@@ -2,7 +2,7 @@ Package: ComplexHeatmap

 Type: Package

 Title: Make Complex Heatmaps

 Version: 1.99.8

-Date: 2019-04-28

+Date: 2019-05-03

 Author: Zuguang Gu

 Maintainer: Zuguang Gu <z.gu@dkfz.de>

 Depends: R (>= 3.1.2), methods, grid, graphics, stats, grDevices

@@ -16,6 +16,7 @@

 # -ylab_gp Graphic parameters for y-labels.

 # -tick_label_gp Graphic parameters for y-ticks.

 # -quantile_gp Graphic parameters for the quantiles.

+# -show_quantiles Whether show quantile lines.

 # -column_order Order of columns.

 # -column_names_side Pass to `Heatmap`.

 # -show_column_names Pass to `Heatmap`.

@@ -73,6 +74,7 @@ densityHeatmap = function(data,

 	ylab_gp = gpar(fontsize = 12),

 	tick_label_gp = gpar(fontsize = 10),

 	quantile_gp = gpar(fontsize = 10),

+	show_quantiles = TRUE,

 	column_order = NULL,

 	column_names_side = "bottom",

@@ -167,16 +169,18 @@ densityHeatmap = function(data,

 		left_annotation = rowAnnotation(axis = anno_empty(border = FALSE, 

 				width = grobHeight(textGrob(ylab, gp = ylab_gp))*2 + max_text_width(bb, gp = tick_label_gp) + unit(4, "mm")),

 			show_annotation_name = FALSE), 

-		right_annotation = rowAnnotation(quantile = anno_empty(border = FALSE, 

+		right_annotation = {if(show_quantiles) {rowAnnotation(quantile = anno_empty(border = FALSE, 

 				width = grobWidth(textGrob("100%", gp = quantile_gp)) + unit(6, "mm")),

-			show_annotation_name = FALSE),

+			show_annotation_name = FALSE)} else NULL},

 		...

 	)

 	random_str = paste(sample(c(letters, LETTERS, 0:9), 8), collapse = "")

 	ht@name = paste0(ht@name, "_", random_str)

 	names(ht@left_annotation) = paste0(names(ht@left_annotation), "_", random_str)

-	names(ht@right_annotation) = paste0(names(ht@right_annotation), "_", random_str)

+	if(show_quantiles) {

+		names(ht@right_annotation) = paste0(names(ht@right_annotation), "_", random_str)

+	}

 	post_fun = function(ht) {

 		column_order = column_order(ht)

@@ -189,16 +193,18 @@ densityHeatmap = function(data,

 			grid.text(ylab, x = grobHeight(textGrob(ylab, gp = ylab_gp)), rot = 90)

 		}, slice = 1)

-		for(i_slice in 1:n_slice) {

-			decorate_heatmap_body(paste0("density_", random_str), {

-				n = length(column_order[[i_slice]])

-				pushViewport(viewport(xscale = c(0.5, n + 0.5), yscale = c(min_x, max_x), clip = TRUE))

-				for(i in seq_len(5)) {

-					grid.lines(1:n, quantile_list[i, column_order[[i_slice]] ], default.units = "native", gp = gpar(lty = 2))

-				}

-				grid.lines(1:n, mean_value[ column_order[[i_slice]] ], default.units = "native", gp = gpar(lty = 2, col = "darkred"))

-				upViewport()

-			}, column_slice = i_slice)

+		if(!is.null(ht@right_annotation)) {

+			for(i_slice in 1:n_slice) {

+				decorate_heatmap_body(paste0("density_", random_str), {

+					n = length(column_order[[i_slice]])

+					pushViewport(viewport(xscale = c(0.5, n + 0.5), yscale = c(min_x, max_x), clip = TRUE))

+					for(i in seq_len(5)) {

+						grid.lines(1:n, quantile_list[i, column_order[[i_slice]] ], default.units = "native", gp = gpar(lty = 2))

+					}

+					grid.lines(1:n, mean_value[ column_order[[i_slice]] ], default.units = "native", gp = gpar(lty = 2, col = "darkred"))

+					upViewport()

+				}, column_slice = i_slice)

+			}

 		}

 		decorate_heatmap_body(paste0("density_", random_str), {

@@ -208,41 +214,43 @@ densityHeatmap = function(data,

 			upViewport()

 		}, column_slice = 1)

-		decorate_heatmap_body(paste0("density_", random_str), {

-			n = length(column_order[[n_slice]])

-			

-			lq = !apply(quantile_list, 1, function(x) all(x > max_x) || all(x < min_x))

-			lq = c(lq, !(all(mean_value > max_x) || all(mean_value < min_x)))

-			if(sum(lq) == 0) {

-				return(NULL)

-			}

+		if(!is.null(ht@right_annotation)) {

+			decorate_heatmap_body(paste0("density_", random_str), {

+				n = length(column_order[[n_slice]])

+				

+				lq = !apply(quantile_list, 1, function(x) all(x > max_x) || all(x < min_x))

+				lq = c(lq, !(all(mean_value > max_x) || all(mean_value < min_x)))

+				if(sum(lq) == 0) {

+					return(NULL)

+				}

-			labels = c(rownames(quantile_list), "mean")

-			y = c(quantile_list[, column_order[[n_slice]][n] ], mean_value[ column_order[[n_slice]][n] ])

-			labels = labels[lq]

-			y = y[lq]

-			od = order(y)

-			y = y[od]

-			labels = labels[od]

-			

-			pushViewport(viewport(xscale = c(0.5, n + 0.5), yscale = c(min_x, max_x), clip = FALSE))

-			text_height = convertHeight(grobHeight(textGrob(labels[1])) * (1 + 0.2), "native", valueOnly = TRUE)

-	        h1 = y - text_height*0.5

-	        h2 = y + text_height*0.5

-	        pos = rev(smartAlign(h1, h2, c(min_x, max_x)))

-	        h = (pos[, 1] + pos[, 2])/2

-	        link_width = unit(6, "mm")

-	        n2 = length(labels)

-	        grid.text(labels, unit(1, "npc") + rep(link_width, n2), h, default.units = "native", just = "left", gp = quantile_gp)

-	        link_width = link_width - unit(1, "mm")

-	        ly = y <= max_x & y >= min_x

-	        if(sum(ly)) {

-		        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")

-		        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")

-		        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")

-		    }

-			upViewport()

-		}, column_slice = n_slice)

+				labels = c(rownames(quantile_list), "mean")

+				y = c(quantile_list[, column_order[[n_slice]][n] ], mean_value[ column_order[[n_slice]][n] ])

+				labels = labels[lq]

+				y = y[lq]

+				od = order(y)

+				y = y[od]

+				labels = labels[od]

+				

+				pushViewport(viewport(xscale = c(0.5, n + 0.5), yscale = c(min_x, max_x), clip = FALSE))

+				text_height = convertHeight(grobHeight(textGrob(labels[1])) * (1 + 0.2), "native", valueOnly = TRUE)

+		        h1 = y - text_height*0.5

+		        h2 = y + text_height*0.5

+		        pos = rev(smartAlign(h1, h2, c(min_x, max_x)))

+		        h = (pos[, 1] + pos[, 2])/2

+		        link_width = unit(6, "mm")

+		        n2 = length(labels)

+		        grid.text(labels, unit(1, "npc") + rep(link_width, n2), h, default.units = "native", just = "left", gp = quantile_gp)

+		        link_width = link_width - unit(1, "mm")

+		        ly = y <= max_x & y >= min_x

+		        if(sum(ly)) {

+			        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")

+			        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")

+			        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")

+			    }

+				upViewport()

+			}, column_slice = n_slice)

+		}

 	}

 	ht@heatmap_param$post_fun = post_fun

@@ -22,6 +22,7 @@ densityHeatmap(data,

     ylab_gp = gpar(fontsize = 12),

     tick_label_gp = gpar(fontsize = 10),

     quantile_gp = gpar(fontsize = 10),

+    show_quantiles = TRUE,

     column_order = NULL,

     column_names_side = "bottom",

@@ -52,6 +53,7 @@ densityHeatmap(data,

   \item{ylab_gp}{Graphic parameters for y-labels.}

   \item{tick_label_gp}{Graphic parameters for y-ticks.}

   \item{quantile_gp}{Graphic parameters for the quantiles.}

+  \item{show_quantiles}{Whether show quantile lines.}

   \item{column_order}{Order of columns.}

   \item{column_names_side}{Pass to \code{\link{Heatmap}}.}

   \item{show_column_names}{Pass to \code{\link{Heatmap}}.}