1. ComplexHeatmap
  2. Commit 7f6dddf098a4c924d47178527a25e27524ca5b63
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
Showing 57 changed files
man/AdditiveUnit-class.rd
History View file @ 7f6dddf
... ... 
@@ -15,5 +15,8 @@ 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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+NULL
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+
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+}
man/AdditiveUnit.rd
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... ... 
@@ -27,5 +27,8 @@ 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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+NULL
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+
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+}
man/ColorMapping-class.rd
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@@ -30,5 +30,8 @@ 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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+NULL
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+
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+}
man/ColorMapping.rd
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... ... 
@@ -34,6 +34,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
36 36 
 \examples{
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+
37 38 
 # discrete color mapping for characters
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 cm = ColorMapping(name = "test",
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     colors = c("blue", "white", "red"),
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@@ -50,4 +51,6 @@ cm
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 require(circlize)
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 cm = ColorMapping(name = "test",
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     col_fun = colorRamp2(c(0, 0.5, 1), c("blue", "white", "red")))
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-cm}
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+cm
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+
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+}
man/Heatmap-class.rd
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@@ -72,5 +72,8 @@ 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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+NULL
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+
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+}
man/Heatmap.rd
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... ... 
@@ -111,6 +111,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
113 113 
 \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))
116 117 
 rownames(mat) = letters[1:12]
... ... 
@@ -181,4 +182,6 @@ Heatmap(mat, rect_gp = gpar(col = "white"),
181 182 
         grid.text(mat[i, j], x = x, y = y)
182 183 
     },
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     cluster_rows = FALSE, cluster_columns = FALSE, row_names_side = "left",
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-    column_names_side = "top")}
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+    column_names_side = "top")
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+
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+}
man/HeatmapAnnotation-class.rd
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... ... 
@@ -29,5 +29,8 @@ 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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+NULL
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+
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+}
man/HeatmapAnnotation.rd
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... ... 
@@ -46,6 +46,7 @@ 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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... ... 
@@ -59,4 +60,6 @@ ha = HeatmapAnnotation(points = anno_points(1:6))
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 ha = HeatmapAnnotation(histogram = anno_points(1:6))
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 mat = matrix(rnorm(36), 6)
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-ha = HeatmapAnnotation(boxplot = anno_boxplot(mat))}
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+ha = HeatmapAnnotation(boxplot = anno_boxplot(mat))
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+
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+}
man/HeatmapList-class.rd
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... ... 
@@ -68,6 +68,7 @@ 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]
... ... 
@@ -83,4 +84,6 @@ ht + ht_list
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 ha = HeatmapAnnotation(points = anno_points(1:12, which = "row"),
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     which = "row")
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 ht + ha
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-ht_list + ha}
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+ht_list + ha
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+
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+}
man/HeatmapList.rd
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@@ -27,7 +27,11 @@ 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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+
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 # no example
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-NULL}
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+NULL
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+
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+}
man/SingleAnnotation-class.rd
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@@ -39,5 +39,8 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
41 41 
 \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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+NULL
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+
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+}
man/SingleAnnotation.rd
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@@ -48,6 +48,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
50 50 
 \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"),
... ... 
@@ -63,4 +64,6 @@ SingleAnnotation(value = 1:10)
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 SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red")))
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 # self-defined graphic function
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-SingleAnnotation(fun = anno_points(1:10))}
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+SingleAnnotation(fun = anno_points(1:10))
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+
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+}
man/add.AdditiveUnit.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(80, 2), 8, 10)
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 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
36 37 
 rownames(mat) = letters[1:12]
... ... 
@@ -48,4 +49,6 @@ ha = HeatmapAnnotation(points = anno_points(1:12, which = "row"),
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 ht + ha
49 50 
 ht_list + ha
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-ha + ha + ht}
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+ha + ha + ht
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+
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+}
man/add_heatmap-Heatmap-method.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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 mat = matrix(rnorm(80, 2), 8, 10)
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 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
33 34 
 rownames(mat) = letters[1:12]
... ... 
@@ -38,4 +39,6 @@ add_heatmap(ht, ht)
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 ha = HeatmapAnnotation(points = anno_points(1:12, which = "row"),
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     which = "row")
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-add_heatmap(ht, ha)}
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+add_heatmap(ht, ha)
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+
44 
+}
man/add_heatmap-HeatmapAnnotation-method.rd
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... ... 
@@ -28,6 +28,7 @@ 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))
33 34 
 rownames(mat) = letters[1:12]
... ... 
@@ -37,4 +38,6 @@ ht = Heatmap(mat)
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 ha = HeatmapAnnotation(points = anno_points(1:12, which = "row"),
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     which = "row")
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-add_heatmap(ha, ht)}
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+add_heatmap(ha, ht)
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+
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+}
man/add_heatmap-HeatmapList-method.rd
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... ... 
@@ -28,6 +28,7 @@ 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)
32 33 
 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
33 34 
 rownames(mat) = letters[1:12]
... ... 
@@ -39,4 +40,6 @@ add_heatmap(ht_list, ht)
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 ha = HeatmapAnnotation(points = anno_points(1:12, which = "row"),
41 42 
     which = "row")
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-add_heatmap(ht_list, ha)}
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+add_heatmap(ht_list, ha)
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+
45 
+}
man/anno_barplot.rd
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... ... 
@@ -31,8 +31,11 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
32 32 
 }
33 33 
 \examples{
34 
+
34 35 
 f = anno_barplot(rnorm(10))
35 36 
 grid.newpage(); f(1:10)
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37 38 
 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)
40 
+
41 
+}
man/anno_boxplot.rd
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@@ -32,6 +32,7 @@ Zuguang Gu <z.gu@dkfz.de>
32 32
33 33 
 }
34 34 
 \examples{
35 
+
35 36 
 mat = matrix(rnorm(32), nrow = 4)
36 37 
 f = anno_boxplot(mat)
37 38 
 grid.newpage(); f(1:8)
... ... 
@@ -41,4 +42,6 @@ grid.newpage(); f(1:4)
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42 43 
 lt = lapply(1:4, function(i) rnorm(8))
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 f = anno_boxplot(lt)
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-grid.newpage(); f(1:4)}
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+grid.newpage(); f(1:4)
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+
47 
+}
man/anno_density.rd
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@@ -28,6 +28,7 @@ Zuguang Gu <z.gu@dkfz.de>
28 28
29 29 
 }
30 30 
 \examples{
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+
31 32 
 mat = matrix(rnorm(32), nrow = 4)
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 f = anno_density(mat)
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 grid.newpage(); f(1:8)
... ... 
@@ -37,4 +38,6 @@ grid.newpage(); f(1:4)
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 lt = lapply(1:4, function(i) rnorm(8))
39 40 
 f = anno_density(lt, type = "heatmap")
40 
-grid.newpage(); f(1:4)}
41 
+grid.newpage(); f(1:4)
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+
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+}
man/anno_histogram.rd
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... ... 
@@ -26,6 +26,7 @@ Zuguang Gu <z.gu@dkfz.de>
26 26
27 27 
 }
28 28 
 \examples{
29 
+
29 30 
 mat = matrix(rnorm(32), nrow = 4)
30 31 
 f = anno_histogram(mat)
31 32 
 grid.newpage(); f(1:8)
... ... 
@@ -35,4 +36,6 @@ grid.newpage(); f(1:4)
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36 37 
 lt = lapply(1:4, function(i) rnorm(8))
37 38 
 f = anno_histogram(lt)
38 
-grid.newpage(); f(1:4)}
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+grid.newpage(); f(1:4)
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+
41 
+}
man/anno_points.rd
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... ... 
@@ -33,5 +33,8 @@ Zuguang Gu <z.gu@dkfz.de>
33 33
34 34 
 }
35 35 
 \examples{
36 
+
36 37 
 f = anno_points(rnorm(10))
37 
-grid.newpage(); f(1:10)}
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+grid.newpage(); f(1:10)
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+
40 
+}
man/anno_text.rd
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... ... 
@@ -29,9 +29,12 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
30 30 
 }
31 31 
 \examples{
32 
+
32 33 
 mat = matrix(rnorm(100), 10)
33 34 
 colnames(mat) = letters[1:10]
34 35 
 rownames(mat) = LETTERS[1:10]
35 36 
 long_cn = do.call("paste0", rep(list(colnames(mat)), 4))  # just to construct long text
36 37 
 ha_rot_cn = HeatmapAnnotation(text = anno_text(long_cn, rot = 45, offset = unit(5, "mm")))
37 
-Heatmap(mat, name = "foo", top_annotation = ha_rot_cn, top_annotation_height = unit(1.2, "cm"))}
38 
+Heatmap(mat, name = "foo", top_annotation = ha_rot_cn, top_annotation_height = unit(1.2, "cm"))
39 
+
40 
+}
man/annotation_legend_size-HeatmapList-method.rd
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... ... 
@@ -33,5 +33,8 @@ Zuguang Gu <z.gu@dkfz.de>
33 33
34 34 
 }
35 35 
 \examples{
36 
+
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 # no example for this internal method
37 
-NULL}
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+NULL
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+
40 
+}
man/color_mapping_legend-ColorMapping-method.rd
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... ... 
@@ -38,6 +38,7 @@ Zuguang Gu <z.gu@dkfz.de>
38 38
39 39 
 }
40 40 
 \examples{
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+
41 42 
 # discrete color mapping for characters
42 43 
 cm = ColorMapping(name = "test",
43 44 
     colors = c("blue", "white", "red"),
... ... 
@@ -57,4 +58,6 @@ require(circlize)
57 58 
 cm = ColorMapping(name = "test",
58 59 
     col_fun = colorRamp2(c(0, 0.5, 1), c("blue", "white", "red")))
59 60 
 grid.newpage()
60 
-color_mapping_legend(cm, legend_title_gp = gpar(fontsize = 16))}
61 
+color_mapping_legend(cm, legend_title_gp = gpar(fontsize = 16))
62 
+
63 
+}
man/columnAnnotation.rd
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... ... 
@@ -31,5 +31,8 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
32 32 
 }
33 33 
 \examples{
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+
34 35 
 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
35 
-ha = rowAnnotation(df = df)}
36 
+ha = rowAnnotation(df = df)
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+
38 
+}
man/component_height-Heatmap-method.rd
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... ... 
@@ -28,4 +28,7 @@ Zuguang Gu <z.gu@dkfz.de>
28 28
29 29 
 }
30 30 
 \examples{
31 
-# no example for this internal method}
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+
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+# no example for this internal method
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+
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+}
man/component_height-HeatmapList-method.rd
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... ... 
@@ -24,4 +24,7 @@ Zuguang Gu <z.gu@dkfz.de>
24 24
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 }
26 26 
 \examples{
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-# no example for this internal method}
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+
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+# no example for this internal method
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+
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+}
man/component_width-Heatmap-method.rd
History View file @ 7f6dddf
... ... 
@@ -20,6 +20,7 @@ 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.
... ... 
@@ -30,4 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>
30 31
31 32 
 }
32 33 
 \examples{
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-# no example for this internal method}
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+
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+# no example for this internal method
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+
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+}
man/component_width-HeatmapList-method.rd
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... ... 
@@ -28,4 +28,7 @@ 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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+
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+# no example for this internal method
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+
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+}
man/dist2.rd
History View file @ 7f6dddf
... ... 
@@ -30,6 +30,7 @@ Zuguang Gu <z.gu@dkfz.de>
30 30
31 31 
 }
32 32 
 \examples{
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+
33 34 
 mat = matrix(rnorm(40), nr = 4, ncol = 10)
34 35 
 rownames(mat) = letters[1:4]
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 colnames(mat) = letters[1:10]
... ... 
@@ -39,4 +40,6 @@ d2 = dist2(mat, pairwise_fun = function(x, y) 1 - cor(x, y))
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 d2 = dist2(mat, pairwise_fun = function(x, y) {
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     l = is.na(x) & is.na(y)
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     sqrt(sum((x[l] - y[l])^2))
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-})}
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+})
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+
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+}
man/draw-Heatmap-method.rd
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... ... 
@@ -31,10 +31,13 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
32 32 
 }
33 33 
 \examples{
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+
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 mat = matrix(rnorm(80, 2), 8, 10)
35 36 
 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
36 37 
 rownames(mat) = letters[1:12]
37 38 
 colnames(mat) = letters[1:10]
38 39
39 40 
 ht = Heatmap(mat)
40 
-draw(ht, heatmap_legend_side = "left")}
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+draw(ht, heatmap_legend_side = "left")
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+
43 
+}
man/draw-HeatmapAnnotation-method.rd
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... ... 
@@ -30,6 +30,7 @@ Zuguang Gu <z.gu@dkfz.de>
30 30
31 31 
 }
32 32 
 \examples{
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+
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 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
34 35 
 ha = HeatmapAnnotation(df = df)
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 grid.newpage(); draw(ha, 1:6)
... ... 
@@ -50,4 +51,6 @@ grid.newpage(); draw(ha, 1:6)
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51 52 
 mat = matrix(rnorm(36), 6)
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 ha = HeatmapAnnotation(boxplot = anno_boxplot(mat))
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-grid.newpage(); draw(ha, 1:6)}
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+grid.newpage(); draw(ha, 1:6)
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+
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+}
man/draw-HeatmapList-method.rd
History View file @ 7f6dddf
... ... 
@@ -33,6 +33,7 @@ Zuguang Gu <z.gu@dkfz.de>
33 33
34 34 
 }
35 35 
 \examples{
36 
+
36 37 
 mat = matrix(rnorm(80, 2), 8, 10)
37 38 
 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
38 39 
 rownames(mat) = letters[1:12]
... ... 
@@ -42,4 +43,6 @@ ht = Heatmap(mat)
42 43 
 ht_list = ht + ht
43 44 
 draw(ht_list)
44 45 
 draw(ht_list, row_title = "row title", column_title = "column title",
45 
-	heatmap_legend_side = "top")}
46 
+	heatmap_legend_side = "top")
47 
+
48 
+}
man/draw-SingleAnnotation-method.rd
History View file @ 7f6dddf
... ... 
@@ -31,6 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
32 32 
 }
33 33 
 \examples{
34 
+
34 35 
 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
35 36 
 grid.newpage(); draw(anno, 1:5)
36 37 
 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
... ... 
@@ -52,4 +53,6 @@ anno = SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red"
52 53 
 grid.newpage(); draw(anno, 1:10)
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54 55 
 anno = SingleAnnotation(fun = anno_points(1:10))
55 
-grid.newpage(); draw(anno, 1:10)}
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+grid.newpage(); draw(anno, 1:10)
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+
58 
+}
man/draw_annotation-Heatmap-method.rd
History View file @ 7f6dddf
... ... 
@@ -34,5 +34,8 @@ Zuguang Gu <z.gu@dkfz.de>
34 34
35 35 
 }
36 36 
 \examples{
37 
+
37 38 
 # no example for this internal method
38 
-NULL}
39 
+NULL
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+
41 
+}
man/draw_annotation_legend-HeatmapList-method.rd
History View file @ 7f6dddf
... ... 
@@ -32,5 +32,8 @@ Zuguang Gu <z.gu@dkfz.de>
32 32
33 33 
 }
34 34 
 \examples{
35 
+
35 36 
 # no example for this internal method
36 
-NULL}
37 
+NULL
38 
+
39 
+}
man/draw_dimnames-Heatmap-method.rd
History View file @ 7f6dddf
... ... 
@@ -35,5 +35,8 @@ Zuguang Gu <z.gu@dkfz.de>
35 35
36 36 
 }
37 37 
 \examples{
38 
+
38 39 
 # no example for this internal method
39 
-NULL}
40 
+NULL
41 
+
42 
+}
man/draw_hclust-Heatmap-method.rd
History View file @ 7f6dddf
... ... 
@@ -42,5 +42,8 @@ Zuguang Gu <z.gu@dkfz.de>
42 42
43 43 
 }
44 44 
 \examples{
45 
+
45 46 
 # no example for this internal method
46 
-NULL}
47 
+NULL
48 
+
49 
+}
man/draw_heatmap_body-Heatmap-method.rd
History View file @ 7f6dddf
... ... 
@@ -36,5 +36,8 @@ Zuguang Gu <z.gu@dkfz.de>
36 36
37 37 
 }
38 38 
 \examples{
39 
+
39 40 
 # no example for this internal method
40 
-NULL}
41 
+NULL
42 
+
43 
+}
man/draw_heatmap_legend-HeatmapList-method.rd
History View file @ 7f6dddf
... ... 
@@ -31,5 +31,8 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
32 32 
 }
33 33 
 \examples{
34 
+
34 35 
 # no example for this internal method
35 
-NULL}
36 
+NULL
37 
+
38 
+}
man/draw_heatmap_list-HeatmapList-method.rd
History View file @ 7f6dddf
... ... 
@@ -30,5 +30,8 @@ Zuguang Gu <z.gu@dkfz.de>
30 30
31 31 
 }
32 32 
 \examples{
33 
+
33 34 
 # no example for this internal method
34 
-NULL}
35 
+NULL
36 
+
37 
+}
man/draw_title-Heatmap-method.rd
History View file @ 7f6dddf
... ... 
@@ -33,5 +33,8 @@ Zuguang Gu <z.gu@dkfz.de>
33 33
34 34 
 }
35 35 
 \examples{
36 
+
36 37 
 # no example for this internal method
37 
-NULL}
38 
+NULL
39 
+
40 
+}
man/draw_title-HeatmapList-method.rd
History View file @ 7f6dddf
... ... 
@@ -31,5 +31,8 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
32 32 
 }
33 33 
 \examples{
34 
+
34 35 
 # no example for this internal method
35 
-NULL}
36 
+NULL
37 
+
38 
+}
man/get_color_mapping_list-HeatmapAnnotation-method.rd
History View file @ 7f6dddf
... ... 
@@ -30,5 +30,8 @@ Zuguang Gu <z.gu@dkfz.de>
30 30
31 31 
 }
32 32 
 \examples{
33 
+
33 34 
 # no example for this internal method
34 
-NULL}
35 
+NULL
36 
+
37 
+}
man/grid.dendrogram.rd
History View file @ 7f6dddf
... ... 
@@ -34,6 +34,7 @@ Zuguang Gu <z.gu@dkfz.de>
34 34
35 35 
 }
36 36 
 \examples{
37 
+
37 38 
 hc = hclust(dist(USArrests[1:5, ]))
38 39 
 dend = as.dendrogram(hc)
39 40
... ... 
@@ -45,4 +46,6 @@ grid.dendrogram(dend, facing = "top", layout.pos.row = 1, layout.pos.col = 2)
45 46 
 grid.dendrogram(dend, facing = "top", order = "reverse", layout.pos.row = 2,
46 47 
     layout.pos.col = 1)
47 48 
 grid.dendrogram(dend, facing = "left", layout.pos.row = 2, layout.pos.col = 2)
48 
-upViewport()}
49 
+upViewport()
50 
+
51 
+}
man/heatmap_legend_size-HeatmapList-method.rd
History View file @ 7f6dddf
... ... 
@@ -29,5 +29,8 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
30 30 
 }
31 31 
 \examples{
32 
+
32 33 
 # no example for this internal method
33 
-NULL}
34 
+NULL
35 
+
36 
+}
man/make_column_cluster-Heatmap-method.rd
History View file @ 7f6dddf
... ... 
@@ -30,5 +30,8 @@ Zuguang Gu <z.gu@dkfz.de>
30 30
31 31 
 }
32 32 
 \examples{
33 
+
33 34 
 # no example for this internal method
34 
-NULL}
35 
+NULL
36 
+
37 
+}
man/make_layout-Heatmap-method.rd
History View file @ 7f6dddf
... ... 
@@ -33,5 +33,8 @@ Zuguang Gu <z.gu@dkfz.de>
33 33
34 34 
 }
35 35 
 \examples{
36 
+
36 37 
 # no example for this internal method
37 
-NULL}
38 
+NULL
39 
+
40 
+}
man/make_layout-HeatmapList-method.rd
History View file @ 7f6dddf
... ... 
@@ -58,5 +58,8 @@ Zuguang Gu <z.gu@dkfz.de>
58 58
59 59 
 }
60 60 
 \examples{
61 
+
61 62 
 # no example for this internal method
62 
-NULL}
63 
+NULL
64 
+
65 
+}
man/make_row_cluster-Heatmap-method.rd
History View file @ 7f6dddf
... ... 
@@ -32,5 +32,8 @@ Zuguang Gu <z.gu@dkfz.de>
32 32
33 33 
 }
34 34 
 \examples{
35 
+
35 36 
 # no example for this internal method
36 
-NULL}
37 
+NULL
38 
+
39 
+}
man/map_to_colors-ColorMapping-method.rd
History View file @ 7f6dddf
... ... 
@@ -29,6 +29,7 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
30 30 
 }
31 31 
 \examples{
32 
+
32 33 
 # discrete color mapping for characters
33 34 
 cm = ColorMapping(name = "test",
34 35 
     colors = c("blue", "white", "red"),
... ... 
@@ -49,4 +50,6 @@ require(circlize)
49 50 
 cm = ColorMapping(name = "test",
50 51 
     col_fun = colorRamp2(c(0, 0.5, 1), c("blue", "white", "red")))
51 52 
 map_to_colors(cm, 0.2)
52 
-map_to_colors(cm, seq(0.2, 0.8, by = 0.1))}
53 
+map_to_colors(cm, seq(0.2, 0.8, by = 0.1))
54 
+
55 
+}
man/plotDataFrame.rd
History View file @ 7f6dddf
... ... 
@@ -46,6 +46,7 @@ Zuguang Gu <z.gu@dkfz.de>
46 46
47 47 
 }
48 48 
 \examples{
49 
+
49 50 
 df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], letters[1:4])),
50 51 
                 large = runif(10)*100,
51 52 
                 t1 = sample(letters[1:3], 10, replace = TRUE),
... ... 
@@ -53,4 +54,6 @@ df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], lett
53 54 
                 t2 = sample(LETTERS[1:3], 10, replace = TRUE))
54 55 
 plotDataFrame(df)
55 56 
 plotDataFrame(df, group = list(1:4, 5, 6, 7:12, 13), group_names = c("mat1", "large", "t1", "mat2", "t2"),
56 
-    main_heatmap = 4, km = 2, column_title = "column title", row_title = "row title")}
57 
+    main_heatmap = 4, km = 2, column_title = "column title", row_title = "row title")
58 
+
59 
+}
man/prepare-Heatmap-method.rd
History View file @ 7f6dddf
... ... 
@@ -37,5 +37,8 @@ Zuguang Gu <z.gu@dkfz.de>
37 37
38 38 
 }
39 39 
 \examples{
40 
+
40 41 
 # no example for this internal method
41 
-NULL}
42 
+NULL
43 
+
44 
+}
man/rowAnnotation.rd
History View file @ 7f6dddf
... ... 
@@ -31,5 +31,8 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
32 32 
 }
33 33 
 \examples{
34 
+
34 35 
 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
35 
-ha = columnAnnotation(df = df)}
36 
+ha = columnAnnotation(df = df)
37 
+
38 
+}
man/set_component_height-Heatmap-method.rd
History View file @ 7f6dddf
... ... 
@@ -30,5 +30,8 @@ Zuguang Gu <z.gu@dkfz.de>
30 30
31 31 
 }
32 32 
 \examples{
33 
+
33 34 
 # no example for this internal method
34 
-NULL}
35 
+NULL
36 
+
37 
+}
man/show-Heatmap-method.rd
History View file @ 7f6dddf
... ... 
@@ -28,6 +28,7 @@ Zuguang Gu <z.gu@dkfz.de>
28 28
29 29 
 }
30 30 
 \examples{
31 
+
31 32 
 mat = matrix(rnorm(80, 2), 8, 10)
32 33 
 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
33 34 
 rownames(mat) = letters[1:12]
... ... 
@@ -35,4 +36,6 @@ colnames(mat) = letters[1:10]
35 36
36 37 
 ht = Heatmap(mat)
37 38 
 ht
38 
-draw(ht, heatmap_legend_side = "left")}
39 
+draw(ht, heatmap_legend_side = "left")
40 
+
41 
+}
man/show-HeatmapList-method.rd
History View file @ 7f6dddf
... ... 
@@ -24,4 +24,7 @@ This function returns no value.
24 24
25 25 
 }
26 26 
 \author{
27 
-Zuguang Gu <z.gu@dkfz.de>}
27 
+
28 
+Zuguang Gu <z.gu@dkfz.de>
29 
+
30 
+}