@@ -1,6 +1,6 @@

 Package: mheatmap

 Type: Package

-Title: plot multiple heatmaps

+Title: Making Complex Heatmaps

 Version: 0.0.1

 Date: 2014-10-6

 Author: Zuguang Gu

@@ -9,7 +9,10 @@ Depends: R (>= 3.1.0), grid

 Imports: methods, circlize (>= 0.2.3), GetoptLong, colorspace

 Suggests: testthat (>= 0.3), knitr, markdown, cluster, dendextend

 VignetteBuilder: knitr

-Description: plot multiple heatmaps

+Description: Complex heatmaps are efficient to visualize associations 

+    between different sources of data sets and reveal potential features. 

+    Here the mheatmap package provides a highly flexible way to arrange 

+    multiple heatmaps and supports self-defined annotation graphics.

 biocViews: Software, Visualization, Sequencing

 URL: https://github.com/jokergoo/mheatmap

 License: GPL (>= 2)

@@ -1,46 +1,51 @@

-export(+.AdditiveUnit)

-exportMethods(add_heatmap)

-exportMethods(draw_title)

-exportMethods(make_row_cluster)

+exportClasses(AdditiveUnit)

+export(AdditiveUnit)

+export(anno_histogram)

+exportMethods(annotation_legend_size)

+exportMethods(component_height)

+exportMethods(draw_hclust)

+export(HeatmapAnnotation)

+exportMethods(draw_annotation_legend)

+exportMethods(draw_heatmap_body)

+export(AdditiveUnit)

+export(anno_simple)

+exportMethods(draw_dimnames)

 exportClasses(HeatmapList)

 export(HeatmapList)

-exportMethods(draw_dimnames)

-exportMethods(component_height)

-exportMethods(initialize)

-exportMethods(prepare)

-exportMethods(make_layout)

-exportMethods(draw_heatmap_list)

-exportMethods(component_width)

-exportMethods(set_component_height)

-exportMethods(draw_annotation)

-exportMethods(map)

-exportMethods(annotation_legend_size)

-export(anno_points)

-export(dist2)

 exportMethods(show)

-exportMethods(color_mapping_legend)

-exportClasses(AdditiveUnit)

-export(AdditiveUnit)

 exportMethods(make_column_cluster)

-exportMethods(draw_heatmap_body)

+exportMethods(draw)

+exportMethods(color_mapping_legend)

 exportClasses(ColorMapping)

 export(ColorMapping)

+export(anno_boxplot)

+exportMethods(add_heatmap)

+exportMethods(make_row_cluster)

+exportMethods(make_layout)

+exportMethods(map)

+exportMethods(draw_heatmap_list)

+exportMethods(draw_heatmap_legend)

+export(Heatmap)

+exportMethods(heatmap_legend_size)

 exportMethods(get_color_mapping_list)

+export(ColorMapping)

 exportClasses(Heatmap)

 export(Heatmap)

-export(anno_histogram)

-exportMethods(heatmap_legend_size)

-exportMethods(draw_annotation_legend)

+export(anno_points)

+exportMethods(set_component_height)

+export(+.AdditiveUnit)

+exportMethods(prepare)

+exportMethods(component_width)

 exportClasses(SingleAnnotation)

 export(SingleAnnotation)

-export(anno_simple)

-exportMethods(draw_heatmap_legend)

-export(grid.dendrogram)

-exportMethods(draw_hclust)

-exportMethods(draw)

+export(HeatmapList)

 exportClasses(HeatmapAnnotation)

 export(HeatmapAnnotation)

-export(anno_boxplot)

+export(SingleAnnotation)

+export(grid.dendrogram)

+exportMethods(draw_title)

+exportMethods(draw_annotation)

+export(dist2)

 import(grid)

 importFrom("methods", setClass)

deleted file mode 100644

@@ -1,3 +0,0 @@

-[Dolphin]

-Timestamp=2015,3,4,16,2,47

-ViewMode=2

@@ -1,44 +1,44 @@

-setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))

+setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))

-setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))

+setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))

-setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))

+setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))

-setGeneric('draw', function(object, ...) standardGeneric('draw'))

+setGeneric('component_width', function(object, ...) standardGeneric('component_width'))

-setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))

+setGeneric('component_height', function(object, ...) standardGeneric('component_height'))

-setGeneric('component_width', function(object, ...) standardGeneric('component_width'))

+setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))

 setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))

-setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))

+setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))

-setGeneric('map', function(object, ...) standardGeneric('map'))

+setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))

-setGeneric('prepare', function(object, ...) standardGeneric('prepare'))

+setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))

-setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))

+setGeneric('map', function(object, ...) standardGeneric('map'))

-setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))

+setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))

 setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))

-setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))

+setGeneric('draw', function(object, ...) standardGeneric('draw'))

 setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))

-setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))

+setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))

 setGeneric('draw_hclust', function(object, ...) standardGeneric('draw_hclust'))

-setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))

+setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))

-setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))

+setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))

-setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))

+setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))

-setGeneric('component_height', function(object, ...) standardGeneric('component_height'))

+setGeneric('prepare', function(object, ...) standardGeneric('prepare'))

 setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))

@@ -3,25 +3,38 @@

 # An internal class

 #

 # == detail

-# This class is a super class for `Heatmap`, `HeatmapList` and `HeatmapAnnotation` classes.

-# And it is only for ``+`` generic method.

+# This class is a super class for `Heatmap-class`, `HeatmapList-class` and `HeatmapAnnotation-class` classes.

+# It is only for ``+`` generic method.

 #

 AdditiveUnit = setClass("AdditiveUnit")

+# == title

+# Constructor method for AdditiveUnit class

+#

+# == param

+# -... arguments.

+#

+# == details

+# This method is not used in the package.

+#

+AdditiveUnit = function(...) {

+    new("AdditiveUnit", ...)

+}

+

 # == title

 # Add heatmaps or row annotations to a heatmap list

 #

 # == param

-# -x a `Heatmap` object, a `HeatmapAnnotation` object or a `HeatmapList` object.

-# -y a `Heatmap` object, a `HeatmapAnnotation` object or a `HeatmapList` object.

+# -x a `Heatmap-class` object, a `HeatmapAnnotation-class` object or a `HeatmapList-class` object.

+# -y a `Heatmap-class` object, a `HeatmapAnnotation-class` object or a `HeatmapList-class` object.

 #

 # == detail

 # It is only a shortcut function. It actually calls `add_heatmap,Heatmap-method`, `add_heatmap,HeatmapList-method`

-# or `add_heatmap,HeatmapAnnotation-method` depending on the class of the input values.

+# or `add_heatmap,HeatmapAnnotation-method` depending on the class of the input objects.

 #

 # == value

-# a `HeatmapList` object.

+# A `HeatmapList-class` object.

 #

 # == author

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

@@ -7,14 +7,14 @@

 # Class to map values to colors

 #

 # == details

-# The `ColorMapping` class handles color mapping with both discrete values and continuous values.

+# The `ColorMapping-class` handles color mapping with both discrete values and continuous values.

 # Discrete values are mapped by setting a vector of colors and continuous values are mapped by setting

 # a color mapping function.

 #

 # == methods

-# The `ColorMapping` class provides following methods:

+# The `ColorMapping-class` provides following methods:

 #

-# - `initialize,ColorMapping-method`: contructor methods

+# - `ColorMapping`: contructor methods

 # - `map,ColorMapping-method`: mapping values to colors

 # - `color_mapping_legend,ColorMapping-method`: draw legend or get the size of the legend

 #

@@ -35,7 +35,6 @@ ColorMapping = setClass("ColorMapping",

 # Constructor methods for ColorMapping class

 #

 # == param

-# -.Object private object

 # -name name for this color mapping. It is used for drawing the title of the legend.

 # -colors discrete colors.

 # -levels levels that correspond to ``colors``. If ``colors`` is name indexed, 

@@ -49,16 +48,16 @@ ColorMapping = setClass("ColorMapping",

 # ``breaks`` are used for continuous color mapping.

 #

 # == value

-# A `ColorMapping` object.

+# A `ColorMapping-class` object.

 #

 # == author

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

 #

-setMethod(f = "initialize",

-	signature = "ColorMapping",

-	definition = function(.Object, name, colors = NULL, levels = NULL, 

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

 	col_fun = NULL, breaks = NULL) {

+	.Object = new("ColorMapping")

+

 	if(is.null(name)) {

 		stop("You should provide name.")

 	}

@@ -106,13 +105,13 @@ setMethod(f = "initialize",

 	.Object@name = name

 	return(.Object)

-})

+}

 # == title

 # Print ColorMapping object

 #

 # == param

-# -object a `ColorMapping` object.

+# -object a `ColorMapping-class` object.

 #

 # == value

 # This function returns no value.

@@ -150,7 +149,7 @@ setMethod(f = "show",

 # Map values to colors

 #

 # == param

-# -object a `ColorMapping` object.

+# -object a `ColorMapping-class` object.

 # -x input values.

 #

 # == details

@@ -189,7 +188,7 @@ setMethod(f = "map",

 # Draw legend based on color mapping

 #

 # == param

-# -object a `ColorMapping` object.

+# -object a `ColorMapping-class` object.

 # -... pass to `grid::viewport`.

 # -plot whether to plot or just return the size of the legend viewport.

 # -legend_grid_height height of each legend grid.

@@ -46,14 +46,14 @@

 # - row cluster on the right, graphics are drawn by `draw_hclust,Heatmap-method`.

 # - title on the right, graphics are drawn by `draw_title,Heatmap-method`.

 #

-# The `Heatmap` class is not responsible for heatmap legend and annotatino legends. The `draw,Heatmap-method` method

-# will construct a `HeatmapList` object which only contains one single heatmap

+# The `Heatmap-class` is not responsible for heatmap legend and annotatino legends. The `draw,Heatmap-method` method

+# will construct a `HeatmapList-class` object which only contains one single heatmap

 # and call `draw,HeatmapList-method` to make a complete heatmap.

 #

 # == methods

-# The `Heatmap` class provides following methods:

+# The `Heatmap-class` provides following methods:

 #

-# - `initialize,Heatmap-method`: contructor method.

+# - `Heatmap`: contructor method.

 # - `draw,Heatmap-method`: draw a single heatmap.

 # - `add_heatmap,Heatmap-method` append heatmaps and row annotations to a list of heatmaps.

 #

@@ -103,11 +103,10 @@ Heatmap = setClass("Heatmap",

 # Constructor method for Heatmap class

 #

 # == param

-# -.Object private object.

 # -matrix a matrix. Either numeric or character. If it is a simple vector, it will be

 #         converted to a one-column matrix.

 # -col a vector of colors if the color mapping is discrete or a color mapping 

-#      function if the matrix is continuous numbers. Pass to `initialize,ColorMapping-method`.

+#      function if the matrix is continuous numbers. Pass to `ColorMapping`.

 # -name name of the heatmap. The name is used as the title of the heatmap legend.

 # -rect_gp graphic parameters for drawing rectangles (for heatmap body).

 # -cell_fun self-defined function to add graphics on each cell. Six parameters will be passed into 

@@ -171,24 +170,22 @@ Heatmap = setClass("Heatmap",

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

 # Then it will be ready for clustering and layout.

 # 

-# Following methods can be applied on the `Heatmap` object:

+# Following methods can be applied on the `Heatmap-class` object:

 #

 # - `show,Heatmap-method`: draw a single heatmap with default parameters

 # - `draw,Heatmap-method`: draw a single heatmap.

 # - `add_heatmap,Heatmap-method` append heatmaps and row annotations to a list of heatmaps.

 #

 # The constructor function pretends to be a high-level graphic function because the ``show`` method

-# of the `Heatmap` object actually plots the graphics.

+# of the `Heatmap-class` object actually plots the graphics.

 #

 # == value

-# A `Heatmap` object.

+# A `Heatmap-class` object.

 #

 # == author

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

 #

-setMethod(f = "initialize",

-    signature = "Heatmap",

-    definition = function(.Object, matrix, col, name, rect_gp = gpar(col = NA), 

+Heatmap = function(matrix, col, name, rect_gp = gpar(col = NA), 

     cell_fun = function(i, j, x, y, width, height, fill) NULL,

     row_title = character(0), row_title_side = c("left", "right"), 

     row_title_gp = gpar(fontsize = 14), column_title = character(0),

@@ -211,6 +208,8 @@ setMethod(f = "initialize",

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

     width = NULL, show_heatmap_legend = TRUE) {

+    .Object = new("Heatmap")

+

     .Object@heatmap_param$width = width

     .Object@heatmap_param$show_heatmap_legend = show_heatmap_legend

@@ -308,7 +307,7 @@ setMethod(f = "initialize",

     .Object@row_names_param$side = match.arg(row_names_side)[1]

     .Object@row_names_param$show = show_row_names

     .Object@row_names_param$gp = row_names_gp

-    .Object@row_names_param$max_width = row_names_max_width

+    .Object@row_names_param$max_width = row_names_max_width + unit(2, "mm")

     if(is.null(colnames(matrix))) {

         show_column_names = FALSE

@@ -316,7 +315,7 @@ setMethod(f = "initialize",

     .Object@column_names_param$side = match.arg(column_names_side)[1]

     .Object@column_names_param$show = show_column_names

     .Object@column_names_param$gp = column_names_gp

-    .Object@column_names_param$max_height = column_names_max_height

+    .Object@column_names_param$max_height = column_names_max_height + unit(2, "mm")

     if(inherits(cluster_rows, "dendrogram") || inherits(cluster_rows, "hclust")) {

         .Object@row_hclust_param$obj = cluster_rows

@@ -409,13 +408,13 @@ setMethod(f = "initialize",

     return(.Object)

-})

+}

 # == title

 # Make cluster on columns

 #

 # == param

-# -object a `Heatmap` object.

+# -object a `Heatmap-class` object.

 # -order a pre-defined order.

 #

 # == details

@@ -424,7 +423,7 @@ setMethod(f = "initialize",

 # This function is only for internal use.

 #

 # == value

-# A `Heatmap` object.

+# A `Heatmap-class` object.

 #

 # == author

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

@@ -460,7 +459,7 @@ setMethod(f = "make_column_cluster",

 # Make cluster on rows

 #

 # == param

-# -object a `Heatmap` object.

+# -object a `Heatmap-class` object.

 # -order a pre-defined order.

 # -km if apply k-means clustering on rows, number of clusters.

 # -split a vector or a data frame by which the rows are be splitted.

@@ -468,10 +467,12 @@ setMethod(f = "make_column_cluster",

 # == details

 # The function will fill or adjust ``row_hclust_list``, ``row_order_list``, ``row_title`` and ``matrix_param`` slots.

 #

+# If ``order`` is defined, no clustering will be applied.

+#

 # This function is only for internal use.

 #

 # == value

-# A `Heatmap` object.

+# A `Heatmap-class` object.

 #

 # == author

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

@@ -581,7 +582,7 @@ setMethod(f = "make_row_cluster",

 # Make the layout of a single heatmap

 #

 # == param

-# -object a `Heatmap` object.

+# -object a `Heatmap-class` object.

 # 

 # == detail

 # The layout of the single heatmap will be established by setting the size of each heatmap components.

@@ -593,7 +594,7 @@ setMethod(f = "make_row_cluster",

 # This function is only for internal use.

 #

 # == value

-# A `Heatmap` object.

+# A `Heatmap-class` object.

 #

 # == author

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

@@ -786,7 +787,7 @@ setMethod(f = "make_layout",

 # Draw the single heatmap with default parameters

 #

 # == param

-# -object a `Heatmap` object.

+# -object a `Heatmap-class` object.

 #

 # == details

 # Actually it calls `draw,Heatmap-method`, but only with default parameters. If users want to customize the heatmap,

@@ -812,14 +813,14 @@ setMethod(f = "show",

 # Add two heatmaps or add row annotations as a heatmap list

 #

 # == param

-# -object a `Heatmap` object.

-# -x a `Heatmap` object, a `HeatmapAnnotation` object or a `HeatmapList` object.

+# -object a `Heatmap-class` object.

+# -x a `Heatmap-class` object, a `HeatmapAnnotation-class` object or a `HeatmapList-class` object.

 #

 # == details

 # There is a shortcut function ``+.Heatmap``.

 #

 # == value

-# A `HeatmapList` object.

+# A `HeatmapList-class` object.

 #

 # == author

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

@@ -839,7 +840,7 @@ setMethod(f = "add_heatmap",

 # Draw the heatmap body

 #

 # == param

-# -object a `Heatmap` object.

+# -object a `Heatmap-class` object.

 # -k a matrix may be splitted by rows, the value identifies which row-slice.

 # -... pass to `grid::viewport`, basically for defining the position of the viewport.

 #

@@ -905,7 +906,7 @@ setMethod(f = "draw_heatmap_body",

 # Draw dendrogram on row or column

 #

 # == params

-# -object a `Heatmap` object.

+# -object a `Heatmap-class` object.

 # -which is dendrogram put on the row or on the column of the heatmap?

 # -k a matrix may be splitted by rows, the value identifies which row-slice.

 # -max_height maximum height of the dendrograms.

@@ -974,7 +975,7 @@ setMethod(f = "draw_hclust",

 # Draw row names or column names

 #

 # == param

-# -object a `Heatmap` object.

+# -object a `Heatmap-class` object.

 # -which are names put on the row or on the column of the heatmap?

 # -k a matrix may be splitted by rows, the value identifies which row-slice.

 # -... pass to `grid::viewport`, basically for defining the position of the viewport.

@@ -1060,7 +1061,7 @@ setMethod(f = "draw_dimnames",

 # Draw heatmap title

 #

 # == param

-# -object a `Heatmap` object.

+# -object a `Heatmap-class` object.

 # -which is title put on the row or on the column of the heatmap?

 # -k a matrix may be splitted by rows, the value identifies which row-slice.

 # -... pass to `grid::viewport`, basically for defining the position of the viewport.

@@ -1114,13 +1115,13 @@ setMethod(f = "draw_title",

 # Draw column annotations

 #

 # == param

-# -object a `Heatmap` object.

+# -object a `Heatmap-class` object.

 # -which are the annotations put on the top or bottom of the heatmap.

 #

 # == details

 # A viewport is created which contains column annotations.

 #

-# Since the column annotations is a `HeatmapAnnotation` object, the function

+# Since the column annotations is a `HeatmapAnnotation-class` object, the function

 # calls `draw,HeatmapAnnotation-method` to draw the annotations.

 #

 # This function is only for internal use.

@@ -1153,7 +1154,7 @@ setMethod(f = "draw_annotation",

 # Width of each heatmap component

 #

 # == param

-# -object a `Heatmap` object.

+# -object a `Heatmap-class` object.

 # -k which components, see `Heatmap-class`.

 #

 # == detials

@@ -1201,7 +1202,7 @@ setMethod(f = "component_width",

 # Height of each heatmap component

 #

 # == param

-# -object a `Heatmap` object.

+# -object a `Heatmap-class` object.

 # -k which components, see `Heatmap-class`.

 #

 # == detail

@@ -1249,7 +1250,7 @@ setMethod(f = "component_height",

 # Set height of each heatmap component

 #

 # == param

-# -object a `Heatmap` object.

+# -object a `Heatmap-class` object.

 # -k which components, see `Heatmap-class`.

 # -v height of the component, a `grid::unit` object.

 #

@@ -1294,13 +1295,13 @@ setMethod(f = "set_component_height",

 # Draw a single heatmap

 #

 # == param

-# -object a `Heatmap` object.

+# -object a `Heatmap-class` object.

 # -internal only for internal use.

 # -test only for testing

 # -... pass to `draw,HeatmapList-method`.

 #

 # == detail

-# The function creates a `HeatmapList` object which only contains a single heatmap

+# The function creates a `HeatmapList-class` object which only contains a single heatmap

 # and call `draw,HeatmapList-method` to make the final heatmap.

 #

 # == value

@@ -1347,7 +1348,7 @@ setMethod(f = "draw",

 # Prepare the heatmap

 #

 # == param

-# -object a `Heatmap` object.

+# -object a `Heatmap-class` object.

 # -row_order orders of rows, pass to `make_row_cluster,Heatmap-method`. Because if more than one heatmaps

 #            are drawn by columns, the order of some heatmap will be adjusted by one certain heatmap, this

 #            argument is used to pass a pre-defined row order.

@@ -1363,7 +1364,7 @@ setMethod(f = "draw",

 # This function is only for internal use.

 #

 # == value

-# A `Heatmap` object.

+# A `Heatmap-class` object.

 #

 # == author

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

@@ -6,13 +6,13 @@

 #

 # == details

 # A complex heatmap contains a list of annotations which represente as different graphics

-# placed on rows and columns. The `HeatmapAnnotation` class is a category of single annotations

-# by a list of `SingleAnnotation` objects with same number of rows or columns.

+# placed on rows and columns. The `HeatmapAnnotation-class` is a category of single annotations

+# by a list of `SingleAnnotation-class` objects with same number of rows or columns.

 #

 # == methods

-# The `HeatmapAnnotation` class provides following methods:

+# The `HeatmapAnnotation-class` provides following methods:

 #

-# - `initialize,HeatmapAnnotation-method`: constructor method

+# - `HeatmapAnnotation`: constructor method

 # - `draw,HeatmapAnnotation-method`

 #

 # == author

@@ -38,10 +38,9 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",

 # Constructor method for HeatmapAnnotation class

 #

 # == param

-# -.Object a private object.

 # -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

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

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

 # -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?

@@ -55,17 +54,17 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",

 # defined by the function list. 

 #

 # == value

-# A `HeatmapAnnotation` object.

+# A `HeatmapAnnotation-class` object.

 #

 # == author

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

 #

-setMethod(f = "initialize",

-	signature = "HeatmapAnnotation",

-	definition = function(.Object, df, name, col, show_legend, ..., 

+HeatmapAnnotation = function(df, name, col, show_legend, ..., 

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

 	height = unit(1, "cm"), width = unit(1, "cm")) {

+	.Object = new("HeatmapAnnotation")

+

 	anno_list = list()

 	which = match.arg(which)[1]

@@ -154,13 +153,13 @@ setMethod(f = "initialize",

     .Object@size = size

     return(.Object)

-})

+}

 # == title

 # Get a list of color mapping objects

 #

 # == param

-# -object a `HeatmapAnnotation` object.

+# -object a `HeatmapAnnotation-class` object.

 #

 # == details

 # Color mapping for visible simple annotations are only returned.

@@ -168,7 +167,7 @@ setMethod(f = "initialize",

 # This function is only for internal use.

 #

 # == values

-# A list of `ColorMapping` list or an empty list.

+# A list of `ColorMapping-class` objects or an empty list.

 #

 # == author

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

@@ -190,7 +189,7 @@ setMethod(f = "get_color_mapping_list",

 # Draw the heatmap annotations

 #

 # == param

-# -object a `HeatmapAnnotation` object.

+# -object a `HeatmapAnnotation-class` object.

 # -index a vector of order.

 # -... pass to `grid::viewport` which contains all annotations.

 #

@@ -228,7 +227,7 @@ setMethod(f = "draw",

 # Print the Heatmap Annotation object

 #

 # == param

-# -object a `HeatmapAnnotation` object.

+# -object a `HeatmapAnnotation-class` object.

 #

 # == value

 # No value is returned.

@@ -259,14 +258,14 @@ setMethod(f = "show",

 # Add two row annotations or add heatmaps as a heatmap list

 #

 # == param

-# -object a `HeatmapAnnotation` object.

-# -x a `Heatmap` object, a `HeatmapAnnotation` object or a `HeatmapList` object.

+# -object a `HeatmapAnnotation-class` object.

+# -x a `Heatmap-class` object, a `HeatmapAnnotation-class` object or a `HeatmapList-class` object.

 #

 # == details

 # There is a shortcut function ``+.HeatmapAnnotation``.

 #

 # == value

-# A `HeatmapList` object.

+# A `HeatmapList-class` object.

 #

 # == author

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

@@ -41,7 +41,7 @@

 # are placed one after the other.

 #

 # == methods

-# The `HeatmapList` class provides following methods:

+# The `HeatmapList-class` provides following methods:

 #

 # - `draw,HeatmapList-method`: draw the list of heatmaps and row annotations.

 # - `add_heatmap,HeatmapList-method` add heatmaps to the list of heatmaps.

@@ -87,18 +87,31 @@ HeatmapList = setClass("HeatmapList",

     contains = "AdditiveUnit"

 )

+# == title

+# Constructor method for HeatmapList class

+#

+# == param

+# -... arguments

+#

+# == detailes

+# There is no public constructor method for the `HeatmapList-class`.

+#

+HeatmapList = function(...) {

+    new("HeatmapList", ...)

+}

+

 # == title

 # Add heatmaps and row annotations to the heatmap list

 #

 # == param

-# -object a `HeatmapList` object.

-# -x a `Heatmap` object or a `HeatmapAnnotation` object or a `HeatmapList` object.

+# -object a `HeatmapList-class` object.

+# -x a `Heatmap-class` object or a `HeatmapAnnotation-class` object or a `HeatmapList-class` object.

 #

 # == details

 # There is a shortcut function ``+.HeatmapList``.

 #

 # == value

-# A `HeatmapList` object.

+# A `HeatmapList-class` object.

 #

 # == author

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

@@ -134,7 +147,7 @@ setMethod(f = "add_heatmap",

 # Make layout for the complete plot

 #

 # == param

-# -object a `HeatmapList` object.

+# -object a `HeatmapList-class` object.

 # -row_title title on the row.

 # -row_title_side will the title be put on the left or right of the heatmap.

 # -row_title_gp graphic parameters for drawing text.

@@ -160,7 +173,7 @@ setMethod(f = "add_heatmap",

 # This function is only for internal use.

 #

 # == value

-# A `HeatmapList` object in which settings for each heatmap are adjusted.

+# A `HeatmapList-class` object in which settings for each heatmap are adjusted.

 #

 # == author

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

@@ -486,7 +499,7 @@ setMethod(f = "make_layout",

 # Draw a list of heatmaps

 #

 # == param

-# -object a `HeatmapList` object

+# -object a `HeatmapList-class` object

 # -... pass to `make_layout,HeatmapList-method`

 # -newpage whether to create a new page

 #

@@ -505,6 +518,10 @@ setMethod(f = "make_layout",

 setMethod(f = "draw",

     signature = "HeatmapList",

     definition = function(object, ..., newpage= TRUE) {

+

+    if(! any(sapply(object@ht_list, inherits, "Heatmap"))) {

+        stop("There should be at least one Heatmap in the heatmap list.")

+    }

     if(newpage) {

         grid.newpage()

@@ -530,7 +547,7 @@ setMethod(f = "draw",

 # Width of each heatmap list component

 #

 # == param

-# -object a `HeatmapList` object.

+# -object a `HeatmapList-class` object.

 # -k which components, see `HeatmapList-class`.

 #

 # == detail

@@ -573,7 +590,7 @@ setMethod(f = "component_width",

 # Height of each heatmap list component

 #

 # == param

-# -object a `HeatmapList` object.

+# -object a `HeatmapList-class` object.

 # -k which components, see `HeatmapList-class`.

 #

 # == value

@@ -614,7 +631,7 @@ setMethod(f = "component_height",

 # Draw the list of heatmaps

 #

 # == param

-# -object a `HeatmapList` object

+# -object a `HeatmapList-class` object

 #

 # == details

 # A viewport is created which contains heatmaps.

@@ -750,7 +767,7 @@ setMethod(f = "draw_heatmap_list",

 # Draw heatmap list title

 #

 # == param

-# -object a `HeatmapList` object

+# -object a `HeatmapList-class` object

 # -which dendrogram on the row or on the column of the heatmap

 #

 # == details

@@ -802,7 +819,7 @@ setMethod(f = "draw_title",

 # Draw legends for all heatmaps

 #

 # == param

-# -object a `HeatmapList` object

+# -object a `HeatmapList-class` object

 #

 # == details

 # A viewport is created which contains heatmap legends.

@@ -859,7 +876,7 @@ setMethod(f = "draw_heatmap_legend",

 # Draw legends for all column annotations

 #

 # == param

-# -object a `HeatmapList` object

+# -object a `HeatmapList-class` object

 # -annotation_legend_list a list of self-defined legend, should be wrapped into `grid::grob` objects.

 #

 # == details

@@ -919,7 +936,7 @@ setMethod(f = "draw_annotation_legend",

 # Size of the heatmap legend viewprot

 #

 # == param

-# -object a `HeatmapList` object

+# -object a `HeatmapList-class` object

 #

 # == detail

 # This function is only for internal use.

@@ -957,7 +974,7 @@ setMethod(f = "heatmap_legend_size",

 # Size of the annotation legend viewport

 #

 # == param

-# -object a `HeatmapList` object

+# -object a `HeatmapList-class` object

 # -annotation_legend_list a list of self-defined legend, should be wrapped into `grid::grob` objects.

 #

 # == detail

@@ -1091,7 +1108,7 @@ draw_legend = function(ColorMappingList, side = c("right", "left", "top", "botto

 # Draw a list of heatmaps with default parameters

 #

 # == param

-# -object a `HeatmapList` object.

+# -object a `HeatmapList-class` object.

 #

 # == details

 # Actually it calls `draw,HeatmapList-method`, but only with default parameters. If users want to customize the heatmap,