update

R/00_S4_generic_methods.R

@@ -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'))

R/zzz.R

@@ -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!

README.md

@@ -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

inst/CITATION

@@ -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

man/Heatmap.Rd

@@ -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.}
 
 }

man/add_heatmap-dispatch.Rd

@@ -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{

man/column_dend-dispatch.Rd

@@ -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{

man/draw-dispatch.Rd

@@ -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{

man/draw_title-dispatch.Rd

@@ -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{

man/row_dend-dispatch.Rd

@@ -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{

man/show-dispatch.Rd

@@ -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{