update

jokergoo · Mar 22, 2023 · 30566f4 · 30566f4
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: ComplexHeatmap
 Type: Package
 Title: Make Complex Heatmaps
-Version: 2.15.1
-Date: 2022-11-24
+Version: 2.15.2
+Date: 2023-03-22
 Authors@R: person("Zuguang", "Gu", email = "[email protected]", role = c("aut", "cre"),
                   comment = c('ORCID'="0000-0002-7395-8709"))
 Depends: R (>= 3.5.0), methods, grid, graphics, stats, grDevices
@@ -13,7 +13,7 @@ Suggests: testthat (>= 1.0.0), knitr, markdown, dendsort,
     jpeg, tiff, fastcluster, EnrichedHeatmap,
     dendextend (>= 1.0.1), grImport, grImport2, glue,
     GenomicRanges, gridtext, pheatmap (>= 1.0.12),
-    gridGraphics, gplots, rmarkdown, Cairo
+    gridGraphics, gplots, rmarkdown, Cairo, magick
 VignetteBuilder: knitr
 Description: Complex heatmaps are efficient to visualize associations 
     between different sources of data sets and reveal potential patterns. 

diff --git a/R/00_S4_generic_methods.R b/R/00_S4_generic_methods.R
@@ -1,32 +1,32 @@
-setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
-setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
+setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
+setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
+setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
+setGeneric('re_size', function(object, ...) standardGeneric('re_size'))
+setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
+setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
+setGeneric('draw', function(object, ...) standardGeneric('draw'))
 setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))
-setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
-setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
-setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
-setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
-setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
 setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
-setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
-setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
-setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
+setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
 setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
-setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
+setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
+setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation'))
+setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
+setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
+setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
 setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
-setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
 setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))
-setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation'))
-setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
-setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
-setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
-setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
-setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
-setGeneric('re_size', function(object, ...) standardGeneric('re_size'))
-setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
-setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
-setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
-setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
-setGeneric('draw', function(object, ...) standardGeneric('draw'))
+setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
+setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
+setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
 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('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_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
+setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
+setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
+setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
 setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
-setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
+setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
diff --git a/R/HeatmapList-class.R b/R/HeatmapList-class.R
@@ -325,7 +325,7 @@ setMethod(f = "draw",
     column_title_gp = gpar(fontsize = 13), 
 
     heatmap_legend_side = c("right", "left", "bottom", "top"), 
-    merge_legends = FALSE,
+    merge_legends = ht_opt$merge_legends,
     show_heatmap_legend = TRUE, 
     heatmap_legend_list = list(),
     annotation_legend_side = c("right", "left", "bottom", "top"), 

diff --git a/R/global.R b/R/global.R
@@ -34,6 +34,7 @@
 # -legend_gap Gap between legends. The value should be a vector of two units. One for gaps between
 #         vertical legends and one for the horizontal legends. If only one single unit is specified,
 #         the same gap set for the vertical and horizontal legends.
+# -merge_legend wether merge heatmap and annotation legends.
 #
 # Following parameters control heatmap annotations:
 #
@@ -117,6 +118,7 @@ ht_opt = setGlobalOptions(
 			}
 		}
 	),
+	merge_legends = FALSE,
 
 	heatmap_border = list(
 		.value = NULL),

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

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/component_height-dispatch.Rd b/man/component_height-dispatch.Rd
@@ -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{

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,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{

diff --git a/man/draw-HeatmapList-method.Rd b/man/draw-HeatmapList-method.Rd
@@ -19,7 +19,7 @@ Draw a list of heatmaps
     column_title_gp = gpar(fontsize = 13),
 
     heatmap_legend_side = c("right", "left", "bottom", "top"),
-    merge_legends = FALSE,
+    merge_legends = ht_opt$merge_legends,
     show_heatmap_legend = TRUE,
     heatmap_legend_list = list(),
     annotation_legend_side = c("right", "left", "bottom", "top"),

diff --git a/man/draw-dispatch.Rd b/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,AnnotationFunction-method}}, \code{\link{AnnotationFunction-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,Legends-method}}, \code{\link{Legends-class}} class method
+\item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method
+\item \code{\link{draw,SingleAnnotation-method}}, \code{\link{SingleAnnotation-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
 }
 }
 \examples{

diff --git a/man/ht_opt.Rd b/man/ht_opt.Rd
@@ -43,6 +43,7 @@ Following parameters control the legends:
   \item{legend_grid_height}{set \code{grid_height} in all heatmap legends and annotation legends.}
   \item{legend_border}{set \code{border} in all heatmap legends and annotation legends.}
   \item{legend_gap}{Gap between legends. The value should be a vector of two units. One for gaps between vertical legends and one for the horizontal legends. If only one single unit is specified, the same gap set for the vertical and horizontal legends.}
+  \item{merge_legend}{wether merge heatmap and annotation legends.}
 }
 
 Following parameters control heatmap annotations:

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
@@ -11,11 +11,11 @@ Method dispatch page for \code{show}.
 
 \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,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
-\item \code{\link{show,Heatmap-method}}, \code{\link{Heatmap-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
 \item \code{\link{show,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
+\item \code{\link{show,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method
 }
 }
 \examples{