@@ -153,6 +153,7 @@ export("dendrogramGrob")

 export("densityHeatmap")

 export("dist2")

 export("getXY_in_parent_vp")

+export("grid.annotation_axis")

 export("grid.boxplot")

 export("grid.dendrogram")

 export("ht_global_opt")

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

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

+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('re_size', function(object, ...) standardGeneric('re_size'))

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@@ -268,6 +268,7 @@ AnnotationFunction = function(fun, fun_name = "", which = c("column", "row"),

 # -k Current slice index.

 # -n Total number of slices.

 # -test Is it in test mode? The value can be logical or a text which is plotted as the title of plot.

+# -... Pass to `grid::viewport`.

 #

 # == detail

 # Normally it is called internally by the `SingleAnnotation-class`.

@@ -277,7 +278,7 @@ AnnotationFunction = function(fun, fun_name = "", which = c("column", "row"),

 # 

 setMethod(f = "draw",

 	signature = "AnnotationFunction",

-	definition = function(object, index, k = 1, n = 1, test = FALSE) {

+	definition = function(object, index, k = 1, n = 1, test = FALSE, ...) {

 	if(is.character(test)) {

 		test2 = TRUE

@@ -302,7 +303,7 @@ setMethod(f = "draw",

     anno_width = object@width

     # names should be passed to the data viewport

-	pushViewport(viewport(width = anno_width, height = anno_height))

+	pushViewport(viewport(width = anno_width, height = anno_height, ...))

 	vp_name1 = current.viewport()$name

 	object@fun(index, k, n)

 	if(test2) {

@@ -310,7 +310,28 @@ setMethod(f = "draw_dimnames",

         "column" = object@column_order_list[[k]])

     pushViewport(viewport(name = paste(object@name, which, "names", k, sep = "_"), ...))

-    draw(anno, index = ind)

+    if(which == "row") {

+        if(object@row_names_param$side == "right" ) {

+            x = unit(0, "npc")

+            y = unit(0.5, "npc")

+            just = "left"

+        } else {

+            x = unit(1, "npc")

+            y = unit(0.5, "npc")

+            just = "right"

+        }

+    } else {

+        if(object@column_names_param$side == "top") {

+            x = unit(0.5, "npc")

+            y = unit(0, "npc")

+            just = "bottom"

+        } else {

+            x = unit(0.5, "npc")

+            y = unit(1, "npc")

+            just = "top"

+        }

+    }

+    draw(anno, index = ind, x = x, y = y, just = just)

     upViewport()

 })

@@ -106,7 +106,7 @@ SingleAnnotation = setClass("SingleAnnotation",

 # == seealso

 # There are following built-in annotation functions that can be directly used to generate complex annotations: 

 # `anno_simple`, `anno_points`, `anno_lines`, `anno_barplot`, `anno_histogram`, `anno_boxplot`, `anno_density`, `anno_text`,

-# `anno_joyplot`, `anno_horizon`, `anno_image`, `anno_lines` and `anno_mark`.

+# `anno_joyplot`, `anno_horizon`, `anno_image`, `anno_block`, `anno_summary` and `anno_mark`.

 # 

 # == value

 # A `SingleAnnotation-class` object.

@@ -23,7 +23,7 @@ The full documentations are available at https://jokergoo.github.io/ComplexHeatm

 ### Install

-`ComplexHeatmap` is available on [Bioconductor](http://www.bioconductor.org/packages/devel/bioc/html/ComplexHeatmap.html), you can intall it by:

+`ComplexHeatmap` is available on [Bioconductor](http://www.bioconductor.org/packages/devel/bioc/html/ComplexHeatmap.html), you can install it by:

 ```{r}

 source("http://bioconductor.org/biocLite.R")

@@ -71,7 +71,7 @@ are those created by annotation names and axes.

 \seealso{

 There are following built-in annotation functions that can be directly used to generate complex annotations: 

 \code{\link{anno_simple}}, \code{\link{anno_points}}, \code{\link{anno_lines}}, \code{\link{anno_barplot}}, \code{\link{anno_histogram}}, \code{\link{anno_boxplot}}, \code{\link{anno_density}}, \code{\link{anno_text}},

-\code{\link{anno_joyplot}}, \code{\link{anno_horizon}}, \code{\link{anno_image}}, \code{\link{anno_lines}} and \code{\link{anno_mark}}.

+\code{\link{anno_joyplot}}, \code{\link{anno_horizon}}, \code{\link{anno_image}}, \code{\link{anno_block}}, \code{\link{anno_summary}} and \code{\link{anno_mark}}.

 }

 \value{

 A \code{\link{SingleAnnotation-class}} object.

@@ -10,9 +10,9 @@ Method dispatch page for \code{add_heatmap}.

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

 \itemize{

-\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,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-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{

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

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

 \itemize{

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

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

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

 }

 }

 \examples{

@@ -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{

@@ -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{

@@ -7,7 +7,7 @@ Draw the AnnotationFunction Object

 Draw the AnnotationFunction Object

 }

 \usage{

-\S4method{draw}{AnnotationFunction}(object, index, k = 1, n = 1, test = FALSE)

+\S4method{draw}{AnnotationFunction}(object, index, k = 1, n = 1, test = FALSE, ...)

 }

 \arguments{

@@ -16,6 +16,7 @@ Draw the AnnotationFunction Object

   \item{k}{Current slice index.}

   \item{n}{Total number of slices.}

   \item{test}{Is it in test mode? The value can be logical or a text which is plotted as the title of plot.}

+  \item{...}{Pass to \code{\link[grid]{viewport}}.}

 }

 \details{

@@ -10,12 +10,12 @@ Method dispatch page for \code{draw}.

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

 \itemize{

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

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

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

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

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

 }

 }

 \examples{

@@ -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{

new file mode 100644

@@ -0,0 +1,30 @@

+\name{grid.annotation_axis}

+\alias{grid.annotation_axis}

+\title{

+Draw Annotation Axis

+}

+\description{

+Draw Annotation Axis

+}

+\usage{

+grid.annotation_axis(at = NULL, labels = at, labels_rot = 0, gp = gpar(),

+    side = "left", facing = "outside")

+}

+\arguments{

+

+  \item{at}{Break values. If it is not specified, it is inferred from data scale in current viewport.}

+  \item{labels}{Corresponding labels.}

+  \item{labels_rot}{Rotations of labels.}

+  \item{gp}{Graphic parameters.}

+  \item{side}{side of the axis of the annotation viewport.}

+  \item{facing}{Facing of the axis.}

+

+}

+\details{

+It uses \code{\link{annotation_axis_grob}} to construct the grob object, then use \code{\link[grid]{grid.draw}}

+to draw the axis.

+}

+\examples{

+# See examples in `annotation_axis_grob`

+NULL

+}

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

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

 \itemize{

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

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

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

 }

 }

 \examples{

@@ -10,12 +10,12 @@ Method dispatch page for \code{show}.

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

 \itemize{

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

 \item \code{\link{show,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method

+\item \code{\link{show,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method

+\item \code{\link{show,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method

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

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

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

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

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

 }

 }

 \examples{

@@ -4,7 +4,7 @@

 -->

-Difference to Older Versions of ComplexHeatmap

+Difference to Older Versions of ComplexHeatmap Package

 =================================================

 **Author**: Zuguang Gu ( z.gu@dkfz.de )

@@ -15,23 +15,14 @@ Difference to Older Versions of ComplexHeatmap

 ---------------------------------------

-```{r, echo = FALSE, message = FALSE}

-library(markdown)

-options(markdown.HTML.options = c(options('markdown.HTML.options')[[1]], "toc"))

-library(knitr)

-knitr::opts_chunk$set(

-    error = FALSE,

-    tidy  = FALSE,

-    message = FALSE,

-    fig.align = "center",

-    fig.width = 6,

-    fig.height = 6)

-options(markdown.HTML.stylesheet = "custom.css")

-options(width = 100)

-```

+<style type="text/css">

+h1, h2, h3, h4, h5 {

+    line-height: 120%;

+}

+</style>

 From version 2.0.0 of **ComplexHeatmap**, there are big changes to the older versions. The major

-functionalities are still the same, but still it is not 100% compatible. This vignette lists the

+functionalities are still the same, but it is not 100% compatible. This vignette lists the

 changes between the new and old versions.

 ## Heatmap() function

@@ -40,18 +31,18 @@ changes between the new and old versions.

   are renamed to `row_km` and `row_split`, although `km` and `split` are still usable.

 - A new argument `border` controls the border of the heatmap body. If heatmap is split into slices,

   all the slices will have borders.

-- Row title and column title allow background color by `column_title_gp = gpar(fill = ...)`.

-- `cluster_rows` and `cluster_columns` also allows objects which can be converted to `dendrogram`.

+- Row title and column title allow background color by e.g. `column_title_gp = gpar(fill = ...)`.

+- `cluster_rows` and `cluster_columns` also allow objects which can be converted to `dendrogram`.

 - If `cluster_rows` and `cluster_columns` are provided as clustering object, dendrogram reordering

   is turned off by default.

-- Add examples of how to integerat seriation

+- Add examples of how to integrate seriation.

   (https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#heatmap-seriation)

 - Row names and column names allow rotation by `row_names_rot` and `column_names_rot`.

 - New arguments `row_labels` and `column_labels` which can be set to replace row names and column

   names on the heatmap.

 - When heatmap is split and clustering is performed, there is a parent dendrogram which is

-  calculated from mean value in slices and put on top of the children dendrograms. There is a dashed

-  line showing the part of the parent dendrogram and emphasize the dendrogram is combined from

+  calculated from mean values in slices and put on top of the children dendrograms. There is a dashed

+  line showing the part of the parent dendrogram and emphasizing the dendrogram is combined from

   several dendrograms.

 - Remove `combined_name_fun` argument and control the titles for the heatmap slices directly by

   `row_title` and `column_title`. The two arguments support a string template which is convinient to

@@ -60,12 +51,13 @@ changes between the new and old versions.

 - New argument `layer_fun` is a vectorized version of `cell_fun`. This functionality is too

   low-level and normally users will not use it.

   (https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#customize-the-heatmap-body)

-- New argument: `width`, `heatmap_width`, `height`, `heatmap_height` to control the size of the

+- New arguments `width`, `heatmap_width`, `height`, `heatmap_height` to control the size of the

   heatmap.

   (https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#size-of-the-heatmap)

-- New argument: `left_annotation` and `right_annotation`.

+- New arguments `left_annotation` and `right_annotation`, which means row annotations can be components

+  of the heatmap, just like column annotations.

 - Remove `top_annotation_height` and `bottom_annotation_height`. The height of annotations should be

-  set in `HeatmapAnnotation()` function.

+  set in `HeatmapAnnotation()` function now.

 ## HeatmapAnnotation() function

@@ -74,7 +66,7 @@ changes between the new and old versions.

 - Provide more annotation functions: `anno_empty()`, `anno_simple`, `anno_image()`, `anno_block()`,

   `anno_lines()`, `anno_joyplot()`, `anno_horizon()`, `anno_summary()`.

   (https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html)

-- The size of the annotations are better to be set in the annotation function, e.g.

+- The size of the annotations are better to be set in the annotation functions, e.g.

   `anno_points(..., height = )`, but you can still set `annotation_height`.

 - The axis for the annotations (e.g. `anno_points()`, ...) can be controlled by the `axis_param`

   argument in the annotation function.

@@ -85,6 +77,8 @@ changes between the new and old versions.

   account for the layout of the final heatmap.

 - Two `HeatmapAnnotation` objects can be added as a single `HeatmapAnnotation` object by `c()`.

   (https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#heatmap-annotation-utility-function)

+- No need to use `row_anno_*()` functions, now `anno_*()` functions can automatically check whether

+  they are in column annotations or row annotations.

 ## A list of heatmaps

@@ -92,15 +86,15 @@ changes between the new and old versions.

   (https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#vertical-concatenation)

 - More arguments for the main heatmap can be controlled directly in `draw()`.

   (https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#control-main-heatmap-in-draw-function)

+- Global options can be temporarily set in `draw()`. (https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#change-parameters-globally, the last paragraph.)

 - Annotations and column names are nicely adjusted.

   (https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#annotations-as-components-are-adjusted)

 ## Legends

-- Legends are reimplemented as a `gTree` object internally. `Legend()` and `packLegend()` all

-  returns a `Legends` object. This object can be treated as a graphic element and to draw by

-  specifying the positions of the legends on the plot.

-  (https://jokergoo.github.io/ComplexHeatmap-reference/book/legends.html)

+- Legends are re-implemented as a `gTree` object internally. `Legend()` and `packLegend()` all

+  returns a `Legends` object. This object can be treated as a single graphic element and can be drawn by

+  specifying the positions on the viewport. (https://jokergoo.github.io/ComplexHeatmap-reference/book/legends.html)

 - Positions of legend labels are automatically adjusted if they overlap.

 - A list of legends are automatically wrapped into multiple columns or rows if they are too long and

   exceed the plotting region.

@@ -109,18 +103,18 @@ changes between the new and old versions.

 - It automatially tests whether functions in `alter_fun` are vectorized.

 - The oncoPrint barplot annotations are now controlled by `anno_oncoprint_barplot()` and they are

-  basically normal heatmap annotations. Also axes is controlled in `anno_oncoprint_barplot()`.

+  basically normal heatmap annotations. Also axis is controlled in `anno_oncoprint_barplot()`.

 - `barplot_ignore` is removed and the subset of alterations in directly controlled in

   `anno_oncoprint_barplot()`.

 - Similar as `Heatmap()`, all the argument related to the size of annotations are removed and they

   should be set directly in `HeatmapAnnotation()` or `anno_oncoprint_barplot()`.

 - New arguments `remove_empty_rows` and `remove_empty_columns`. If the number of rows and columns

-  gets smaller, all the oncoPrint component (e.g. row names, annotations) will be adjusted as well.

+  gets smaller, all the oncoPrint components (e.g. row names, annotations) will be adjusted as well.

 - `oncoPrint()` now returns a `Heatmap` object which can be concatenated to other

   heatmaps/annotations horizontally or vertically.

 ## densityHeatmap() function

-- Columns can be clustered by the Kolmogorov-Smirnov statistic between distributions.

+- Columns can be clustered by the Kolmogorov-Smirnov distance between distributions.

 - `densityHeatmap()` returns a vertical heatmap that more heatmaps and annotations can concatenate

   to it vertically.

@@ -14,55 +14,66 @@ Most Probably Asked Questions

 ---------------------------------------

-```{r, echo = FALSE, message = FALSE}

-library(markdown)

-options(markdown.HTML.options = c(options('markdown.HTML.options')[[1]], "toc"))

-library(knitr)

-knitr::opts_chunk$set(

-    error = FALSE,

-    tidy  = FALSE,

-    message = FALSE,

-    fig.align = "center",

-    fig.width = 6,

-    fig.height = 6)

-options(markdown.HTML.stylesheet = "custom.css")

-options(width = 100)

-```

+<style type="text/css">

+h1, h2, h3, h4, h5 {

+    line-height: 120%;

+}

+</style>

-## There is no plot comming out after running `Heatmap()` function.

+### There is no plot comming out after running Heatmap() function.

 In this case, you need to use `draw()` function explicitly. See https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#plot-the-heatmap.

-## Retrieve orders and dendrograms.

+### Retrieve orders and dendrograms.

-For retrieving orders and dendrograms from a single heatmap, see https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#get-orders-and-dendrograms-from-heatmap.

+For retrieving orders and dendrograms from a single heatmap. See https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#get-orders-and-dendrograms-from-heatmap.

-For retrieving orders and dendrograms from a list of heatmaps, see https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#get-orders-and-dendrograms.

+For retrieving orders and dendrograms from a list of heatmaps. See https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#get-orders-and-dendrograms-from-a-list-of-heatmaps.

-## How to control the style of legends.

+### How to control the style of legends?

 The style of legends can be controlled by `heatmap_legend_param` in `Heatmap()`, or

 `annotation_legend_param` in `HeatmapAnnotation()`. The parameters for controlling legends are those

-arguments in `Legend()` function, see

+arguments in `Legend()` function. See

 https://jokergoo.github.io/ComplexHeatmap-reference/book/legends.html#heatmap-and-annotation-legends.

-## Some text are cut by the plotting region

+### Some text are cut by the plotting region.

 The layout of the **ComplexHeatmap** is not perfect that it is still possible some of the text are

-drawn out of the plotting region. In this case, you set the `padding` argument in `draw()` function

-to increase the blank areas around the final plot.

+drawn out of the plotting region. In this case, you can set the `padding` argument in `draw()` function

+to increase the blank areas around the final plot. See https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#manually-increase-space-around-the-plot.

-## Can the heatmaps be added vertically?

+### Can the heatmaps be added vertically?

-Yes, use `%v%` instead of `+`.

+Yes, use `%v%` instead of `+`. See https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#vertical-concatenation.

-## Does Heatmap titles supports mathematical expression?

+### Does Heatmap title supports mathematical expression?

 Yes, all the text-related elements (e.g. titles, row names, legend titles, legend labels, ...) allow

 methematical expression.

-## I have many heatmaps and I want to put them into panels for a big figure for my paper.

+### I have many heatmaps and I want to put them into different panels for a big figure for my paper.

 You can set `newpage = FALSE` in `draw()` function and use `grid.layout()` to manage the layout of

-your panels. But I suggest more to use `grid.grabExpr()` to directly capture the output of the

+your panels. 

+

+```{r, eval = FALSE}

+pushViewport(viewport(layout = grid.layout(...)))

+pushViewport(viewport(layout.pos.row = ..., layout.pos.col = ...))

+draw(ht, newpage = FALSE) # or draw(ht_list, newpage = FALSE)

+popViewport()

+...

+```

+

+But I more suggest to use `grid.grabExpr()` to directly capture the output of the

 heatmap and later draw the whole plot as a single graphic element by `grid.draw()`.

+

+```{r, eval = FALSE}

+ht_grob = grid.grabExpr(draw(ht, ...))

+

+pushViewport(viewport(layout = grid.layout(...)))

+pushViewport(viewport(layout.pos.row = ..., layout.pos.col = ...))

+grid.draw(ht_grob)

+popViewport()

+...

+```