update

ztsin · Mar 31, 2023 · 772822f · 772822f
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Showing 11 changed files with 51 additions and 36 deletions.
diff --git a/NEWS b/NEWS
@@ -1,3 +1,9 @@
+CHANGES in VERSION 2.15.3
+
+* `Legend()`: `legend_gp` also controls line color, width and style.
+
+=======================
+
 CHANGES in VERSION 2.15.1
 
 * `Legend()`: allows `NA` in `pch`.

diff --git a/R/00_S4_generic_methods.R b/R/00_S4_generic_methods.R
@@ -1,32 +1,32 @@
-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('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
+setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
+setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
+setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
+setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
+setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation'))
+setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
+setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
 setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))
+setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
+setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))
+setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
+setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
+setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
 setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
 setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
-setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
-setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
-setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation'))
+setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
+setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
 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('draw_title', function(object, ...) standardGeneric('draw_title'))
-setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
+setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
 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('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
+setGeneric('row_order', function(object, ...) standardGeneric('row_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('re_size', function(object, ...) standardGeneric('re_size'))
+setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
+setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
 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('component_width', function(object, ...) standardGeneric('component_width'))
+setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
+setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
+setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
diff --git a/R/ColorMapping-class.R b/R/ColorMapping-class.R
@@ -262,6 +262,7 @@ setMethod(f = "map_to_colors",
 # -nrow Pass to `Legend`. It controls the layout of legend grids if they are arranged in multiple rows or columns.
 # -ncol Pass to `Legend`. It controls the layout of legend grids if they are arranged in multiple rows or columns.
 # -by_row Pass to `Legend`. It controls the order of legend grids if they are arranged in multiple rows or columns.
+# -legend_gp Graphic parameters for legend.
 # -legend_height Height of the legend body. It only works when ``color_bar`` is ``continuous`` and ``direction`` is ``vertical``. Pass to `Legend`.
 # -legend_width Width of the legend body. It only works when ``color_bar`` is ``continuous`` and ``direction`` is ``horizontal``. Pass to `Legend`.
 # -legend_direction When ``color_bar`` is ``continuous``, whether the legend is vertical or horizontal? Pass to `Legend`.
@@ -300,6 +301,7 @@ setMethod(f = "color_mapping_legend",
 	nrow = NULL,
 	ncol = 1,
 	by_row = FALSE,
+	legend_gp = gpar(),
 	legend_height = NULL, 
 	legend_width = NULL,
 	legend_direction = c("vertical", "horizontal"),
@@ -356,19 +358,21 @@ setMethod(f = "color_mapping_legend",
 			labels = rev(labels)
 		}
 		if(length(at) == 0) {
+			legend_gp$fill = object@na_col
 			gf = Legend(at = "NA", labels = "NA", name = object@name, title = title, title_gp = title_gp, grid_height = grid_height,
 				grid_width = grid_width, tick_length = tick_length, border = border, labels_gp = labels_gp, direction = legend_direction, nrow = nrow, ncol = ncol,
-				legend_gp = gpar(fill = object@na_col), title_position = title_position, by_row = by_row, graphics = graphics, break_dist = break_dist)
+				legend_gp = legend_gp, title_position = title_position, by_row = by_row, graphics = graphics, break_dist = break_dist)
 		} else {
+			legend_gp$fill = map_to_colors(object, at)
 			gf = Legend(at = at, labels = labels, name = object@name, title = title, title_gp = title_gp, grid_height = grid_height,
 				grid_width = grid_width, tick_length = tick_length, border = border, labels_gp = labels_gp, direction = legend_direction, nrow = nrow, ncol = ncol,
-				legend_gp = gpar(fill = map_to_colors(object, at)), title_position = title_position, by_row = by_row, graphics = graphics, break_dist = break_dist)
+				legend_gp = legend_gp, title_position = title_position, by_row = by_row, graphics = graphics, break_dist = break_dist)
 		}
 
 	} else {
 		gf = Legend(at = at, labels = labels, name = object@name, col_fun = object@col_fun, title = title, title_gp = title_gp, grid_height = grid_height,
 				grid_width = grid_width, tick_length = tick_length, border = border, labels_gp = labels_gp, labels_rot = labels_rot, direction = legend_direction,
-				legend_width = legend_width, legend_height = legend_height, title_position = title_position, by_row = by_row, break_dist = break_dist)
+				legend_gp = legend_gp, legend_width = legend_width, legend_height = legend_height, title_position = title_position, by_row = by_row, break_dist = break_dist)
 
 	}
 

diff --git a/R/grid.Legend.R b/R/grid.Legend.R
@@ -526,6 +526,9 @@ discrete_legend_body = function(at, labels = at, nrow = NULL, ncol = 1, by_row =
 		} else {
 			sgd2$fill = background
 		}
+		if(identical(legend_gp$col, "asis")) {
+			border = "asis"
+		}
 		if(identical(border, "asis")) {
 			sgd2$col = sgd2$fill	
 		} else {

diff --git a/man/add_heatmap-dispatch.Rd b/man/add_heatmap-dispatch.Rd
@@ -11,8 +11,8 @@ Method dispatch page for \code{add_heatmap}.
 
 \itemize{
 \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
 \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
 }
 }
 \examples{

diff --git a/man/color_mapping_legend-ColorMapping-method.Rd b/man/color_mapping_legend-ColorMapping-method.Rd
@@ -27,6 +27,7 @@ Draw Legend Based on Color Mapping
     nrow = NULL,
     ncol = 1,
     by_row = FALSE,
+    legend_gp = gpar(),
     legend_height = NULL,
     legend_width = NULL,
     legend_direction = c("vertical", "horizontal"),
@@ -55,6 +56,7 @@ Draw Legend Based on Color Mapping
   \item{nrow}{Pass to \code{\link{Legend}}. It controls the layout of legend grids if they are arranged in multiple rows or columns.}
   \item{ncol}{Pass to \code{\link{Legend}}. It controls the layout of legend grids if they are arranged in multiple rows or columns.}
   \item{by_row}{Pass to \code{\link{Legend}}. It controls the order of legend grids if they are arranged in multiple rows or columns.}
+  \item{legend_gp}{Graphic parameters for legend.}
   \item{legend_height}{Height of the legend body. It only works when \code{color_bar} is \code{continuous} and \code{direction} is \code{vertical}. Pass to \code{\link{Legend}}.}
   \item{legend_width}{Width of the legend body. It only works when \code{color_bar} is \code{continuous} and \code{direction} is \code{horizontal}. Pass to \code{\link{Legend}}.}
   \item{legend_direction}{When \code{color_bar} is \code{continuous}, whether the legend is vertical or horizontal? Pass to \code{\link{Legend}}.}

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,Heatmap-method}}, \code{\link{Heatmap-class}} class method
 \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
 }
 }
 \examples{

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

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,Heatmap-method}}, \code{\link{Heatmap-class}} class method
 \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
 }
 }
 \examples{

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/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,SingleAnnotation-method}}, \code{\link{SingleAnnotation-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,ColorMapping-method}}, \code{\link{ColorMapping-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
+\item \code{\link{show,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
 }
 }
 \examples{