@@ -8,9 +8,7 @@ Maintainer: Zuguang Gu <z.gu@dkfz.de>

 Depends: R (>= 3.1.2), methods, grid, graphics, stats, grDevices

 Imports: circlize (>= 0.4.1), GetoptLong, colorspace,

     RColorBrewer, GlobalOptions (>= 0.1.0)

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

-    dendsort, HilbertCurve (>= 1.11.1), Cairo, png, jpeg, tiff, fastcluster,

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

+Suggests: testthat (>= 0.3), knitr, markdown

 VignetteBuilder: knitr

 Description: Complex heatmaps are efficient to visualize associations 

     between different sources of data sets and reveal potential patterns. 

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

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

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

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

@@ -1,3 +1,5 @@

+<a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/"><img src="https://jokergoo.github.io/ComplexHeatmap-reference/book/complexheatmap-cover.jpg" width=240 align="right" style="border:2px solid black;" ></a>

+

 [![Build Status](https://travis-ci.org/jokergoo/ComplexHeatmap.svg)](https://travis-ci.org/jokergoo/ComplexHeatmap) 

 [![codecov](https://img.shields.io/codecov/c/github/jokergoo/ComplexHeatmap.svg)](https://codecov.io/github/jokergoo/ComplexHeatmap) 

 [![bioc](http://www.bioconductor.org/shields/downloads/ComplexHeatmap.svg)](https://bioconductor.org/packages/stats/bioc/ComplexHeatmap/) 

@@ -6,40 +8,18 @@

 ## Make Complex Heatmaps

-Complex heatmaps are efficient to visualize associations 

-between different sources of data sets and reveal potential structures. 

-Here the **ComplexHeatmap** package provides a highly flexible way to arrange 

-multiple heatmaps and supports self-defined annotation graphics.

+Complex heatmaps are efficient to visualize associations between different

+sources of data sets and reveal potential patterns. Here the

+**ComplexHeatmap** package provides a highly flexible way to arrange multiple

+heatmaps and supports various annotation graphics.

 ### Citation

 Zuguang Gu, Roland Eils and Matthias Schlesner, [Complex heatmaps reveal patterns and correlations in multidimensional genomic data](http://bioinformatics.oxfordjournals.org/content/early/2016/05/20/bioinformatics.btw313.abstract), Bioinformatics, 2016

-### General design

-

-Generally, a heatmap list contains several heatmaps and row annotations.

-

-![default](https://cloud.githubusercontent.com/assets/449218/6541828/75c77f8a-c4e5-11e4-80af-6ebb5e649898.png)

-

-Surrounding the heatmap list,

-there are legends for heatmaps and annotations, also there are titles which are placed

-on the four sides of the heatmap list. And for each heatmap, there are also different components

-surrounding the heatmap body.

-

-The **ComplexHeatmap** package is implemented in an object-oriented way. To describe a heatmap list, 

-there are following classes:

-

-- `Heatmap` class: a single heatmap containing heatmap body, row/column names, titles, dendrograms and column annotations.

-- `HeatmapList` class: a list of heatmaps and row annotations.

-- `HeatmapAnnotation` class: defines a list of row annotations and column annotations.

-

-There are also several internal classes:

-

-- `SingleAnnotation` class: defines a single row annotation or column annotation.

-- `ColorMapping` class: mapping from values to colors.

+### Documentation

-**ComplexHeatmap** is implemented under **grid** system, so users should know basic **grid** functionality

-to get full use of the package.

+The full documentations are available at https://jokergoo.github.io/ComplexHeatmap-reference/book/.

 ### Install

@@ -85,108 +65,25 @@ ha = HeatmapAnnotation(df = anno1, anno_fun = anno2, ..., which = "row")

 Heatmap(mat1, ...) + Heatmap(mat2, ...) + ha

 ```

-### As a base package

-

-**ComplexHeatmap** can be used as a base package to build other packages which focus

-On specific applications. E.g. [EnrichedHeatmap](http://github.com/jokergoo/EnrichedHeatmap) package

-uses **ComplexHeatmap** as base to make heatmaps which visualize the enrichment of genomic signals

-to specific target regions.

-

-### Vignettes

-

-There are several vignettes in the package. Each vignette focuses on a specific topic. Following

-lists the general topics discussed in these vignettes:

-

-  1. [**Making a Single Heatmap**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s2.single_heatmap.html)

-

-    This vignette introduces the basic configuration for making a single heatmap. Similar as other

-    R functions/packages, the basic usage is quite similar, but there are several unique features

-    for **ComplexHeamtap** package.

-    - Works both for numeric matrix and character matrix

-    - For numeric matrix which contains continuous values, the package allows a color mapping function

-      which can give more accurate colors and be robust to outliers.

-    - Highly flexible for clustering. You can define the distance method for clustering by:

-          * a pre-defined distance such as "euclidean" or "pearson"

-          * a self-defined function which calculates distance from a matrix.

-          * a self-defined function which calculates distance from two vectors

-        

-        You can define the clustering method by:

-          * a clustering function such as `diana()` from **cluster** package

-          * a `hclust` or `dendrogram` object.

-    - `NA` is allowed for clustering and heatmap visualization.

-    - Dendrogram and dimension names can be put on any side of the heatmap.

-    - Rows on the heatmap can be split by `cutree`, by `kmeans` or by a data frame which contains 

-      different levels that split the heatmap.

-    - The heatmap body itself can be completely self-defined.

-

-  2. [**Making a List of Heatmaps**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s3.a_list_of_heatmaps.html)

-

-    This vignette introduces how to concatenate a list of heatmaps and how adjustment is applied to keep

-    the correspondence of the heatmaps.

+### Examples

-  3. [**Heatmap Annotations**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s4.heatmap_annotation.html)

+#### Visualize Methylation Profile with Complex Annotations

-    This vignette introduces the concept of the heatmap annotation and demonstrate how to make simple annotations

-    as well as complex annotations. Also, the vignette explains the difference between column annotations

-    and row annotations.

+![complexheatmap_example4](https://user-images.githubusercontent.com/449218/47718635-2ec22980-dc49-11e8-9f01-37becb19e0d5.png)

-  4. [**Heatmap and Annotation Legends**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s5.legend.html)

+#### Correlations between methylation, expression and other genomic features

-    This vignette introduces how to configurate the heatmap legend and annotation legend, also

-    how to add self-defined legends.

+![complexheatmap_example3](https://user-images.githubusercontent.com/449218/47718636-2ec22980-dc49-11e8-8db0-1659c27dcf40.png)

-  5. [**Heatmap Decoration**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s6.heatmap_decoration.html)

+#### Visualize Cell Heterogeneity from Single Cell RNASeq

-    This vignette introduces methods to add more self-defined graphics to the heatmaps after the heatmaps

-    are generated.

+![complexheatmap_example2](https://user-images.githubusercontent.com/449218/47718637-2ec22980-dc49-11e8-925e-955c16cfa982.png)

-  6. [**Interactive with Heatmaps**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s7.interactive.html)

+#### Making Enhanced OncoPrint

-    How to select a region in the heatmap to retrieve the sub-matrix.

-  

-  7. [**OncoPrint**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s8.oncoprint.html)

-

-    How to make an oncoPrint.

-

-  8. [**Examples**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s9.examples.html)

-

-    More simulated and real-world examples are shown in this vignette.

-    

-

-### Visualize high dimensional genomic data

-

-The examples visualizes correlation between methylation and expression, as well as other annotation information (data are randomly generated). In the heatmap, each row corresponds to a differentially methylated regions (DMRs). 

-From left to right, heatmaps are:

-

-1. methylation for each DMRs in samples.

-2. direction of the methylation (one column heatmap), i.e. is methylation hyper in tumor or hypo?

-3. expression for the genes that are associated with corresponding DMRs (e.g. closest gene).

-4. signiciance for the correlation between methylation and expression (-log10(p-value)).

-5. type of genes, i.e. is the gene a protein coding gene or a lincRNA?

-6. annotation to gene models, i.e. is the DMR located in the intragenic region of the corresponding gene or the DMR is intergenic?

-7. distance from the DMR to the TSS of the corresponding gene.

-8. overlapping between DMRs and enhancers (Color shows how much the DMR is covered by the enhancers).

-

-![download](https://cloud.githubusercontent.com/assets/449218/9685180/dddf30c0-531c-11e5-805a-4cc5a36e9197.png)

-

-### OncoPrint

-

-<a href="http://www.cbioportal.org/faq.jsp#what-are-oncoprints">OncoPrint</a> visualize multiple genomic alteration

-events through a heatmap. From verion 1.3.0, **ComplexHeatmap** package provides a new `oncoPrint()` function. By this

-function, users can define their own graphics which correspond to differnet alteration events. Also the function additionally

-add barplots on two sides of the heatmap which tell number of different alterations in patients or samples.

-

-With general functionality of **ComplexHeamtap**, you can add more heatmaps / row annotations to the oncoPrint, even split the

-oncoPrint to enphasize sub groups.

-

-![oncoprint](https://cloud.githubusercontent.com/assets/449218/9370313/9c9b6b00-46cf-11e5-9740-c5c2a7a40eb5.png)

-

-### Interact with heatmaps

-

-You can use mouse to select a region on the heatmap, it will return row index and column index which correspond to the selected region.

-

-<p><img src="https://cloud.githubusercontent.com/assets/449218/10479344/2981c27a-7264-11e5-9868-7400c5dc620d.gif", width="600"></p>

+![complexheatmap_example1](https://user-images.githubusercontent.com/449218/47718638-2ec22980-dc49-11e8-845e-21e51d3b8e73.png)

 ### License

-GPL (>= 2)

+MIT @ Zuguang Gu

+

@@ -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,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

+\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

 }

 }

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

 \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

 }

 }

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

 \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

 }

 }

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

 \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

 }

 }

 \examples{

@@ -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,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,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-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,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

 \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

 }

 }

 \examples{

@@ -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,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

 \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

 }

 }

 \examples{

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

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

 \itemize{

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

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

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

 }

 }

 \examples{

@@ -3,3 +3,124 @@

 %\VignetteIndexEntry{Difference to older versions}

 -->

+

+Difference to Older Versions of ComplexHeatmap

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

+

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

+

+**Date**: `r Sys.Date()`

+

+**Package version**: `r installed.packages()["ComplexHeatmap", "Version"]`

+

+---------------------------------------

+

+```{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)

+```

+

+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

+changes between the new and old versions.

+

+## Heatmap() function

+

+- New arguments `column_km` and `column_split` to split heatmap by columns. The old `km` and `split`

+  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`.

+- 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

+  (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

+  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

+  control the title for each slice.

+  (https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#titles-for-splitting)

+- 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

+  heatmap.

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

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

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

+  set in `HeatmapAnnotation()` function.

+

+## HeatmapAnnotation() function

+

+- All annotations have default width/height now. E.g. the column simple annotation has height of 5mm

+  and the column barplot annotation has height of 1cm.

+- 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.

+  `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.

+- `anno_link()` is now renamed to `anno_mark()`. This annotation has default width and no need to

+  manually calcualte.

+- `anno_text()`: the size of the annotation is automatically calculated.

+- By default, the annotation names and axes are drawn and the space for them are also taken into

+  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)

+

+## A list of heatmaps

+

+- Heatmaps and annotations can be concatenated vertically by `%v%`.

+  (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)

+- 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)

+- 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.

+

+## oncoPrint() function

+

+- 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()`.

+- `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.

+- `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.

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

+  to it vertically.

@@ -3,3 +3,67 @@

 %\VignetteIndexEntry{Most probably asked questions}

 -->

+Most Probably Asked Questions

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

+

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

+

+**Date**: `r Sys.Date()`

+

+**Package version**: `r installed.packages()["ComplexHeatmap", "Version"]`

+

+---------------------------------------

+

+```{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)

+```

+

+## 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.

+

+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

+

+## 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

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

+

+## 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.

+

+## Can the heatmaps be added vertically?

+

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

+

+## Does Heatmap titles 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 them into 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

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

+ 

\ No newline at end of file