rename rect3D to bar3D

jokergoo · Mar 24, 2021 · 7caac70 · 7caac70
1 parent 49e4fa6
commit 7caac70
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: ComplexHeatmap
 Type: Package
 Title: Make Complex Heatmaps
-Version: 2.7.9.1004
+Version: 2.7.9.1005
 Date: 2021-3-24
 Author: Zuguang Gu
 Maintainer: Zuguang Gu <[email protected]>

diff --git a/NAMESPACE b/NAMESPACE
@@ -149,6 +149,7 @@ export("anno_summary")
 export("anno_text")
 export("anno_zoom")
 export("annotation_axis_grob")
+export("bar3D")
 export("bin_genome")
 export("cluster_between_groups")
 export("cluster_within_group")
@@ -203,7 +204,6 @@ export("order.comb_mat")
 export("packLegend")
 export("pheatmap")
 export("pindex")
-export("rect3D")
 export("restore_matrix")
 export("rowAnnotation")
 export("row_anno_barplot")

diff --git a/R/00_S4_generic_methods.R b/R/00_S4_generic_methods.R
@@ -1,32 +1,32 @@
-setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
+setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
+setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
+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('make_layout', function(object, ...) standardGeneric('make_layout'))
-setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
-setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
-setGeneric('re_size', function(object, ...) standardGeneric('re_size'))
+setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
 setGeneric('draw', function(object, ...) standardGeneric('draw'))
-setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
-setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
-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_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('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
 setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
+setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
 setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
-setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
-setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
+setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
 setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))
-setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
-setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
-setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
-setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
-setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))
-setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
-setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
-setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
+setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
 setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
-setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
+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('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('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
-setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
+setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
 setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
-setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
+setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
+setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
+setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
diff --git a/R/3d.R b/R/3d.R
@@ -15,9 +15,9 @@
 #
 # == example
 # grid.newpage()
-# rect3D(c(0.3, 0.7), 0.5, 0.2, 0.2, 0.2, fill = 2:3)
+# bar3D(c(0.3, 0.7), 0.5, 0.2, 0.2, 0.2, fill = 2:3)
 #
-rect3D = function(x, y, w, h, l, theta = 60, default.units = "npc", fill = "white", col = "black") {
+bar3D = function(x, y, w, h, l, theta = 60, default.units = "npc", fill = "white", col = "black") {
 
 	if(!is.unit(x)) x = unit(x, default.units)
 	if(!is.unit(y)) y = unit(y, default.units)
@@ -165,7 +165,7 @@ Heatmap3D = function(matrix,
 			v = pindex(matrix, i, j)
 			od = rank(order(-as.numeric(y), -as.numeric(x)))
 			grid.rect(x[od], y[od], w[od], h[od], gp = gpar(col = "white", fill = "#EEEEEE"))
-			rect3D(x[od], y[od], w[od]*bar_rel_width, h[od]*bar_rel_height, v[od]/max(matrix)*bar_max_length, theta = bar_angle, fill = f[od])	
+			bar3D(x[od], y[od], w[od]*bar_rel_width, h[od]*bar_rel_height, v[od]/max(matrix)*bar_max_length, theta = bar_angle, fill = f[od])	
 		},
 		show_row_dend = show_row_dend,
 		show_column_dend = show_column_dend,

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,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,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
 \item \code{\link{add_heatmap,Heatmap-method}}, \code{\link{Heatmap-class}} class method
 }
 }

diff --git a/man/rect3D.Rd → man/bar3D.Rd b/man/rect3D.Rd → man/bar3D.Rd
@@ -1,13 +1,13 @@
-\name{rect3D}
-\alias{rect3D}
+\name{bar3D}
+\alias{bar3D}
 \title{
 Draw 3D bars
 }
 \description{
 Draw 3D bars
 }
 \usage{
-rect3D(x, y, w, h, l, theta = 60, default.units = "npc", fill = "white", col = "black")
+bar3D(x, y, w, h, l, theta = 60, default.units = "npc", fill = "white", col = "black")
 }
 \arguments{
 
@@ -24,5 +24,5 @@ rect3D(x, y, w, h, l, theta = 60, default.units = "npc", fill = "white", col = "
 }
 \examples{
 grid.newpage()
-rect3D(c(0.3, 0.7), 0.5, 0.2, 0.2, 0.2, fill = 2:3)
+bar3D(c(0.3, 0.7), 0.5, 0.2, 0.2, 0.2, fill = 2:3)
 }
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/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/component_width-dispatch.Rd b/man/component_width-dispatch.Rd
@@ -10,8 +10,8 @@ Method dispatch page for \code{component_width}.
 \code{component_width} can be dispatched on following classes:
 
 \itemize{
-\item \code{\link{component_width,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
 \item \code{\link{component_width,Heatmap-method}}, \code{\link{Heatmap-class}} class method
+\item \code{\link{component_width,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-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,Heatmap-method}}, \code{\link{Heatmap-class}} class method
+\item \code{\link{draw,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-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,AnnotationFunction-method}}, \code{\link{AnnotationFunction-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
 }
 }
 \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/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,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
 \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
 }
 }
 \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,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,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
+\item \code{\link{show,Heatmap-method}}, \code{\link{Heatmap-class}} class method
 }
 }
 \examples{