4 +36,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
Browse code

rename to anno_textbox()

Zuguang Gu authored on 15/06/2022 10:11:58
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@@ -36,5 +36,4 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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-
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 }
Browse code

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

Zuguang Gu authored on 28/09/2021 11:13:16
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@@ -8,7 +8,7 @@ Barplot Annotation for oncoPrint
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 }
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 \usage{
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 anno_oncoprint_barplot(type = NULL, which = c("column", "row"),
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-    bar_width = 0.6, ylim = NULL, show_fraction = FALSE, axis = TRUE,
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+    bar_width = 0.6, beside = FALSE, ylim = NULL, show_fraction = FALSE, axis = TRUE,
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     axis_param = if(which == "column") default_axis_param("column") else list(side = "top", labels_rot = 0),
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     width = NULL, height = NULL, border = FALSE)
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 }
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@@ -17,6 +17,7 @@ anno_oncoprint_barplot(type = NULL, which = c("column", "row"),
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   \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.}
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   \item{which}{Is it a row annotation or a column annotation?}
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   \item{bar_width}{Width of the bars.}
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+  \item{beside}{Will bars be stacked or be positioned beside each other?}
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   \item{ylim}{Data range.}
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   \item{show_fraction}{Whether to show the numbers or the fractions?}
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   \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
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@@ -35,4 +35,5 @@ Zuguang Gu <z.gu@dkfz.de>
35 35
 \examples{
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 # There is no example
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 NULL
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+
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 }
Browse code

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

Zuguang Gu authored on 13/12/2020 20:54:51
Showing1 changed files
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@@ -35,5 +35,4 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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-
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 }
Browse code

pheatmap(): adjust the setting of color and breaks

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

update

Zuguang Gu authored on 20/10/2019 06:57:30
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@@ -34,4 +34,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
Browse code

generate documentations by pkgdown

Zuguang Gu authored on 18/10/2019 11:34:02
Showing1 changed files
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new file mode 100644
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@@ -0,0 +1,37 @@
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+\name{anno_oncoprint_barplot}
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+\alias{anno_oncoprint_barplot}
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+\title{
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+Barplot Annotation for oncoPrint
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+}
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+\description{
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+Barplot Annotation for oncoPrint
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+}
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+\usage{
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+anno_oncoprint_barplot(type = NULL, which = c("column", "row"),
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+    bar_width = 0.6, ylim = NULL, axis = TRUE,
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+    axis_param = if(which == "column") default_axis_param("column") else list(side = "top", labels_rot = 0),
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+    width = NULL, height = NULL, border = FALSE)
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+}
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+\arguments{
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+
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+  \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.}
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+  \item{which}{Is it a row annotation or a column annotation?}
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+  \item{bar_width}{Width of the bars.}
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+  \item{ylim}{Data range.}
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+  \item{axis}{Whether draw axis?}
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+  \item{axis_param}{Parameters for controlling axis.}
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+  \item{width}{Width of the annotation.}
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+  \item{height}{Height of the annotation.}
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+  \item{border}{Whether draw the border?}
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+
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+}
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+\details{
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+This annotation function should always be used with \code{\link{oncoPrint}}.
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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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+\examples{
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+# There is no example
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+NULL
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+}