@@ -1,7 +1,7 @@

 Package: ComplexHeatmap

 Type: Package

 Title: Making Complex Heatmaps

-Version: 1.2.3

+Version: 1.2.4

 Date: 2015-7-11

 Author: Zuguang Gu

 Maintainer: Zuguang Gu <z.gu@dkfz.de>

@@ -1,3 +1,9 @@

+CHANGES in VERSION 1.2.4

+

+*  legend for continuous values can be set as continuous legends

+

+==========================================

+

 CHANGES in VERSION 1.2.3

 * `color_mapping_legend` can produce a continuous color legend

@@ -28,7 +28,8 @@ ColorMapping = setClass("ColorMapping",

 		col_fun = "function", # function to map values to colors

 		type    = "character",  # continuous or discrete

 		name    = "character",  # used to map to the dataset and taken as the title of the legend

-		na_col  = "character"

+		na_col  = "character",

+		color_bar = "character"

 	)

 )

@@ -46,6 +47,7 @@ ColorMapping = setClass("ColorMapping",

 # -enforce_breaks If it is set to `TRUE`, values of ``breaks`` will be the final break value in the legend.

 #            If it is ``FALSE``, proper breaks values will be automatically generated.

 # -na_col colors for ``NA`` values.

+# -color_bar if the color mapping is continuous, whether draw the legend discrete or continuous.

 #

 # == detail

 # ``colors`` and ``levels`` are used for discrete color mapping, ``col_fun`` and 

@@ -58,7 +60,8 @@ ColorMapping = setClass("ColorMapping",

 # Zuguang Gu <z.gu@dkfz.de>

 #

 ColorMapping = function(name, colors = NULL, levels = NULL, 

-	col_fun = NULL, breaks = NULL, enforce_breaks = FALSE, na_col = "#FFFFFF") {

+	col_fun = NULL, breaks = NULL, enforce_breaks = FALSE, na_col = "#FFFFFF",

+	color_bar = c("discrete", "continuous")) {

 	.Object = new("ColorMapping")

@@ -113,6 +116,12 @@ ColorMapping = function(name, colors = NULL, levels = NULL,

 	.Object@name = name

 	.Object@na_col = na_col

+	color_bar = match.arg(color_bar)[1]

+	if(.Object@type == "discrete" && color_bar == "continuous") {

+		stop("Continuous color bar can only be applied to continuous color mapping.")

+	}

+	.Object@color_bar = color_bar

+

 	return(.Object)

 }

@@ -213,7 +222,6 @@ setMethod(f = "map_to_colors",

 # -legend_grid_border color for legend grid borders.

 # -legend_title_gp graphic parameter for legend title.

 # -legend_label_gp graphic parameter for legend label.

-# -color_bar if the color mapping is continuous, whether draw the legend discrete or continuous.

 #

 # == details

 # A viewport is created which contains a legend title, legend grids and corresponding labels.

@@ -229,15 +237,12 @@ setMethod(f = "color_mapping_legend",

 	definition = function(object, ..., plot = TRUE, legend_grid_height = unit(4, "mm"),

 	legend_grid_width = unit(4, "mm"), legend_grid_border = "white",

 	legend_title_gp = gpar(fontsize = 10, fontface = "bold"),

-	legend_label_gp = gpar(fontsize = 10), color_bar = c("discrete", "continuous")) {

+	legend_label_gp = gpar(fontsize = 10)) {

 	legend_title_gp = check_gp(legend_title_gp)

 	legend_label_gp = check_gp(legend_label_gp)

-	color_bar = match.arg(color_bar)[1]

-	if(object@type == "discrete" && color_bar == "continuous") {

-		stop("Continuous color bar can only be applied to continuous color mapping.")

-	}

+	color_bar = object@color_bar

 	# add title

 	legend_title_grob = textGrob(object@name, just = c("left", "top"), gp = legend_title_gp)

@@ -178,6 +178,7 @@ Heatmap = setClass("Heatmap",

 # -width the width of the single heatmap, should be a fixed `grid::unit` object. It is used for the layout when the heatmap

 #        is appended to a list of heatmaps.

 # -show_heatmap_legend whether show heatmap legend?

+# -heatmap_legend_color_bar if the matrix is continuous, whether should the legend as continuous color bar as well?

 #

 # == details

 # The initialization function only applies parameter checking and fill values to each slot with proper ones.

@@ -223,7 +224,8 @@ Heatmap = function(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),

     bottom_annotation_height = unit(5*length(bottom_annotation@anno_list), "mm"),

     km = 1, split = NULL, gap = unit(1, "mm"), 

     combined_name_fun = function(x) paste(x, collapse = "/"),

-    width = NULL, show_heatmap_legend = TRUE) {

+    width = NULL, show_heatmap_legend = TRUE,

+    heatmap_legend_color_bar = c("discrete", "continuous")) {

     .Object = new("Heatmap")

@@ -292,27 +294,28 @@ Heatmap = function(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),

         .Object@matrix = matrix

     }

+    heatmap_legend_color_bar = match.arg(heatmap_legend_color_bar)[1]

     # color for main matrix

     if(ncol(matrix) > 0) {

         if(missing(col)) {

             col = default_col(matrix, main_matrix = TRUE)

         }

         if(is.function(col)) {

-            .Object@matrix_color_mapping = ColorMapping(col_fun = col, name = name, na_col = na_col)

+            .Object@matrix_color_mapping = ColorMapping(col_fun = col, name = name, na_col = na_col, color_bar = heatmap_legend_color_bar)

         } else {

             if(is.null(names(col))) {

                 if(length(col) == length(unique(matrix))) {

                     names(col) = unique(matrix)

-                    .Object@matrix_color_mapping = ColorMapping(colors = col, name = name, na_col = na_col)

+                    .Object@matrix_color_mapping = ColorMapping(colors = col, name = name, na_col = na_col, color_bar = heatmap_legend_color_bar)

                 } else if(is.numeric(matrix)) {

                     col = colorRamp2(seq(min(matrix, na.rm = TRUE), max(matrix, na.rm = TRUE), length = length(col)),

                                      col)

-                    .Object@matrix_color_mapping = ColorMapping(col_fun = col, name = name, na_col = na_col)

+                    .Object@matrix_color_mapping = ColorMapping(col_fun = col, name = name, na_col = na_col, color_bar = heatmap_legend_color_bar)

                 } else {

                     stop("`col` should have names to map to values in `mat`.")

                 }

             } else {

-                .Object@matrix_color_mapping = ColorMapping(colors = col, name = name, na_col = na_col)

+                .Object@matrix_color_mapping = ColorMapping(colors = col, name = name, na_col = na_col, color_bar = heatmap_legend_color_bar)

             }

         }

     }

@@ -42,6 +42,7 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",

 # -df a data frame. Each column will be treated as a simple annotation. The data frame must have column names.

 # -name name of the heatmap annotation, optional.

 # -col a list of colors which contains color mapping to columns in ``df``. See `SingleAnnotation` for how to set colors.

+# -color_bar if there are continuous values in ``df``, show the legend as discrete or continuous

 # -show_legend whether show legend for each column in ``df``.

 # -... functions which define complex annotations. Values should be named arguments.

 # -which are the annotations row annotations or column annotations?

@@ -65,7 +66,8 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",

 # == author

 # Zuguang Gu <z.gu@dkfz.de>

 #

-HeatmapAnnotation = function(df, name, col, show_legend = rep(TRUE, n_anno), ..., 

+HeatmapAnnotation = function(df, name, col, color_bar = rep("discrete", ncol(df)), 

+	show_legend = rep(TRUE, n_anno), ..., 

 	which = c("column", "row"), annotation_height = 1, annotation_width = 1, 

 	height = unit(1, "cm"), width = unit(1, "cm"), gp = gpar(col = NA),

 	gap = unit(0, "null")) {

@@ -94,16 +96,18 @@ HeatmapAnnotation = function(df, name, col, show_legend = rep(TRUE, n_anno), ...

 	    	show_legend = rep(show_legend, n_anno)

 	    }

+	    if(length(color_bar) == 1) color_bar = rep(color_bar, ncol(df))

+

 	    if(missing(col)) {

 	        for(i in seq_len(n_anno)) {

-	        	anno_list = c(anno_list, list(SingleAnnotation(name = anno_name[i], value = df[, i], which = which, show_legend = show_legend[i], gp = gp)))

+	        	anno_list = c(anno_list, list(SingleAnnotation(name = anno_name[i], value = df[, i], which = which, show_legend = show_legend[i], gp = gp, color_bar = color_bar[i])))

 	        }

 	    } else {

 	        for(i in seq_len(n_anno)) {

 	        	if(is.null(col[[ anno_name[i] ]])) { # if the color is not provided

-	        		anno_list = c(anno_list, list(SingleAnnotation(name = anno_name[i], value = df[, i], which = which, show_legend = show_legend[i], gp = gp)))

+	        		anno_list = c(anno_list, list(SingleAnnotation(name = anno_name[i], value = df[, i], which = which, show_legend = show_legend[i], gp = gp, color_bar = color_bar[i])))

 	        	} else {

-	        		anno_list = c(anno_list, list(SingleAnnotation(name = anno_name[i], value = df[, i], col = col[[ anno_name[i] ]], which = which, show_legend = show_legend[i], gp = gp)))

+	        		anno_list = c(anno_list, list(SingleAnnotation(name = anno_name[i], value = df[, i], col = col[[ anno_name[i] ]], which = which, show_legend = show_legend[i], gp = gp, color_bar = color_bar[i])))

 	        	}

 	        }

 	    }

@@ -55,6 +55,7 @@ SingleAnnotation = setClass("SingleAnnotation",

 # -which is the annotation a row annotation or a column annotation?

 # -show_legend if it is a simple annotation, whether show legend when making the complete heatmap.

 # -gp graphic parameters for simple annotations.

+# -color_bar if the color mapping is continuous, whether draw the legend discrete or continuous. Onl works for simple annotation.

 #

 # == details

 # The most simple annotation is one row or one column grids in which different colors

@@ -80,7 +81,7 @@ SingleAnnotation = setClass("SingleAnnotation",

 # Zuguang Gu <z.gu@dkfz.de>

 #

 SingleAnnotation = function(name, value, col, fun, which = c("column", "row"), 

-	show_legend = TRUE, gp = gpar(col = NA)) {

+	show_legend = TRUE, gp = gpar(col = NA), color_bar = c("discrete", "continuous")) {

 	.Object = new("SingleAnnotation")

@@ -104,15 +105,17 @@ SingleAnnotation = function(name, value, col, fun, which = c("column", "row"),

 	    }

 	}

+	color_bar = match.arg(color_bar)[1]

+

     if(missing(fun)) {

     	if(missing(col)) {

     		col = default_col(value)

     	}

     	if(is.atomic(col)) {

-            color_mapping = ColorMapping(name = name, colors = col)

+            color_mapping = ColorMapping(name = name, colors = col, color_bar = color_bar)

         } else if(is.function(col)) {

-            color_mapping = ColorMapping(name = name, col_fun = col)

+            color_mapping = ColorMapping(name = name, col_fun = col, color_bar = color_bar)

         }

         .Object@color_mapping = color_mapping

@@ -15,5 +15,7 @@ It is only designed for \code{+} generic method so that above three classes can

 }

 \examples{

+

+

 # no example

 NULL}

@@ -27,5 +27,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example

 NULL}

@@ -30,5 +30,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # for examples, please go to `ColorMapping` method page

 NULL}

@@ -10,7 +10,8 @@ Constructor methods for ColorMapping class

 }

 \usage{

 ColorMapping(name, colors = NULL, levels = NULL,

-    col_fun = NULL, breaks = NULL, enforce_breaks = FALSE, na_col = "#FFFFFF")}

+    col_fun = NULL, breaks = NULL, enforce_breaks = FALSE, na_col = "#FFFFFF",

+    color_bar = c("discrete", "continuous"))}

 \arguments{

   \item{name}{name for this color mapping. It is used for drawing the title of the legend.}

@@ -20,6 +21,7 @@ ColorMapping(name, colors = NULL, levels = NULL,

   \item{breaks}{breaks for the continuous color mapping. If \code{col_fun} isgenerated by \code{\link[circlize]{colorRamp2}}, \code{breaks} can be ignored.}

   \item{enforce_breaks}{If it is set to \code{\link{TRUE}}, values of \code{breaks} will be the final break value in the legend.If it is \code{FALSE}, proper breaks values will be automatically generated.}

   \item{na_col}{colors for \code{NA} values.}

+  \item{color_bar}{if the color mapping is continuous, whether draw the legend discrete or continuous.}

 }

 \details{

 \code{colors} and \code{levels} are used for discrete color mapping, \code{col_fun} and 

@@ -35,6 +37,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # discrete color mapping for characters

 cm = ColorMapping(name = "test",

     colors = c("blue", "white", "red"),

@@ -72,5 +72,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # for examples, please go to `Heatmap` method page

 NULL}

@@ -34,7 +34,8 @@ Heatmap(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),

     bottom_annotation_height = unit(5*length(bottom_annotation@anno_list), "mm"),

     km = 1, split = NULL, gap = unit(1, "mm"),

     combined_name_fun = function(x) paste(x, collapse = "/"),

-    width = NULL, show_heatmap_legend = TRUE)}

+    width = NULL, show_heatmap_legend = TRUE,

+    heatmap_legend_color_bar = c("discrete", "continuous"))}

 \arguments{

   \item{matrix}{a matrix. Either numeric or character. If it is a simple vector, it will beconverted to a one-column matrix.}

@@ -85,6 +86,7 @@ Heatmap(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),

   \item{combined_name_fun}{if the heatmap is split by rows, how to make a combined row title for each slice?The input parameter for this function is a vector which contains level names under each column in \code{split}.}

   \item{width}{the width of the single heatmap, should be a fixed \code{\link[grid]{unit}} object. It is used for the layout when the heatmapis appended to a list of heatmaps.}

   \item{show_heatmap_legend}{whether show heatmap legend?}

+  \item{heatmap_legend_color_bar}{if the matrix is continuous, whether should the legend as continuous color bar as well?}

 }

 \details{

 The initialization function only applies parameter checking and fill values to each slot with proper ones.

@@ -111,6 +113,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -29,5 +29,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # for examples, please go to `HeatmapAnnotation` method page

 NULL}

@@ -9,7 +9,8 @@ Constructor method for HeatmapAnnotation class

 }

 \usage{

-HeatmapAnnotation(df, name, col, show_legend = rep(TRUE, n_anno), ...,

+HeatmapAnnotation(df, name, col, color_bar = rep("discrete", ncol(df)),

+    show_legend = rep(TRUE, n_anno), ...,

     which = c("column", "row"), annotation_height = 1, annotation_width = 1,

     height = unit(1, "cm"), width = unit(1, "cm"), gp = gpar(col = NA),

     gap = unit(0, "null"))}

@@ -18,6 +19,7 @@ HeatmapAnnotation(df, name, col, show_legend = rep(TRUE, n_anno), ...,

   \item{df}{a data frame. Each column will be treated as a simple annotation. The data frame must have column names.}

   \item{name}{name of the heatmap annotation, optional.}

   \item{col}{a list of colors which contains color mapping to columns in \code{df}. See \code{\link{SingleAnnotation}} for how to set colors.}

+  \item{color_bar}{if there are continuous values in \code{df}, show the legend as discrete or continuous}

   \item{show_legend}{whether show legend for each column in \code{df}.}

   \item{...}{functions which define complex annotations. Values should be named arguments.}

   \item{which}{are the annotations row annotations or column annotations?}

@@ -46,6 +48,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))

 ha = HeatmapAnnotation(df = df)

@@ -68,6 +68,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -27,7 +27,11 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \section{Detailes}{

+

+

 There is no public constructor method for the \code{\link{HeatmapList-class}}.}

 \examples{

+

+

 # no example

 NULL}

@@ -39,5 +39,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # for examples, please go to `SingleAnnotation` method page

 NULL}

@@ -10,7 +10,7 @@ Constructor method for SingleAnnotation class

 }

 \usage{

 SingleAnnotation(name, value, col, fun, which = c("column", "row"),

-    show_legend = TRUE, gp = gpar(col = NA))}

+    show_legend = TRUE, gp = gpar(col = NA), color_bar = c("discrete", "continuous"))}

 \arguments{

   \item{name}{name for this annotation.}

@@ -20,6 +20,7 @@ SingleAnnotation(name, value, col, fun, which = c("column", "row"),

   \item{which}{is the annotation a row annotation or a column annotation?}

   \item{show_legend}{if it is a simple annotation, whether show legend when making the complete heatmap.}

   \item{gp}{graphic parameters for simple annotations.}

+  \item{color_bar}{if the color mapping is continuous, whether draw the legend discrete or continuous. Onl works for simple annotation.}

 }

 \details{

 The most simple annotation is one row or one column grids in which different colors

@@ -48,6 +49,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # discrete character

 SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))

 SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"), 

@@ -31,6 +31,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -28,6 +28,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -28,6 +28,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -28,6 +28,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -31,6 +31,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 f = anno_barplot(rnorm(10))

 grid.newpage(); f(1:10)

@@ -32,6 +32,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(32), nrow = 4)

 f = anno_boxplot(mat)

 grid.newpage(); f(1:8)

@@ -28,6 +28,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(32), nrow = 4)

 f = anno_density(mat)

 grid.newpage(); f(1:8)

@@ -26,6 +26,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(32), nrow = 4)

 f = anno_histogram(mat)

 grid.newpage(); f(1:8)

@@ -33,5 +33,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 f = anno_points(rnorm(10))

 grid.newpage(); f(1:10)}

@@ -29,6 +29,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(100), 10)

 colnames(mat) = letters[1:10]

 rownames(mat) = LETTERS[1:10]

@@ -33,5 +33,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -13,7 +13,7 @@ Draw legend based on color mapping

 \S4method{color_mapping_legend}{ColorMapping}(object, ..., plot = TRUE, legend_grid_height = unit(4, "mm"),

     legend_grid_width = unit(4, "mm"), legend_grid_border = "white",

     legend_title_gp = gpar(fontsize = 10, fontface = "bold"),

-    legend_label_gp = gpar(fontsize = 10), color_bar = c("discrete", "continuous"))}

+    legend_label_gp = gpar(fontsize = 10))}

 \arguments{

   \item{object}{a \code{\link{ColorMapping-class}} object.}

@@ -24,7 +24,6 @@ Draw legend based on color mapping

   \item{legend_grid_border}{color for legend grid borders.}

   \item{legend_title_gp}{graphic parameter for legend title.}

   \item{legend_label_gp}{graphic parameter for legend label.}

-  \item{color_bar}{if the color mapping is continuous, whether draw the legend discrete or continuous.}

 }

 \details{

 A viewport is created which contains a legend title, legend grids and corresponding labels.

@@ -39,6 +38,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # discrete color mapping for characters

 cm = ColorMapping(name = "test",

     colors = c("blue", "white", "red"),

@@ -31,5 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))

 ha = rowAnnotation(df = df)}

@@ -28,4 +28,6 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method}

@@ -24,4 +24,6 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method}

@@ -20,6 +20,8 @@ This function is only for internal use.

 }

 \section{Detials}{

+

+

 This function is only for internal use.}

 \value{

 A \code{\link[grid]{unit}} object.

@@ -30,4 +32,6 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method}

@@ -28,4 +28,6 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method}

@@ -30,6 +30,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(40), nr = 4, ncol = 10)

 rownames(mat) = letters[1:4]

 colnames(mat) = letters[1:10]

@@ -31,6 +31,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -30,6 +30,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))

 ha = HeatmapAnnotation(df = df)

 grid.newpage(); draw(ha, 1:6)

@@ -33,6 +33,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -31,6 +31,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))

 grid.newpage(); draw(anno, 1:5)

 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))

@@ -34,5 +34,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -32,5 +32,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -35,5 +35,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -42,5 +42,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -36,5 +36,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -32,5 +32,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -30,5 +30,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -33,5 +33,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -31,5 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -30,5 +30,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -34,6 +34,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 hc = hclust(dist(USArrests[1:5, ]))

 dend = as.dendrogram(hc)

@@ -30,5 +30,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -30,5 +30,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -33,5 +33,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -59,5 +59,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -32,5 +32,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -29,6 +29,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # discrete color mapping for characters

 cm = ColorMapping(name = "test",

     colors = c("blue", "white", "red"),

@@ -25,5 +25,7 @@ This function returns no value.

 }

 \examples{

+

+

 # no example 

 NULL}

@@ -46,6 +46,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], letters[1:4])),

                 large = runif(10)*100,

                 t1 = sample(letters[1:3], 10, replace = TRUE),

@@ -37,5 +37,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -25,5 +25,7 @@ This function returns no value.

 }

 \examples{

+

+

 # no example 

 NULL}

@@ -31,5 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))

 ha = columnAnnotation(df = df)}

@@ -30,5 +30,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -28,6 +28,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -24,4 +24,6 @@ This function returns no value.

 }

 \author{

+

+

 Zuguang Gu <z.gu@dkfz.de>}