neighbour annotation grids are merged if they have the same value

jokergoo · Aug 3, 2021 · 7e46f0a · 7e46f0a
1 parent a5c8bc3
commit 7e46f0a
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diff --git a/NEWS b/NEWS
@@ -5,6 +5,8 @@ CHANGES in VERSION 2.9.3
 * set `wrap = TRUE` in `grid.grabExpr()` when capturing the legend objects.
 * `make_comb_mat()`: support `GRangesList` object as input.
 * legends: fixed a bug of the grid heights were not correctedly calculated.
+* discrete annotations: neighbour grids are merged into one single grid if they have the 
+  same values.
 
 =========================
 

diff --git a/R/00_S4_generic_methods.R b/R/00_S4_generic_methods.R
@@ -1,32 +1,32 @@
-setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
-setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
-setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
-setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
-setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
-setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
+setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))
+setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
+setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation'))
 setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
-setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
-setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
-setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
-setGeneric('draw', function(object, ...) standardGeneric('draw'))
-setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
 setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
-setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
+setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
 setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
-setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation'))
-setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
-setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
+setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
+setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
 setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
-setGeneric('re_size', function(object, ...) standardGeneric('re_size'))
+setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
+setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
+setGeneric('draw', function(object, ...) standardGeneric('draw'))
+setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
+setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
+setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))
+setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
 setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
+setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
+setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
+setGeneric('re_size', function(object, ...) standardGeneric('re_size'))
 setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
-setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
-setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
+setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
+setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
 setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
-setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
-setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
-setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
-setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
-setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))
+setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
+setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
+setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
+setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
+setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
 setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
-setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))
+setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
diff --git a/R/AnnotationFunction-function.R b/R/AnnotationFunction-function.R
@@ -160,7 +160,7 @@ subset_vector = function(x, i) x[i]
 # anno = anno_simple(cbind(1:10, 10:1), pch = pch)
 # draw(anno, test = "matrix, pch is a matrix with NA values")
 anno_simple = function(x, col, na_col = "grey", 
-	which = c("column", "row"), border = FALSE, gp = gpar(col = NA),
+	which = c("column", "row"), border = FALSE, gp = gpar(),
 	pch = NULL, pt_size = unit(1, "snpc")*0.8, pt_gp = gpar(), 
 	simple_anno_size = ht_opt$simple_anno_size,
 	width = NULL, height = NULL) {
@@ -230,8 +230,16 @@ anno_simple = function(x, col, na_col = "grey",
 			pch = pch[index, , drop = FALSE]
 
 			for(i in seq_len(nc)) {
-			    fill = map_to_colors(color_mapping, value[index, i])
-			    grid.rect(x = (i-0.5)/nc, y, height = 1/n, width = 1/nc, gp = do.call("gpar", c(list(fill = fill), gp)))
+				if(color_mapping@type == "continuous") {
+				    fill = map_to_colors(color_mapping, value[index, i])
+				    if(is.null(gp$col)) gp$col = fill
+				    grid.rect(x = (i-0.5)/nc, y, height = 1/n, width = 1/nc, gp = do.call("gpar", c(list(fill = fill), gp)))
+				} else {
+					r = rle(value[index, i])
+					fill = map_to_colors(color_mapping, r$values)
+					if(is.null(gp$col)) gp$col = fill
+					grid.rect(x = (i-0.5)/nc, y = 1 - cumsum(r$lengths)/n, height = r$length/n, width = 1/nc, just = "bottom", gp = do.call("gpar", c(list(fill = fill), gp)))
+				}
 			    if(!is.null(pch)) {
 					l = !is.na(pch[, i])
 					if(any(l)) {
@@ -249,8 +257,16 @@ anno_simple = function(x, col, na_col = "grey",
 			    }
 			}
 	    } else {
-			fill = map_to_colors(color_mapping, value[index])
-			grid.rect(x = 0.5, y, height = 1/n, width = 1, gp = do.call("gpar", c(list(fill = fill), gp)))
+	    	if(color_mapping@type == "continuous") {
+				fill = map_to_colors(color_mapping, value[index])
+				if(is.null(gp$col)) gp$col = fill
+				grid.rect(x = 0.5, y, height = 1/n, width = 1, gp = do.call("gpar", c(list(fill = fill), gp)))
+			} else {
+				r = rle(value[index])
+				fill = map_to_colors(color_mapping, r$values)
+				if(is.null(gp$col)) gp$col = fill
+				grid.rect(x = 0.5, y = 1 - cumsum(r$lengths)/n, height = r$length/n, width = 1, just = "bottom", gp = do.call("gpar", c(list(fill = fill), gp)))
+			}
 			if(!is.null(pch)) {
 			    pch = pch[index]
 			    pt_size = pt_size[index]
@@ -282,8 +298,16 @@ anno_simple = function(x, col, na_col = "grey",
 		    pch = pch[index, , drop = FALSE]
 
 	        for(i in seq_len(nc)) {
-                fill = map_to_colors(color_mapping, value[index, i])
-                grid.rect(x, y = (nc-i +0.5)/nc, width = 1/n, height = 1/nc, gp = do.call("gpar", c(list(fill = fill), gp)))
+	        	if(color_mapping@type == "continuous") {
+	                fill = map_to_colors(color_mapping, value[index, i])
+	                if(is.null(gp$col)) gp$col = fill
+	                grid.rect(x, y = (nc-i +0.5)/nc, width = 1/n, height = 1/nc, gp = do.call("gpar", c(list(fill = fill), gp)))
+	            } else {
+	            	r = rle(value[index, i])
+					fill = map_to_colors(color_mapping, r$values)
+					if(is.null(gp$col)) gp$col = fill
+					grid.rect(cumsum(r$lengths)/n, y = (nc-i +0.5)/nc, width = r$length/n, height = 1/nc, just = "right", gp = do.call("gpar", c(list(fill = fill), gp)))
+	            }
 				if(!is.null(pch)){
 				    l = !is.na(pch[, i])
 				    if(any(l)) {
@@ -301,8 +325,16 @@ anno_simple = function(x, col, na_col = "grey",
 				}
 		    }
         } else {
-			fill = map_to_colors(color_mapping, value[index])
-			grid.rect(x, y = 0.5, width = 1/n, height = 1, gp = do.call("gpar", c(list(fill = fill), gp)))
+        	if(color_mapping@type == "continuous") {
+				fill = map_to_colors(color_mapping, value[index])
+				if(is.null(gp$col)) gp$col = fill
+				grid.rect(x, y = 0.5, width = 1/n, height = 1, gp = do.call("gpar", c(list(fill = fill), gp)))
+			} else {
+				r = rle(value[index])
+				fill = map_to_colors(color_mapping, r$values)
+				if(is.null(gp$col)) gp$col = fill
+				grid.rect(cumsum(r$lengths)/n, y = 0.5, width = r$length/n, height = 1, just = "right", gp = do.call("gpar", c(list(fill = fill), gp)))
+			}
 			if(!is.null(pch)) {
 				pch = pch[index]
 				pt_size = pt_size[index]
@@ -361,6 +393,7 @@ anno_simple = function(x, col, na_col = "grey",
 	return(anno)      
 }
 
+
 # == title
 # Image Annotation
 #

diff --git a/man/add_heatmap-dispatch.Rd b/man/add_heatmap-dispatch.Rd
@@ -10,9 +10,9 @@ 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,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,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
 }
 }
 \examples{

diff --git a/man/anno_simple.Rd b/man/anno_simple.Rd
@@ -8,7 +8,7 @@ Simple Annotation
 }
 \usage{
 anno_simple(x, col, na_col = "grey",
-    which = c("column", "row"), border = FALSE, gp = gpar(col = NA),
+    which = c("column", "row"), border = FALSE, gp = gpar(),
     pch = NULL, pt_size = unit(1, "snpc")*0.8, pt_gp = gpar(),
     simple_anno_size = ht_opt$simple_anno_size,
     width = NULL, height = NULL)

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