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a0neup03 · Mar 25, 2021 · 56b3b3e · 56b3b3e
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: ComplexHeatmap
 Type: Package
 Title: Make Complex Heatmaps
-Version: 2.7.9.1005
-Date: 2021-3-24
+Version: 2.7.9.1006
+Date: 2021-3-25
 Author: Zuguang Gu
 Maintainer: Zuguang Gu <[email protected]>
 Depends: R (>= 3.1.2), methods, grid, graphics, stats, grDevices

diff --git a/R/00_S4_generic_methods.R b/R/00_S4_generic_methods.R
@@ -1,32 +1,32 @@
+setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
 setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
-setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
+setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
 setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
-setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
-setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
-setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
-setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
-setGeneric('draw', function(object, ...) standardGeneric('draw'))
-setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
-setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
-setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
-setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
+setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
+setGeneric('re_size', function(object, ...) standardGeneric('re_size'))
 setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
-setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
+setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
 setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
+setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
+setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))
 setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
-setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
+setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
+setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
+setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
+setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
+setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
+setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
 setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))
-setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
-setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
+setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
 setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
-setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
-setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
-setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))
+setGeneric('draw', function(object, ...) standardGeneric('draw'))
+setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
 setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
-setGeneric('re_size', function(object, ...) standardGeneric('re_size'))
-setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation'))
-setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
-setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
 setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
+setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
+setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
 setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
-setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
+setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
+setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
+setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation'))
+setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
diff --git a/R/3d.R b/R/3d.R
@@ -160,7 +160,7 @@ Heatmap3D = function(matrix,
 		stop_wrap("`bar_rel_height` can only be set to a value between 0 and 1.")
 	}
 
-	Heatmap(matrix, ..., rect_gp = gpar(type = "none"),
+	ht = Heatmap(matrix, ..., rect_gp = gpar(type = "none"),
 		layer_fun = function(j, i, x, y, w, h, f) {
 			v = pindex(matrix, i, j)
 			od = rank(order(-as.numeric(y), -as.numeric(x)))
@@ -171,4 +171,6 @@ Heatmap3D = function(matrix,
 		show_column_dend = show_column_dend,
 		row_names_side = row_names_side,
 	)
+	ht@heatmap_param$type = "Heatmap3D"
+	ht
 }
diff --git a/R/Upset.R b/R/Upset.R
@@ -1450,6 +1450,7 @@ UpSet = function(m,
 			right_annotation = ra, col = c("0" = bg_pt_col, "1" = comb_col[1]),
 			row_order = comb_order, column_order = set_order, ...)
 	}
+	ht@heatmap_param$type = "UpSet"
 	attr(ht, "UpSet") = TRUE
 	ht
 }

diff --git a/R/global.R b/R/global.R
@@ -44,7 +44,7 @@
 #
 # -DENDROGRAM_PADDING space bewteen dendrograms and heatmap body.
 # -DIMNAME_PADDING space between row/column names and heatmap body.
-# -TITLE_PADDING space between row/column titles and heatmap body.
+# -TITLE_PADDING space between row/column titles and heatmap body. The value can have length of two which corresponds to the botton and top padding.
 # -COLUMN_ANNO_PADDING space between column annotations and heatmap body.
 # -ROW_ANNO_PADDING space between row annotations and heatmap body.
 # -HEATMAP_LEGEND_PADDING space between heatmap legends and heatmaps

diff --git a/man/add_heatmap-dispatch.Rd b/man/add_heatmap-dispatch.Rd
@@ -10,8 +10,8 @@ Method dispatch page for \code{add_heatmap}.
 \code{add_heatmap} can be dispatched on following classes:
 
 \itemize{
-\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
 }
 }

diff --git a/man/column_order-dispatch.Rd b/man/column_order-dispatch.Rd
@@ -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,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
 \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
 }
 }
 \examples{

diff --git a/man/copy_all-dispatch.Rd b/man/copy_all-dispatch.Rd
@@ -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{

diff --git a/man/draw-dispatch.Rd b/man/draw-dispatch.Rd
@@ -10,11 +10,11 @@ Method dispatch page for \code{draw}.
 \code{draw} can be dispatched on following classes:
 
 \itemize{
-\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,Legends-method}}, \code{\link{Legends-class}} class method
 \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,Legends-method}}, \code{\link{Legends-class}} class method
-\item \code{\link{draw,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
+\item \code{\link{draw,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
 \item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method
 }
 }

diff --git a/man/draw_title-dispatch.Rd b/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{

diff --git a/man/ht_opt.Rd b/man/ht_opt.Rd
@@ -57,7 +57,7 @@ Following parameters control the space between heatmap components:
 \describe{
   \item{DENDROGRAM_PADDING}{space bewteen dendrograms and heatmap body.}
   \item{DIMNAME_PADDING}{space between row/column names and heatmap body.}
-  \item{TITLE_PADDING}{space between row/column titles and heatmap body.}
+  \item{TITLE_PADDING}{space between row/column titles and heatmap body. The value can have length of two which corresponds to the botton and top padding.}
   \item{COLUMN_ANNO_PADDING}{space between column annotations and heatmap body.}
   \item{ROW_ANNO_PADDING}{space between row annotations and heatmap body.}
   \item{HEATMAP_LEGEND_PADDING}{space between heatmap legends and heatmaps}

diff --git a/man/make_layout-dispatch.Rd b/man/make_layout-dispatch.Rd
@@ -10,8 +10,8 @@ Method dispatch page for \code{make_layout}.
 \code{make_layout} can be dispatched on following classes:
 
 \itemize{
-\item \code{\link{make_layout,Heatmap-method}}, \code{\link{Heatmap-class}} class method
 \item \code{\link{make_layout,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
+\item \code{\link{make_layout,Heatmap-method}}, \code{\link{Heatmap-class}} class method
 }
 }
 \examples{

diff --git a/man/row_dend-dispatch.Rd b/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{

diff --git a/man/row_order-dispatch.Rd b/man/row_order-dispatch.Rd
@@ -10,8 +10,8 @@ Method dispatch page for \code{row_order}.
 \code{row_order} can be dispatched on following classes:
 
 \itemize{
-\item \code{\link{row_order,Heatmap-method}}, \code{\link{Heatmap-class}} class method
 \item \code{\link{row_order,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
+\item \code{\link{row_order,Heatmap-method}}, \code{\link{Heatmap-class}} class method
 }
 }
 \examples{

diff --git a/man/show-dispatch.Rd b/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,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method
-\item \code{\link{show,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
-\item \code{\link{show,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method
-\item \code{\link{show,HeatmapList-method}}, \code{\link{HeatmapList-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,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method
+\item \code{\link{show,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method
 }
 }
 \examples{