@@ -1,32 +1,32 @@

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@@ -7,9 +7,11 @@ Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/

 Github page: https://github.com/jokergoo/ComplexHeatmap

 Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

-If you use it in published research, please cite:

-Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 

-  genomic data. Bioinformatics 2016.

+If you use it in published research, please cite either one:

+- Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 

+    genomic data. Bioinformatics 2016.

+- Gu, Z. Complex Heatmap Visualization. iMeta 2022.

+

 The new InteractiveComplexHeatmap package can directly export static 

 complex heatmaps into an interactive Shiny app with zero effort. Have a try!

@@ -17,7 +17,9 @@ The [**InteractiveComplexHeatmap**](https://github.com/jokergoo/InteractiveCompl

 ## Citation

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

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

+

+Zuguang Gu. [Complex Heatmap Visualization](https://doi.org/10.1002/imt2.43), iMeta, 2022. 

 ## Install

@@ -11,6 +11,17 @@ citEntry(

    textVersion = "Gu, Z. (2016) Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics. https://doi.org/10.1093/bioinformatics/btw313."

 )

+

+citEntry(

+   entry="article",

+   title = "Complex Heatmap Visualization",

+   author = personList(as.person("Zuguang Gu")),

+   journal = "iMeta",

+   year = 2022,

+   textVersion = "Gu, Z. (2022) Complex Heatmap Visualization. iMeta. https://doi.org/10.1002/imt2.43."

+)

+

+

 citFooter("This free open-source software implements academic

 research by the authors and co-workers. If you use it,

 please support the project by citing the appropriate

@@ -181,8 +181,8 @@ Heatmap(matrix, col, name,

   \item{raster_quality}{A value larger than 1.}

   \item{raster_device_param}{A list of further parameters for the selected graphic device. For raster image support, please check \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#heatmap-as-raster-image} .}

   \item{raster_resize_mat}{Whether resize the matrix to let the dimension of the matrix the same as the dimension of the raster image? The value can be logical. If it is \code{TRUE}, \code{\link[base]{mean}} is used to summarize the sub matrix which corresponds to a single pixel. The value can also be a summary function, e.g. \code{\link[base:Extremes]{max}}.}

-  \item{raster_by_magick}{Whether to use \code{\link[magick]{image_resize}} to scale the image.}

-  \item{raster_magick_filter}{Pass to \code{filter} argument of \code{\link[magick]{image_resize}}. A character scalar and all possible values are in \code{\link[magick]{filter_types}}. The default is \code{"Lanczos"}.}

+  \item{raster_by_magick}{Whether to use \code{\link[magick:transform]{image_resize}} to scale the image.}

+  \item{raster_magick_filter}{Pass to \code{filter} argument of \code{\link[magick:transform]{image_resize}}. A character scalar and all possible values are in \code{\link[magick:options]{filter_types}}. The default is \code{"Lanczos"}.}

   \item{post_fun}{A function which will be executed after the heatmap list is drawn.}

 }

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

 \itemize{

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

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

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

 \itemize{

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

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

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

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

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

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

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

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

 }

 }

 \examples{