1. ComplexHeatmap
  2. Commit 10b246c08948bd690c0c27292d53672c8adcf0e4
Browse code

Commit made by the Bioconductor Git-SVN bridge.

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
Showing 61 changed files
R/densityHeatmap.R
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@@ -14,6 +14,9 @@
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 # Here we use colors to map to the density values and visualize distribution of values
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 # in each column (or each list element) through a heatmap.
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 #
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+# == value
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+# No value is returned.
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+#
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 # == example
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 # matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10]
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 # densityHeatmap(matrix)
man/AdditiveUnit-class.rd
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@@ -16,6 +16,7 @@ It is only designed for \code{+} generic method so that above three classes can
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 }
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 \examples{
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+
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 # no example
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 NULL
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man/AdditiveUnit.rd
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@@ -28,6 +28,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # no example
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 NULL
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man/ColorMapping-class.rd
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@@ -31,6 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # for examples, please go to `ColorMapping` method page
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 NULL
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man/ColorMapping.rd
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@@ -35,6 +35,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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 # discrete color mapping for characters
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 cm = ColorMapping(name = "test",
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     colors = c("blue", "white", "red"),
man/Heatmap-class.rd
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@@ -73,6 +73,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # for examples, please go to `Heatmap` method page
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 NULL
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man/Heatmap.rd
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@@ -112,6 +112,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 mat = matrix(rnorm(80, 2), 8, 10)
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 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
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 rownames(mat) = letters[1:12]
man/HeatmapAnnotation-class.rd
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@@ -30,6 +30,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # for examples, please go to `HeatmapAnnotation` method page
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 NULL
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man/HeatmapAnnotation.rd
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@@ -47,6 +47,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
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 ha = HeatmapAnnotation(df = df)
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man/HeatmapList-class.rd
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@@ -69,6 +69,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 mat = matrix(rnorm(80, 2), 8, 10)
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 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
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 rownames(mat) = letters[1:12]
man/HeatmapList.rd
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@@ -28,9 +28,11 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \section{Detailes}{
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+
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 There is no public constructor method for the \code{\link{HeatmapList-class}}.}
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 \examples{
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 # no example
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 NULL
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man/SingleAnnotation-class.rd
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@@ -40,6 +40,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # for examples, please go to `SingleAnnotation` method page
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 NULL
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man/SingleAnnotation.rd
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@@ -49,6 +49,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # discrete character
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 SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
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 SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"),
man/add.AdditiveUnit.rd
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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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 mat = matrix(rnorm(80, 2), 8, 10)
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 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
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 rownames(mat) = letters[1:12]
man/add_heatmap-Heatmap-method.rd
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@@ -29,6 +29,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 mat = matrix(rnorm(80, 2), 8, 10)
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 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
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 rownames(mat) = letters[1:12]
man/add_heatmap-HeatmapAnnotation-method.rd
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@@ -29,6 +29,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 mat = matrix(rnorm(80, 2), 8, 10)
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 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
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 rownames(mat) = letters[1:12]
man/add_heatmap-HeatmapList-method.rd
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@@ -29,6 +29,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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 mat = matrix(rnorm(80, 2), 8, 10)
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 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
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 rownames(mat) = letters[1:12]
man/anno_barplot.rd
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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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 f = anno_barplot(rnorm(10))
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 grid.newpage(); f(1:10)
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man/anno_boxplot.rd
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@@ -33,6 +33,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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 mat = matrix(rnorm(32), nrow = 4)
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 f = anno_boxplot(mat)
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 grid.newpage(); f(1:8)
man/anno_density.rd
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@@ -29,6 +29,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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 mat = matrix(rnorm(32), nrow = 4)
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 f = anno_density(mat)
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 grid.newpage(); f(1:8)
man/anno_histogram.rd
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@@ -27,6 +27,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 mat = matrix(rnorm(32), nrow = 4)
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 f = anno_histogram(mat)
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 grid.newpage(); f(1:8)
man/anno_points.rd
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@@ -34,6 +34,7 @@ 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_points(rnorm(10))
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 grid.newpage(); f(1:10)
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man/anno_text.rd
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@@ -30,6 +30,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 mat = matrix(rnorm(100), 10)
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 colnames(mat) = letters[1:10]
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 rownames(mat) = LETTERS[1:10]
man/annotation_legend_size-HeatmapList-method.rd
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@@ -34,6 +34,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # no example for this internal method
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 NULL
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man/color_mapping_legend-ColorMapping-method.rd
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@@ -39,6 +39,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # discrete color mapping for characters
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 cm = ColorMapping(name = "test",
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     colors = c("blue", "white", "red"),
man/columnAnnotation.rd
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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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 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
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 ha = rowAnnotation(df = df)
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man/component_height-Heatmap-method.rd
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@@ -29,6 +29,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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 # no example for this internal method
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 }
man/component_height-HeatmapList-method.rd
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@@ -25,6 +25,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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 # no example for this internal method
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 }
man/component_width-Heatmap-method.rd
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@@ -21,6 +21,7 @@ This function is only for internal use.
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 }
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 \section{Detials}{
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+
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 This function is only for internal use.}
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 \value{
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 A \code{\link[grid]{unit}} object.
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@@ -32,6 +33,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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 # no example for this internal method
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 }
man/component_width-HeatmapList-method.rd
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@@ -29,6 +29,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # no example for this internal method
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 }
man/densityHeatmap.rd
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@@ -25,6 +25,10 @@ To visualize distribution of columns in a matrix or in a list, sometimes we use
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 Here we use colors to map to the density values and visualize distribution of values
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 in each column (or each list element) through a heatmap.
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+}
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+\value{
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+No value is returned.
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+
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 }
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 \examples{
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 matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10]
man/dist2.rd
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@@ -31,6 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 mat = matrix(rnorm(40), nr = 4, ncol = 10)
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 rownames(mat) = letters[1:4]
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 colnames(mat) = letters[1:10]
man/draw-Heatmap-method.rd
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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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 mat = matrix(rnorm(80, 2), 8, 10)
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 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
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 rownames(mat) = letters[1:12]
man/draw-HeatmapAnnotation-method.rd
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@@ -31,6 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
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 ha = HeatmapAnnotation(df = df)
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 grid.newpage(); draw(ha, 1:6)
man/draw-HeatmapList-method.rd
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@@ -34,6 +34,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 mat = matrix(rnorm(80, 2), 8, 10)
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 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
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 rownames(mat) = letters[1:12]
man/draw-SingleAnnotation-method.rd
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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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 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
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 grid.newpage(); draw(anno, 1:5)
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 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
man/draw_annotation-Heatmap-method.rd
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 }
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 \examples{
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 # no example for this internal method
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 NULL
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man/draw_annotation_legend-HeatmapList-method.rd
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@@ -33,6 +33,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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 # no example for this internal method
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 NULL
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man/draw_dimnames-Heatmap-method.rd
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@@ -36,6 +36,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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 # no example for this internal method
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 NULL
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man/draw_hclust-Heatmap-method.rd
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@@ -43,6 +43,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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 # no example for this internal method
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 NULL
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man/draw_heatmap_body-Heatmap-method.rd
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@@ -37,6 +37,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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 # no example for this internal method
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 NULL
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man/draw_heatmap_legend-HeatmapList-method.rd
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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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 # no example for this internal method
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 NULL
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man/draw_heatmap_list-HeatmapList-method.rd
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@@ -31,6 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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 # no example for this internal method
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 NULL
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man/draw_title-Heatmap-method.rd
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 }
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 \examples{
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 # no example for this internal method
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 NULL
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man/draw_title-HeatmapList-method.rd
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 }
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 \examples{
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 # no example for this internal method
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 NULL
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man/get_color_mapping_list-HeatmapAnnotation-method.rd
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@@ -31,6 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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 # no example for this internal method
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 NULL
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man/grid.dendrogram.rd
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@@ -35,6 +35,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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 hc = hclust(dist(USArrests[1:5, ]))
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 dend = as.dendrogram(hc)
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man/heatmap_legend_size-HeatmapList-method.rd
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@@ -30,6 +30,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # no example for this internal method
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 NULL
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man/make_column_cluster-Heatmap-method.rd
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@@ -31,6 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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 # no example for this internal method
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 NULL
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man/make_layout-Heatmap-method.rd
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@@ -34,6 +34,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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 # no example for this internal method
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 NULL
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man/make_layout-HeatmapList-method.rd
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@@ -59,6 +59,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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 # no example for this internal method
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 NULL
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man/make_row_cluster-Heatmap-method.rd
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@@ -33,6 +33,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # no example for this internal method
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 NULL
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man/map_to_colors-ColorMapping-method.rd
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@@ -30,6 +30,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # discrete color mapping for characters
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 cm = ColorMapping(name = "test",
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     colors = c("blue", "white", "red"),
man/plot.HeatmapList.rd
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@@ -24,3 +24,8 @@ they can pass parameters directly to \code{\link{draw,HeatmapList-method}}.
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 This function returns no value.
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 }
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+\examples{
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+
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+# no example
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+NULL
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+}
man/plotDataFrame.rd
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@@ -47,6 +47,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], letters[1:4])),
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                 large = runif(10)*100,
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                 t1 = sample(letters[1:3], 10, replace = TRUE),
man/prepare-Heatmap-method.rd
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@@ -38,6 +38,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # no example for this internal method
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 NULL
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man/print.HeatmapList.rd
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@@ -24,3 +24,8 @@ they can pass parameters directly to \code{\link{draw,HeatmapList-method}}.
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 This function returns no value.
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 }
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+\examples{
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+
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+# no example
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+NULL
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+}
man/rowAnnotation.rd
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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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 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
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 ha = columnAnnotation(df = df)
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man/set_component_height-Heatmap-method.rd
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@@ -31,6 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # no example for this internal method
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 NULL
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man/show-Heatmap-method.rd
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@@ -29,6 +29,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
30 30 
 \examples{
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+
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 mat = matrix(rnorm(80, 2), 8, 10)
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 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
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 rownames(mat) = letters[1:12]
man/show-HeatmapList-method.rd
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@@ -25,6 +25,7 @@ This function returns no value.
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 }
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 \author{
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+
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 Zuguang Gu <z.gu@dkfz.de>
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 }