@@ -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.

 =========================

@@ -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'))

@@ -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

 #

@@ -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{

@@ -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)

@@ -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{

@@ -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{

@@ -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{

@@ -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{

@@ -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{

@@ -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{

@@ -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{