@@ -10,7 +10,7 @@ Imports: circlize (>= 0.4.1), GetoptLong, colorspace,

     RColorBrewer, GlobalOptions (>= 0.1.0)

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

     dendsort, HilbertCurve, Cairo, png, jpeg, tiff, fastcluster,

-    dendextend (>= 1.0.1), grImport, grImport2, rsvg

+    dendextend (>= 1.0.1), grImport, grImport2, rsvg, glue

 VignetteBuilder: knitr

 Description: Complex heatmaps are efficient to visualize associations 

     between different sources of data sets and reveal potential structures. 

@@ -1,31 +1,31 @@

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@@ -97,8 +97,8 @@ anno_width_and_height = function(which, width = NULL, height = NULL,

 # -show_name It is used to turn off the drawing of annotation names in `HeatmapAnnotation`. Annotations always have names

 #        associated and normally they will be drawn beside the annotation graphics to tell what the annotation is about.

 #        e.g. the annotation names put beside the points annotation graphics. However, for some of the annotations, the names

-#        are not necessarily to be drawn, such as text annotations drawn by `anno_text` or an empty annotation drawn by `anno_empty()`.

-#        In this case, when `show_names` is set to `FALSE`, there will be no annotation names drawn for the annotation.

+#        are not necessarily to be drawn, such as text annotations drawn by `anno_text` or an empty annotation drawn by `anno_empty`.

+#        In this case, when ``show_names`` is set to ``FALSE``, there will be no annotation names drawn for the annotation.

 # -width The width of the plotting region (the viewport) that the annotation is drawn. If it is a row annotation,

 #        the width must be an absolute unit. Since the ``AnnotationFunction`` object is always contained by the `SingleAnnotation-class`object,

 #        you can only set the width of row annotations or height of column annotations, while e.g. the height of the row annotation is always ``unit(1, "npc")``

@@ -348,6 +348,9 @@ setMethod(f = "draw",

 	if(test2) {

         grid.newpage()

         pushViewport(viewport(width = 0.8, height = 0.8))

+        if(is.na(object@n)) {

+        	object@n = 1

+        }

     }

     verbose = ht_opt$verbose

@@ -1,3 +1,4 @@

+# -anno_simple_size size of the simple annotation.# -anno_simple_size size of the simple annotation.# -anno_simple_size size of the simple annotation.

 # == title

 # Empty Annotation

@@ -110,6 +111,7 @@ subset_vector = function(x, i) x[i]

 #          the value of ``pt_size`` can be a vector, while if ``x`` is a matrix, ``pt_size`` can

 #          only be a single value.

 # -pt_gp Graphic parameters for points/symbols. The length setting is same as ``pt_size``.

+# -anno_simple_size size of the simple annotation.

 # -width Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.

 # -height Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.

 #

@@ -170,7 +170,7 @@ setMethod(f = "add_heatmap",

 #

 # == param

 # -object a `HeatmapList-class` object.

-# -newpage whether create a new page for the graphics. If you want to arrange multiple plots in one page, I suggest to use `grid::grabExpr`.

+# -newpage whether create a new page for the graphics. If you want to arrange multiple plots in one page, I suggest to use `grid::grid.grabExpr`.

 # -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.

@@ -190,7 +190,8 @@ setMethod(f = "add_heatmap",

 # -ht_gap same as ``gap``.

 # -main_heatmap index of main heatmap. The value can be a numeric index or the heatmap name

 # -padding padding of the whole plot. The value is a unit vector of length 4, which corresponds to bottom, left, top and right.

-# -adjust_annotation_name whether take annotation name into account when calculating positions of graphic elements.

+# -adjust_annotation_extension whether take annotation name into account when calculating positions of graphic elements.

+# -auto_adjust whether auto adjust

 # -row_dend_side side of the dendrogram from the main heatmap

 # -row_sub_title_side side of the row title from the main heatmap

 # -column_dend_side side of the dendrogram from the main heatmap

@@ -208,7 +209,8 @@ setMethod(f = "add_heatmap",

 # -split this modifies ``split`` of the main heatmap

 # -row_km this modifies ``row_km`` of the main heatmap

 # -row_split this modifies ``row_split`` of the main heatmap

-# -heatmap_body_height this modifies ``heatmap_body_height`` of the main heatmap

+# -height this modifies ``height`` of the main heatmap

+# -heatmap_height this modifies ``heatmap_height`` of the main heatmap

 # -column_gap this modifies ``column_gap`` of the main heatmap

 # -cluster_columns this modifies ``cluster_columns`` of the main heatmap

 # -clustering_distance_columns this modifies ``clustering_distance_columns`` of the main heatmap

@@ -220,7 +222,8 @@ setMethod(f = "add_heatmap",

 # -column_order this modifies ``column_order`` of the main heatmap

 # -column_km this modifies ``column_km`` of the main heatmap

 # -column_split this modifies ``column_split`` of the main heatmap

-# -heatmap_body_width this set the value in `ht_opt` and reset back after the plot is done

+# -width this modifies ``width`` of the main heatmap

+# -heatmap_width this modifies ``heatmap_width`` of the main heatmap

 # -heatmap_row_names_gp  this set the value in `ht_opt` and reset back after the plot is done

 # -heatmap_column_names_gp this set the value in `ht_opt` and reset back after the plot is done

 # -heatmap_row_title_gp this set the value in `ht_opt` and reset back after the plot is done

@@ -20,6 +20,7 @@

 # -ht_gap gap between heatmaps, should be a `grid::unit` object.

 # -main_heatmap name or index for the main heatmap

 # -padding padding of the plot

+# -auto_adjust whether autoadjust

 # -row_dend_side if auto adjust, where to put the row dendrograms for the main heatmap

 # -row_sub_title_side row sub title

 # -column_dend_side column dend

@@ -140,7 +141,7 @@ setMethod(f = "make_layout",

         grid::upViewport()

         object@layout$page_size = unit.c(convertWidth(unit(1, "npc"), "mm"),

                                          convertHeight(unit(1, "npc"), "mm"))

-        grid::downViewport()

+        grid::downViewport(current_vp)

     }

     object@ht_list_param$padding = padding

@@ -283,7 +284,7 @@ setMethod(f = "make_layout",

             if(row_dend_width[[1]] == 0) {

                 object@ht_list[[i_main]]@row_dend_param$width = unit(0, "mm")

             } else {

-                object@ht_list[[i_main]]@row_dend_param$width = row_dend_width + DENDROGRAM_PADDING  # append the gap

+                object@ht_list[[i_main]]@row_dend_param$width = row_dend_width + ht_opt$DENDROGRAM_PADDING  # append the gap

             }

         }

         if(!is.null(show_row_dend)) {

@@ -402,7 +403,7 @@ setMethod(f = "make_layout",

             if(column_dend_width[[1]] == 0) {

                 object@ht_list[[i_main]]@column_dend_param$width = unit(0, "mm")

             } else {

-                object@ht_list[[i_main]]@column_dend_param$width = column_dend_width + DENDROGRAM_PADDING  # append the gap

+                object@ht_list[[i_main]]@column_dend_param$width = column_dend_width + ht_opt$DENDROGRAM_PADDING  # append the gap

             }

         }

         if(!is.null(show_column_dend)) {

@@ -73,6 +73,7 @@ SingleAnnotation = setClass("SingleAnnotation",

 # -name_offset Offset to the annotation, a `grid::unit` object.

 # -name_side 'right' and 'left' for column annotations and 'top' and 'bottom' for row annotations

 # -name_rot Rotation of the annotation name, it can only take values in ``c(0, 90, 180, 270)``.

+# -anno_simple_size size of the simple annotation.

 # -width The width of the plotting region (the viewport) that the annotation is drawn. If it is a row annotation,

 #        the width must be an absolute unit.

 # -height The height of the plotting region (the viewport) that the annotation is drawn. If it is a column annotation,

@@ -22,7 +22,7 @@

 # -heatmap_column_names_gp set ``column_names_gp`` in all `Heatmap`.

 # -heatmap_row_title_gp set ``row_title_gp`` in all `Heatmap`.

 # -heatmap_column_title_gp set ``column_title_gp`` in all `Heatmap`.

-# -heatmap_border set `border` in all `Heatmap`.

+# -heatmap_border set ``border`` in all `Heatmap`.

 #

 # Following parameters to control the legends: 

 #

@@ -734,6 +734,8 @@ horizontal_continuous_legend_body = function(at, labels = at, col_fun,

 # == param

 # -... A list of objects returned by `Legend`.

 # -gap Gap between two neighbouring legends. The value is a `grid::unit` object with length of one.

+# -row_gap Horizontal gaps between legends.

+# -column_gap Vertical gaps between legends.

 # -direction The direction to arrange legends.

 # -max_width The maximal width of the total packed legends. It only works for horizontal arrangement.

 #           If the total width of the legends exceeds it, the legends will be arranged into several rows.

@@ -290,7 +290,7 @@ rep.list = function(x, n) {

 # A vector of viewport names.

 #

 list_component = function() {

-    vp = grid.ls(viewports = TRUE, grob = FALSE, flatten = FALSE, print = FALSE)

+    vp = grid.ls(viewports = TRUE, grobs = FALSE, flatten = FALSE, print = FALSE)

     vp = unlist(vp)

     attributes(vp) = NULL

     vp = vp[!grepl("^\\d+$", vp)]

@@ -15,4 +15,5 @@ method so that above three classes can be appended to each other.

 \examples{

 # There is no example

 NULL

+

 }

@@ -26,4 +26,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -23,4 +23,5 @@ See \code{\link{AnnotationFunction}} constructor for details.

 \examples{

 # There is no example

 NULL

+

 }

@@ -21,7 +21,7 @@ AnnotationFunction(fun, fun_name = "", which = c("column", "row"),

   \item{data_scale}{The data scale on the data axis (y-axis for column annotation and x-axis for row annotation). It is only used when \code{\link{decorate_annotation}} is used with "native" unit coordinates.}

   \item{subset_rule}{The rule of subsetting variables in \code{var_import}. It should be set when users want the final object to be subsetable. See **Details** section.}

   \item{subsetable}{Whether the object is subsetable?}

-  \item{show_name}{It is used to turn off the drawing of annotation names in \code{\link{HeatmapAnnotation}}. Annotations always have names associated and normally they will be drawn beside the annotation graphics to tell what the annotation is about. e.g. the annotation names put beside the points annotation graphics. However, for some of the annotations, the names are not necessarily to be drawn, such as text annotations drawn by \code{\link{anno_text}} or an empty annotation drawn by \code{\link{anno_empty()}}. In this case, when \code{\link{show_names}} is set to \code{\link{FALSE}}, there will be no annotation names drawn for the annotation.}

+  \item{show_name}{It is used to turn off the drawing of annotation names in \code{\link{HeatmapAnnotation}}. Annotations always have names associated and normally they will be drawn beside the annotation graphics to tell what the annotation is about. e.g. the annotation names put beside the points annotation graphics. However, for some of the annotations, the names are not necessarily to be drawn, such as text annotations drawn by \code{\link{anno_text}} or an empty annotation drawn by \code{\link{anno_empty}}. In this case, when \code{show_names} is set to \code{FALSE}, there will be no annotation names drawn for the annotation.}

   \item{width}{The width of the plotting region (the viewport) that the annotation is drawn. If it is a row annotation, the width must be an absolute unit. Since the \code{AnnotationFunction} object is always contained by the \code{\link{SingleAnnotation-class}}object, you can only set the width of row annotations or height of column annotations, while e.g. the height of the row annotation is always \code{unit(1, "npc")} which means it always fully filled in the parent \code{SingleAnnotation} and only in \code{\link{SingleAnnotation}} or even \code{\link{HeatmapAnnotation}} can adjust the height of the row annotations.}

   \item{height}{The height of the plotting region (the viewport) that the annotation is drawn. If it is a column annotation, the width must be an absolute unit.}

@@ -121,4 +121,5 @@ ComplexHeatmap Complete Reference ().

 \examples{

 # There is no example

 NULL

+

 }

@@ -26,4 +26,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -36,4 +36,5 @@ You can refer to the ComplexHeatmap Complete Reference for all the information o

 \examples{

 # There is no example

 NULL

+

 }

@@ -23,4 +23,5 @@ If the heatmap list is horizontal, \code{i} is the real row indices and \code{j}

 \examples{

 # There is no example

 NULL

+

 }

@@ -30,4 +30,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -185,4 +185,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -25,4 +25,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -74,4 +74,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -26,4 +26,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -26,4 +26,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -28,4 +28,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -39,6 +39,7 @@ SingleAnnotation(name, value, col, fun,

   \item{name_offset}{Offset to the annotation, a \code{\link[grid]{unit}} object.}

   \item{name_side}{'right' and 'left' for column annotations and 'top' and 'bottom' for row annotations}

   \item{name_rot}{Rotation of the annotation name, it can only take values in \code{c(0, 90, 180, 270)}.}

+  \item{anno_simple_size}{size of the simple annotation.}

   \item{width}{The width of the plotting region (the viewport) that the annotation is drawn. If it is a row annotation, the width must be an absolute unit.}

   \item{height}{The height of the plotting region (the viewport) that the annotation is drawn. If it is a column annotation, the width must be an absolute unit.}

@@ -40,4 +40,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -28,4 +28,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -28,4 +28,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -28,4 +28,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -11,8 +11,8 @@ Method dispatch page for \code{add_heatmap}.

 \itemize{

 \item \code{\link{add_heatmap,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method

-\item \code{\link{add_heatmap,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 \item \code{\link{add_heatmap,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

+\item \code{\link{add_heatmap,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 }

 }

 \examples{

@@ -1,5 +1,6 @@

 \name{adjust_heatmap_list-HeatmapList-method}

 \alias{adjust_heatmap_list,HeatmapList-method}

+\alias{adjust_heatmap_list}

 \title{

 Adjust heatmap list

 }

@@ -22,8 +23,8 @@ This function is only for internal use.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{adjust_heatmap_list}

 \examples{

 # There is no example

 NULL

+

 }

@@ -20,4 +20,5 @@ anno_link(...)

 \examples{

 # There is no example

 NULL

+

 }

@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -24,6 +24,7 @@ anno_simple(x, col, na_col = "grey",

   \item{pch}{Points/symbols that are added on top of the annotation grids. The value can be numeric or single letters. It can be a vector if \code{x} is a vector and a matrix if \code{x} is a matrix. No points are drawn if the corresponding values are NA.}

   \item{pt_size}{Size of the points/symbols. It should be a \code{\link[grid]{unit}} object. If \code{x} is a vector, the value of \code{pt_size} can be a vector, while if \code{x} is a matrix, \code{pt_size} can only be a single value.}

   \item{pt_gp}{Graphic parameters for points/symbols. The length setting is same as \code{pt_size}.}

+  \item{anno_simple_size}{size of the simple annotation.}

   \item{width}{Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.}

   \item{height}{Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.}

@@ -26,4 +26,5 @@ A \code{\link[grid]{grob}} object.

 \examples{

 # There is no example

 NULL

+

 }

@@ -1,5 +1,6 @@

 \name{annotation_legend_size-HeatmapList-method}

 \alias{annotation_legend_size,HeatmapList-method}

+\alias{annotation_legend_size}

 \title{

 Size of the annotation legend viewport

 }

@@ -28,8 +29,8 @@ A \code{\link[grid]{unit}} object.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{annotation_legend_size}

 \examples{

 # There is no example

 NULL

+

 }

@@ -1,5 +1,6 @@

 \name{color_mapping_legend-ColorMapping-method}

 \alias{color_mapping_legend,ColorMapping-method}

+\alias{color_mapping_legend}

 \title{

 Draw Legend Based on Color Mapping

 }

@@ -65,8 +66,8 @@ A \code{\link{Legends-class}} object.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{color_mapping_legend}

 \examples{

 # There is no example

 NULL

+

 }

@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -10,8 +10,8 @@ Method dispatch page for \code{column_order}.

 \code{column_order} can be dispatched on following classes:

 \itemize{

-\item \code{\link{column_order,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 \item \code{\link{column_order,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

+\item \code{\link{column_order,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 }

 }

 \examples{

@@ -31,4 +31,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -24,4 +24,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -10,8 +10,8 @@ Method dispatch page for \code{component_height}.

 \code{component_height} can be dispatched on following classes:

 \itemize{

-\item \code{\link{component_height,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 \item \code{\link{component_height,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

+\item \code{\link{component_height,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 }

 }

 \examples{

@@ -30,4 +30,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -26,4 +26,5 @@ The environment is at \code{object@var_env}.

 \examples{

 # There is no example

 NULL

+

 }

@@ -21,4 +21,5 @@ it calls \code{\link{copy_all,AnnotationFunction-method}} to hard copy the varia

 \examples{

 # There is no example

 NULL

+

 }

@@ -10,8 +10,8 @@ Method dispatch page for \code{copy_all}.

 \code{copy_all} can be dispatched on following classes:

 \itemize{

-\item \code{\link{copy_all,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method

 \item \code{\link{copy_all,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method

+\item \code{\link{copy_all,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method

 }

 }

 \examples{

@@ -17,4 +17,5 @@ dend_heights(x)

 \examples{

 # There is no example

 NULL

+

 }

@@ -28,4 +28,5 @@ A \code{\link{grob}} object which is generally contructed by \code{\link[grid]{s

 \examples{

 # There is no example

 NULL

+

 }

@@ -17,4 +17,5 @@ Dimension of the Heatmap

 \examples{

 # There is no example

 NULL

+

 }

@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -27,4 +27,5 @@ which is generally for testing purpose.

 \examples{

 # There is no example

 NULL

+

 }

@@ -33,4 +33,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -89,7 +89,7 @@ Draw a list of heatmaps

 \arguments{

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

-  \item{newpage}{whether create a new page for the graphics. If you want to arrange multiple plots in one page, I suggest to use \code{\link[grid]{grabExpr}}.}

+  \item{newpage}{whether create a new page for the graphics. If you want to arrange multiple plots in one page, I suggest to use \code{\link[grid]{grid.grabExpr}}.}

   \item{row_title}{title on the row.}

   \item{row_title_side}{will the title be put on the left or right of the heatmap.}

   \item{row_title_gp}{graphic parameters for drawing text.}

@@ -109,7 +109,8 @@ Draw a list of heatmaps

   \item{ht_gap}{same as \code{gap}.}

   \item{main_heatmap}{index of main heatmap. The value can be a numeric index or the heatmap name}

   \item{padding}{padding of the whole plot. The value is a unit vector of length 4, which corresponds to bottom, left, top and right.}

-  \item{adjust_annotation_name}{whether take annotation name into account when calculating positions of graphic elements.}

+  \item{adjust_annotation_extension}{whether take annotation name into account when calculating positions of graphic elements.}

+  \item{auto_adjust}{whether auto adjust}

   \item{row_dend_side}{side of the dendrogram from the main heatmap}

   \item{row_sub_title_side}{side of the row title from the main heatmap}

   \item{column_dend_side}{side of the dendrogram from the main heatmap}

@@ -127,7 +128,8 @@ Draw a list of heatmaps

   \item{split}{this modifies \code{split} of the main heatmap}

   \item{row_km}{this modifies \code{row_km} of the main heatmap}

   \item{row_split}{this modifies \code{row_split} of the main heatmap}

-  \item{heatmap_body_height}{this modifies \code{heatmap_body_height} of the main heatmap}

+  \item{height}{this modifies \code{height} of the main heatmap}

+  \item{heatmap_height}{this modifies \code{heatmap_height} of the main heatmap}

   \item{column_gap}{this modifies \code{column_gap} of the main heatmap}

   \item{cluster_columns}{this modifies \code{cluster_columns} of the main heatmap}

   \item{clustering_distance_columns}{this modifies \code{clustering_distance_columns} of the main heatmap}

@@ -139,7 +141,8 @@ Draw a list of heatmaps

   \item{column_order}{this modifies \code{column_order} of the main heatmap}

   \item{column_km}{this modifies \code{column_km} of the main heatmap}

   \item{column_split}{this modifies \code{column_split} of the main heatmap}

-  \item{heatmap_body_width}{this set the value in \code{\link{ht_opt}} and reset back after the plot is done}

+  \item{width}{this modifies \code{width} of the main heatmap}

+  \item{heatmap_width}{this modifies \code{heatmap_width} of the main heatmap}

   \item{heatmap_row_names_gp}{this set the value in \code{\link{ht_opt}} and reset back after the plot is done}

   \item{heatmap_column_names_gp}{this set the value in \code{\link{ht_opt}} and reset back after the plot is done}

   \item{heatmap_row_title_gp}{this set the value in \code{\link{ht_opt}} and reset back after the plot is done}

@@ -171,4 +174,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -11,11 +11,11 @@ Method dispatch page for \code{draw}.

 \itemize{

 \item \code{\link{draw,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method

-\item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

-\item \code{\link{draw,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method

+\item \code{\link{draw,Legends-method}}, \code{\link{Legends-class}} class method

 \item \code{\link{draw,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method

+\item \code{\link{draw,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method

+\item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

 \item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method

-\item \code{\link{draw,Legends-method}}, \code{\link{Legends-class}} class method

 }

 }

 \examples{

@@ -1,5 +1,6 @@

 \name{draw_annotation-Heatmap-method}

 \alias{draw_annotation,Heatmap-method}

+\alias{draw_annotation}

 \title{

 Draw Heatmap Annotations on the Heatmap

 }

@@ -30,8 +31,8 @@ This function returns no value.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{draw_annotation}

 \examples{

 # There is no example

 NULL

+

 }

@@ -1,5 +1,6 @@

 \name{draw_annotation_legend-HeatmapList-method}

 \alias{draw_annotation_legend,HeatmapList-method}

+\alias{draw_annotation_legend}

 \title{

 Draw legends for all column annotations

 }

@@ -27,8 +28,8 @@ This function returns no value.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{draw_annotation_legend}

 \examples{

 # There is no example

 NULL

+

 }

@@ -1,5 +1,6 @@

 \name{draw_dend-Heatmap-method}

 \alias{draw_dend,Heatmap-method}

+\alias{draw_dend}

 \title{

 Draw Heatmap Dendrograms

 }

@@ -33,8 +34,8 @@ This function returns no value.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{draw_dend}

 \examples{

 # There is no example

 NULL

+

 }

@@ -1,5 +1,6 @@

 \name{draw_dimnames-Heatmap-method}

 \alias{draw_dimnames,Heatmap-method}

+\alias{draw_dimnames}

 \title{

 Draw row names or column names

 }

@@ -29,8 +30,8 @@ This function returns no value.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{draw_dimnames}

 \examples{

 # There is no example

 NULL

+

 }

@@ -1,5 +1,6 @@

 \name{draw_heatmap_body-Heatmap-method}

 \alias{draw_heatmap_body,Heatmap-method}

+\alias{draw_heatmap_body}

 \title{

 Draw the Heatmap Body

 }

@@ -28,8 +29,8 @@ This function returns no value.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{draw_heatmap_body}

 \examples{

 # There is no example

 NULL

+

 }

@@ -1,5 +1,6 @@

 \name{draw_heatmap_legend-HeatmapList-method}

 \alias{draw_heatmap_legend,HeatmapList-method}

+\alias{draw_heatmap_legend}

 \title{

 Draw legends for all heatmaps

 }

@@ -27,8 +28,8 @@ This function returns no value.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{draw_heatmap_legend}

 \examples{

 # There is no example

 NULL

+

 }

@@ -1,5 +1,6 @@

 \name{draw_heatmap_list-HeatmapList-method}

 \alias{draw_heatmap_list,HeatmapList-method}

+\alias{draw_heatmap_list}

 \title{

 Draw the list of heatmaps

 }

@@ -25,8 +26,8 @@ This function returns no value.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{draw_heatmap_list}

 \examples{

 # There is no example

 NULL

+

 }

@@ -32,4 +32,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -30,4 +30,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -10,8 +10,8 @@ Method dispatch page for \code{draw_title}.

 \code{draw_title} can be dispatched on following classes:

 \itemize{

-\item \code{\link{draw_title,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 \item \code{\link{draw_title,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

+\item \code{\link{draw_title,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 }

 }

 \examples{

@@ -1,5 +1,6 @@

 \name{get_color_mapping_list-HeatmapAnnotation-method}

 \alias{get_color_mapping_list,HeatmapAnnotation-method}

+\alias{get_color_mapping_list}

 \title{

 Get a List of ColorMapping objects

 }

@@ -25,8 +26,8 @@ A list of \code{\link{ColorMapping-class}} objects or an empty list.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{get_color_mapping_list}

 \examples{

 # There is no example

 NULL

+

 }

@@ -1,5 +1,6 @@

 \name{get_legend_param_list-HeatmapAnnotation-method}

 \alias{get_legend_param_list,HeatmapAnnotation-method}

+\alias{get_legend_param_list}

 \title{

 Get a List of Annotation Legend Parameters