Zuguang Gu authored on 08/05/2019 19:52:39
Showing3 changed files

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@@ -2,7 +2,7 @@ Package: ComplexHeatmap
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 Type: Package
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 Title: Make Complex Heatmaps
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 Version: 2.1.0
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-Date: 2019-04-28
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+Date: 2019-05-03
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 Author: Zuguang Gu
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 Maintainer: Zuguang Gu <z.gu@dkfz.de>
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 Depends: R (>= 3.1.2), methods, grid, graphics, stats, grDevices
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@@ -16,6 +16,7 @@
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 # -ylab_gp Graphic parameters for y-labels.
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 # -tick_label_gp Graphic parameters for y-ticks.
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 # -quantile_gp Graphic parameters for the quantiles.
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+# -show_quantiles Whether show quantile lines.
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 # -column_order Order of columns.
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 # -column_names_side Pass to `Heatmap`.
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 # -show_column_names Pass to `Heatmap`.
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@@ -73,6 +74,7 @@ densityHeatmap = function(data,
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 	ylab_gp = gpar(fontsize = 12),
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 	tick_label_gp = gpar(fontsize = 10),
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 	quantile_gp = gpar(fontsize = 10),
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+	show_quantiles = TRUE,
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 	column_order = NULL,
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 	column_names_side = "bottom",
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@@ -167,16 +169,18 @@ densityHeatmap = function(data,
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 		left_annotation = rowAnnotation(axis = anno_empty(border = FALSE, 
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 				width = grobHeight(textGrob(ylab, gp = ylab_gp))*2 + max_text_width(bb, gp = tick_label_gp) + unit(4, "mm")),
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 			show_annotation_name = FALSE), 
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-		right_annotation = rowAnnotation(quantile = anno_empty(border = FALSE, 
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+		right_annotation = {if(show_quantiles) {rowAnnotation(quantile = anno_empty(border = FALSE, 
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 				width = grobWidth(textGrob("100%", gp = quantile_gp)) + unit(6, "mm")),
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-			show_annotation_name = FALSE),
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+			show_annotation_name = FALSE)} else NULL},
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 		...
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 	)
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 	random_str = paste(sample(c(letters, LETTERS, 0:9), 8), collapse = "")
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 	ht@name = paste0(ht@name, "_", random_str)
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 	names(ht@left_annotation) = paste0(names(ht@left_annotation), "_", random_str)
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-	names(ht@right_annotation) = paste0(names(ht@right_annotation), "_", random_str)
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+	if(show_quantiles) {
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+		names(ht@right_annotation) = paste0(names(ht@right_annotation), "_", random_str)
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+	}
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 	post_fun = function(ht) {
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 		column_order = column_order(ht)
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@@ -189,16 +193,18 @@ densityHeatmap = function(data,
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 			grid.text(ylab, x = grobHeight(textGrob(ylab, gp = ylab_gp)), rot = 90)
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 		}, slice = 1)
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-		for(i_slice in 1:n_slice) {
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-			decorate_heatmap_body(paste0("density_", random_str), {
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-				n = length(column_order[[i_slice]])
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-				pushViewport(viewport(xscale = c(0.5, n + 0.5), yscale = c(min_x, max_x), clip = TRUE))
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-				for(i in seq_len(5)) {
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-					grid.lines(1:n, quantile_list[i, column_order[[i_slice]] ], default.units = "native", gp = gpar(lty = 2))
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-				}
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-				grid.lines(1:n, mean_value[ column_order[[i_slice]] ], default.units = "native", gp = gpar(lty = 2, col = "darkred"))
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-				upViewport()
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-			}, column_slice = i_slice)
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+		if(!is.null(ht@right_annotation)) {
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+			for(i_slice in 1:n_slice) {
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+				decorate_heatmap_body(paste0("density_", random_str), {
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+					n = length(column_order[[i_slice]])
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+					pushViewport(viewport(xscale = c(0.5, n + 0.5), yscale = c(min_x, max_x), clip = TRUE))
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+					for(i in seq_len(5)) {
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+						grid.lines(1:n, quantile_list[i, column_order[[i_slice]] ], default.units = "native", gp = gpar(lty = 2))
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+					}
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+					grid.lines(1:n, mean_value[ column_order[[i_slice]] ], default.units = "native", gp = gpar(lty = 2, col = "darkred"))
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+					upViewport()
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+				}, column_slice = i_slice)
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+			}
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 		}
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 		decorate_heatmap_body(paste0("density_", random_str), {
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@@ -208,41 +214,43 @@ densityHeatmap = function(data,
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 			upViewport()
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 		}, column_slice = 1)
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-		decorate_heatmap_body(paste0("density_", random_str), {
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-			n = length(column_order[[n_slice]])
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-			
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-			lq = !apply(quantile_list, 1, function(x) all(x > max_x) || all(x < min_x))
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-			lq = c(lq, !(all(mean_value > max_x) || all(mean_value < min_x)))
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-			if(sum(lq) == 0) {
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-				return(NULL)
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-			}
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+		if(!is.null(ht@right_annotation)) {
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+			decorate_heatmap_body(paste0("density_", random_str), {
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+				n = length(column_order[[n_slice]])
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+				
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+				lq = !apply(quantile_list, 1, function(x) all(x > max_x) || all(x < min_x))
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+				lq = c(lq, !(all(mean_value > max_x) || all(mean_value < min_x)))
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+				if(sum(lq) == 0) {
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+					return(NULL)
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+				}
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-			labels = c(rownames(quantile_list), "mean")
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-			y = c(quantile_list[, column_order[[n_slice]][n] ], mean_value[ column_order[[n_slice]][n] ])
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-			labels = labels[lq]
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-			y = y[lq]
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-			od = order(y)
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-			y = y[od]
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-			labels = labels[od]
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-			
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-			pushViewport(viewport(xscale = c(0.5, n + 0.5), yscale = c(min_x, max_x), clip = FALSE))
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-			text_height = convertHeight(grobHeight(textGrob(labels[1])) * (1 + 0.2), "native", valueOnly = TRUE)
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-	        h1 = y - text_height*0.5
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-	        h2 = y + text_height*0.5
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-	        pos = rev(smartAlign(h1, h2, c(min_x, max_x)))
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-	        h = (pos[, 1] + pos[, 2])/2
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-	        link_width = unit(6, "mm")
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-	        n2 = length(labels)
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-	        grid.text(labels, unit(1, "npc") + rep(link_width, n2), h, default.units = "native", just = "left", gp = quantile_gp)
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-	        link_width = link_width - unit(1, "mm")
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-	        ly = y <= max_x & y >= min_x
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-	        if(sum(ly)) {
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-		        grid.segments(unit(rep(1, n2), "npc")[ly], y[ly], unit(1, "npc") + rep(link_width * (1/3), n2)[ly], y[ly], default.units = "native")
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-		        grid.segments(unit(1, "npc") + rep(link_width * (1/3), n2)[ly], y[ly], unit(1, "npc") + rep(link_width * (2/3), n2)[ly], h[ly], default.units = "native")
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-		        grid.segments(unit(1, "npc") + rep(link_width * (2/3), n2)[ly], h[ly], unit(1, "npc") + rep(link_width, n2)[ly], h[ly], default.units = "native")
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-		    }
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-			upViewport()
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-		}, column_slice = n_slice)
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+				labels = c(rownames(quantile_list), "mean")
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+				y = c(quantile_list[, column_order[[n_slice]][n] ], mean_value[ column_order[[n_slice]][n] ])
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+				labels = labels[lq]
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+				y = y[lq]
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+				od = order(y)
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+				y = y[od]
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+				labels = labels[od]
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+				
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+				pushViewport(viewport(xscale = c(0.5, n + 0.5), yscale = c(min_x, max_x), clip = FALSE))
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+				text_height = convertHeight(grobHeight(textGrob(labels[1])) * (1 + 0.2), "native", valueOnly = TRUE)
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+		        h1 = y - text_height*0.5
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+		        h2 = y + text_height*0.5
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+		        pos = rev(smartAlign(h1, h2, c(min_x, max_x)))
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+		        h = (pos[, 1] + pos[, 2])/2
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+		        link_width = unit(6, "mm")
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+		        n2 = length(labels)
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+		        grid.text(labels, unit(1, "npc") + rep(link_width, n2), h, default.units = "native", just = "left", gp = quantile_gp)
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+		        link_width = link_width - unit(1, "mm")
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+		        ly = y <= max_x & y >= min_x
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+		        if(sum(ly)) {
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+			        grid.segments(unit(rep(1, n2), "npc")[ly], y[ly], unit(1, "npc") + rep(link_width * (1/3), n2)[ly], y[ly], default.units = "native")
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+			        grid.segments(unit(1, "npc") + rep(link_width * (1/3), n2)[ly], y[ly], unit(1, "npc") + rep(link_width * (2/3), n2)[ly], h[ly], default.units = "native")
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+			        grid.segments(unit(1, "npc") + rep(link_width * (2/3), n2)[ly], h[ly], unit(1, "npc") + rep(link_width, n2)[ly], h[ly], default.units = "native")
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+			    }
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+				upViewport()
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+			}, column_slice = n_slice)
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+		}
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 	}
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 	ht@heatmap_param$post_fun = post_fun
... ...
@@ -22,6 +22,7 @@ densityHeatmap(data,
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     ylab_gp = gpar(fontsize = 12),
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     tick_label_gp = gpar(fontsize = 10),
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     quantile_gp = gpar(fontsize = 10),
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+    show_quantiles = TRUE,
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     column_order = NULL,
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     column_names_side = "bottom",
... ...
@@ -52,6 +53,7 @@ densityHeatmap(data,
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   \item{ylab_gp}{Graphic parameters for y-labels.}
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   \item{tick_label_gp}{Graphic parameters for y-ticks.}
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   \item{quantile_gp}{Graphic parameters for the quantiles.}
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+  \item{show_quantiles}{Whether show quantile lines.}
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   \item{column_order}{Order of columns.}
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   \item{column_names_side}{Pass to \code{\link{Heatmap}}.}
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   \item{show_column_names}{Pass to \code{\link{Heatmap}}.}