@@ -7,6 +7,7 @@ CHANGES in VERSION 1.2.6

 * insert `k = NULL` into anno_function if they are row annotations

 * add a new vignette "quick examples"

 * change style for continuous legend color bar

+* label order of discrete legend has been adjusted (now it is from top to bottom)

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

@@ -276,10 +276,17 @@ setMethod(f = "color_mapping_legend",

 		x = unit(rep(0, nlevel), "npc")

 		y = (0:(nlevel-1))*(legend_grid_height)

 		y = unit(1, "npc") - y

-		gf = packGrob(gf, row = 2, col = 1, grob = rectGrob(x, rev(y), width = legend_grid_width, height = rev(legend_grid_height), just = c("left", "top"),

-				gp = gpar(col = legend_grid_border, fill = object@colors)))

-		gf = packGrob(gf, row = 2, col = 2, grob = textGrob(object@levels, x + grid_padding, rev(y) - legend_grid_height*0.5, 

-	 		just = c("left", "center"), gp = legend_label_gp), width = grid_padding + legend_label_max_width, force.width = TRUE)

+		if(object@type == "discrete") {

+			gf = packGrob(gf, row = 2, col = 2, grob = textGrob(object@levels, x + grid_padding, y - legend_grid_height*0.5, 

+		 		just = c("left", "center"), gp = legend_label_gp), width = grid_padding + legend_label_max_width, force.width = TRUE)

+			gf = packGrob(gf, row = 2, col = 1, grob = rectGrob(x, y, width = legend_grid_width, height = legend_grid_height, just = c("left", "top"),

+					gp = gpar(col = legend_grid_border, fill = object@colors)))

+		} else {

+			gf = packGrob(gf, row = 2, col = 2, grob = textGrob(object@levels, x + grid_padding, rev(y) - legend_grid_height*0.5, 

+		 		just = c("left", "center"), gp = legend_label_gp), width = grid_padding + legend_label_max_width, force.width = TRUE)

+			gf = packGrob(gf, row = 2, col = 1, grob = rectGrob(x, rev(y), width = legend_grid_width, height = rev(legend_grid_height), just = c("left", "top"),

+					gp = gpar(col = legend_grid_border, fill = object@colors)))

+		}

 	} else {

 		label_height = grobHeight(textGrob("foo", gp = legend_label_gp))

 		gf = frameGrob(layout = grid.layout(nrow = 2, ncol = 2, widths = unit.c(legend_grid_width, grid_padding + legend_label_max_width),

@@ -291,6 +298,8 @@ setMethod(f = "color_mapping_legend",

 		x = unit(rep(0, nlevel), "npc")

 		y = seq(0, 1, length = nlevel) * (unit(1, "npc") - label_height) + label_height*0.5

 		y = unit(1, "npc") - y

+		gf = packGrob(gf, row = 2, col = 2, grob = textGrob(object@levels, x + grid_padding, rev(y), 

+	 		just = c("left", "center"), gp = legend_label_gp), width = grid_padding + legend_label_max_width, force.width = TRUE, height = (2*nlevel-1)*label_height, force.height = TRUE)

 		colors = unlist(lapply(seq_len(nlevel-1), function(i) object@col_fun(seq(as.numeric(object@levels[i]), as.numeric(object@levels[i+1]), length = 16))))

 		x2 = unit(rep(0, length(colors)), "npc")

@@ -298,8 +307,7 @@ setMethod(f = "color_mapping_legend",

 		y2 = y2[-length(y2)] * unit(1, "npc")

 		gf = packGrob(gf, row = 2, col = 1, grob = rectGrob(x2, rev(y2), width = legend_grid_width, height = (unit(1, "npc"))*(1/length(colors)), just = c("left", "top"),

 				gp = gpar(col = rev(colors), fill = rev(colors))), height = (2*nlevel-1)*label_height, force.height = TRUE)

-		gf = packGrob(gf, row = 2, col = 2, grob = textGrob(object@levels, x + grid_padding, rev(y) - label_height*0.5, 

-	 		just = c("left", "center"), gp = legend_label_gp), width = grid_padding + legend_label_max_width, force.width = TRUE, height = (2*nlevel-1)*label_height, force.height = TRUE)

+		

 	}

@@ -225,9 +225,9 @@ Heatmap = function(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),

     show_column_names = TRUE, column_names_max_height = unit(4, "cm"), 

     column_names_gp = gpar(fontsize = 12),

     top_annotation = new("HeatmapAnnotation"),

-    top_annotation_height = unit(5*length(top_annotation@anno_list), "mm"),

+    top_annotation_height = unit(5*length(top_annotation@anno_list), "mm") + sum(top_annotation@gap),

     bottom_annotation = new("HeatmapAnnotation"),

-    bottom_annotation_height = unit(5*length(bottom_annotation@anno_list), "mm"),

+    bottom_annotation_height = unit(5*length(bottom_annotation@anno_list), "mm") + sum(bottom_annotation@gap),

     km = 1, split = NULL, gap = unit(1, "mm"), 

     combined_name_fun = function(x) paste(x, collapse = "/"),

     width = NULL, show_heatmap_legend = TRUE,

@@ -28,7 +28,8 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",

 	prototype = list(

 		anno_list = list(),

 		size = unit(0, "null"),

-		which = "row"

+		which = "row",

+		gap = unit(0, "null")

 	),

     contains = "AdditiveUnit"

 )

@@ -126,7 +127,7 @@ HeatmapAnnotation = function(df, name, col, color_bar = rep("discrete", ncol(df)

 		if(is.null(fun_name)) {

 			stop("functions should be specified as named arguments.")

 		}

-		if(any(fun_name %in% c("df", "col", "show_legend", "which", "height", "width", "annotation_height", "annotation_width", "gp"))) {

+		if(any(fun_name %in% c("df", "col", "show_legend", "which", "height", "width", "annotation_height", "annotation_width", "gp", "color_bar"))) {

 			stop("function names should be same as other argument names.")

 		}

@@ -137,6 +138,18 @@ HeatmapAnnotation = function(df, name, col, color_bar = rep("discrete", ncol(df)

 	n_anno = length(anno_list)

+	if(is.null(gap)) gap = unit(0, "null")

+

+    if(length(gap) == 1) {

+    	.Object@gap = rep(gap, n_anno)

+    } else if(length(gap) == n_anno - 1) {

+    	.Object@gap = unit.c(gap, unit(0, "null"))

+    } else if(length(gap) < n_anno - 1) {

+    	stop("Length of `gap` is wrong.")

+    } else {

+    	.Object@gap = gap

+    }

+

 	anno_size = switch(which,

 		column = annotation_height,

 		row = annotation_width)

@@ -148,7 +161,7 @@ HeatmapAnnotation = function(df, name, col, color_bar = rep("discrete", ncol(df)

 	}

 	if(!is.unit(anno_size)) {

-		anno_size = unit(anno_size/sum(anno_size), "npc")

+		anno_size = anno_size/sum(anno_size)*(unit(1, "npc") - sum(.Object@gap))

 	}

@@ -162,17 +175,7 @@ HeatmapAnnotation = function(df, name, col, color_bar = rep("discrete", ncol(df)

     .Object@size = size

-    if(is.null(gap)) gap = unit(0, "null")

-

-    if(length(gap) == 1) {

-    	.Object@gap = rep(gap, n_anno)

-    } else if(length(gap) == n_anno - 1) {

-    	.Object@gap = unit.c(gap, unit(0, "null"))

-    } else if(length(gap) < n_anno - 1) {

-    	stop("Length of `gap` is wrong.")

-    } else {

-    	.Object@gap = gap

-    }

+    

     return(.Object)

 }

@@ -30,9 +30,9 @@ Heatmap(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),

     show_column_names = TRUE, column_names_max_height = unit(4, "cm"),

     column_names_gp = gpar(fontsize = 12),

     top_annotation = new("HeatmapAnnotation"),

-    top_annotation_height = unit(5*length(top_annotation@anno_list), "mm"),

+    top_annotation_height = unit(5*length(top_annotation@anno_list), "mm") + sum(top_annotation@gap),

     bottom_annotation = new("HeatmapAnnotation"),

-    bottom_annotation_height = unit(5*length(bottom_annotation@anno_list), "mm"),

+    bottom_annotation_height = unit(5*length(bottom_annotation@anno_list), "mm") + sum(bottom_annotation@gap),

     km = 1, split = NULL, gap = unit(1, "mm"),

     combined_name_fun = function(x) paste(x, collapse = "/"),

     width = NULL, show_heatmap_legend = TRUE,

@@ -212,7 +212,8 @@ Heatmap(mat, name = "foo", column_hclust_height = unit(2, "cm"))

 There are three ways to specify distance metric for clustering:

 - specify distance as a pre-defined option. The valid values are the supported methods

-  in `dist()` function and within `pearson`, `spearman` and `kendall`.

+  in `dist()` function and within `pearson`, `spearman` and `kendall`. `NA` values are ignored

+  for pre-defined clustering but with giving a warning.

 - a self-defined function which calculates distance from a matrix. The function should

   only contain one argument. Please note for clustering on columns, the matrix will be transposed

   automatically.

@@ -517,7 +518,9 @@ draw(ha, 1:10)

 You can combine more than one annotations into the object.

 ```{r heatmap_annotation_mixed_with_complex, fig.width = 7, fig.height = 2}

-ha = HeatmapAnnotation(df = df, points = anno_points(value))

+ha = HeatmapAnnotation(df = df, points = anno_points(value),

+    col = list(type = c("a" = "red", "b" = "blue"),

+               age = colorRamp2(c(0, 20), c("white", "red"))))

 ha

 draw(ha, 1:10)

 ```

@@ -529,12 +532,16 @@ annotations shown in the heatmap.

 ```{r, fig.width = 7, fig.height = 3}

 ha = HeatmapAnnotation(df = df, points = anno_points(value), boxplot = anno_boxplot(mat),

+    col = list(type = c("a" = "red", "b" = "blue"),

+               age = colorRamp2(c(0, 20), c("white", "red"))),

     annotation_height = c(1, 2, 3, 4))

 draw(ha, 1:10)

 ```

 ```{r, fig.width = 7, fig.height = 3}

 ha = HeatmapAnnotation(df = df, points = anno_points(value), boxplot = anno_boxplot(mat),

+    col = list(type = c("a" = "red", "b" = "blue"),

+               age = colorRamp2(c(0, 20), c("white", "red"))),

     annotation_height = unit.c((unit(1, "npc") - unit(4, "cm"))*0.5, (unit(1, "npc") - unit(4, "cm"))*0.5, 

         unit(2, "cm"), unit(2, "cm")))

 draw(ha, 1:10)

@@ -547,16 +554,29 @@ and `anno_boxplot()` support axes. Please note we didn't allocate space for axes

 we only assume there are empty spaces for showing axes.

 ```{r add_annotation}

-ha = HeatmapAnnotation(df = df, points = anno_points(value))

+ha = HeatmapAnnotation(df = df, points = anno_points(value),

+    col = list(type = c("a" = "red", "b" = "blue"),

+               age = colorRamp2(c(0, 20), c("white", "red"))))

 ha_boxplot = HeatmapAnnotation(boxplot = anno_boxplot(mat, axis = TRUE))

 Heatmap(mat, name = "foo", top_annotation = ha, bottom_annotation = ha_boxplot, 

     bottom_annotation_height = unit(3, "cm"))

 ```

+Gaps below each annotation can be specified by `gap` in `HeatmapAnnotation()`. 

+

+```{r}

+ha = HeatmapAnnotation(df = df, points = anno_points(value), gap = unit(c(2, 4), "mm"),

+    col = list(type = c("a" = "red", "b" = "blue"),

+               age = colorRamp2(c(0, 20), c("white", "red"))))

+Heatmap(mat, name = "foo", top_annotation = ha)

+```

+

 You can suppress some of the annotation legend by specifying `show_legend` to `FALSE` when creating the `HeatmapAnnotation` object.

 ```{r annotation_show}

-ha = HeatmapAnnotation(df = df, show_legend = FALSE)

+ha = HeatmapAnnotation(df = df, show_legend = FALSE,

+    col = list(type = c("a" = "red", "b" = "blue"),

+               age = colorRamp2(c(0, 20), c("white", "red"))))

 Heatmap(mat, name = "foo", top_annotation = ha)

 ```

@@ -712,7 +732,9 @@ If you don't like the default discrete color bar for legends, you can specify `h

 For the simple annotation which contains continuous values, `color_bar` can also be set to `continuous`.

 ```{r}

-ha = HeatmapAnnotation(df = data.frame(value = runif(10)), color_bar = "continuous")

+ha = HeatmapAnnotation(df = data.frame(value = runif(10)), 

+    col = list(value = colorRamp2(c(0, 1), c("white", "blue"))), 

+    color_bar = "continuous")

 Heatmap(mat, name = "ht1", top_annotation = ha, heatmap_legend_color_bar = "continuous")

 ```

@@ -784,14 +806,15 @@ Row annotation is also defined by the `HeatmapAnnotation` class, but with specif

 ```{r row_annotation, fig.width = 1, fig.height = 7}

 df = data.frame(type = c(rep("a", 6), rep("b", 6)))

-ha = HeatmapAnnotation(df = df, which = "row", width = unit(1, "cm"))

+ha = HeatmapAnnotation(df = df, col = list(type = c("a" = "red", "b" = "blue")),

+    which = "row", width = unit(1, "cm"))

 draw(ha, 1:12)

 ```

 There is a shortcut function `rowAnnotation()` which is same as `HeatmapAnnotation(..., which = "row")`.

 ```{r, eval = FALSE}

-ha = rowAnnotation(df = df, width = unit(1, "cm"))

+ha = rowAnnotation(df = df, col = list(type = c("a" = "red", "b" = "blue")), width = unit(1, "cm"))

 ```

 Similar, there can be more than one row annotation. Note in `anno_boxplot()`, `which` is set to `row`

@@ -799,6 +822,7 @@ to tell that boxplot is calcualted by rows.

 ```{r, fig.width = 3, fig.height = 7}

 ha_combined = rowAnnotation(df = df, boxplot = anno_boxplot(mat, which = "row"), 

+    col = list(type = c("a" = "red", "b" = "blue")),

     annotation_width = c(1, 3))

 draw(ha_combined, 1:12)

 ```

@@ -879,7 +903,7 @@ split row annotaitons:

 ```{r all_row_annotations, fig.width = 7}

 nr = nrow(mat)

-ha = rowAnnotation(df = df, width = NULL)

+ha = rowAnnotation(df = df, col = list(type = c("a" = "red", "b" = "blue")), width = NULL)

 text = paste0("row", seq_len(nr))

 ha_text = rowAnnotation(text = anno_text(text, which = "row"), width = max(grobWidth(textGrob(text))))

 Heatmap(matrix(nrow = nr, ncol = 0), split = sample(c("A", "B"), nr, replace = TRUE)) + 

@@ -918,7 +942,8 @@ ha_column1 = HeatmapAnnotation(points = anno_points(rnorm(10)))

 ht1 = Heatmap(mat, name = "ht1", km = 2, row_title = "Heatmap 1", column_title = "Heatmap 1", 

     top_annotation = ha_column1)

-ha_column2 = HeatmapAnnotation(df = data.frame(type = c(rep("a", 5), rep("b", 5))))

+ha_column2 = HeatmapAnnotation(df = data.frame(type = c(rep("a", 5), rep("b", 5))),

+    col = list(type = c("a" = "red", "b" = "blue")))

 ht2 = Heatmap(mat, name = "ht2", row_title = "Heatmap 2", column_title = "Heatmap 2",

     bottom_annotation = ha_column2)

@@ -1023,7 +1048,8 @@ it will be exceeding the figure region.

 ```{r}

 df = data.frame(type1 = c(rep("a", 5), rep("b", 5)),

                 type2 = c(rep("A", 3), rep("B", 7)))

-ha = HeatmapAnnotation(df)

+ha = HeatmapAnnotation(df, col = list(type1 = c("a" = "red", "b" = "blue"),

+                                      type2 = c("A" = "green", "B" = "orange")))

 Heatmap(mat, name = "ht", top_annotation = ha)

 for(an in colnames(df)) {

     seekViewport(qq("annotation_@{an}"))

@@ -1129,6 +1155,7 @@ Here the package has a `densityHeatmap()` function, the usage is quite straightf

 ```{r, density}

 matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10]

 ha = HeatmapAnnotation(df = data.frame(anno = rep(c("A", "B"), each = 5)),

+    col = list(anno = c("A" = "green", "B" = "orange")),

     points = anno_points(runif(10)))

 densityHeatmap(matrix, anno = ha)

 ```

@@ -1,5 +1,6 @@

 library(ComplexHeatmap)

 library(circlize)

+library(RColorBrewer)

 rand_meth = function(k, mean) {

 	(runif(k) - 0.5)*min(c(1-mean), mean) + mean

@@ -97,8 +98,8 @@ ht_list = Heatmap(mat_meth, name = "methylation", col = colorRamp2(c(0, 0.5, 1),

 	Heatmap(mat_expr[, column_tree$order], name = "expression", col = colorRamp2(c(-2, 0, 2), c("green", "white", "red")),

 		cluster_columns = FALSE, top_annotation = ha2, column_names_gp = gpar(fontsize = 8), column_title = "Expression", column_title_gp = gpar(fontsize = 10)) +

 	Heatmap(cor_pvalue, name = "-log10(cor_p)", col = colorRamp2(c(0, 2, 4), c("white", "white", "red")), column_names_gp = gpar(fontsize = 8)) +

-	Heatmap(gene_type, name = "gene type", column_names_gp = gpar(fontsize = 8)) +

-	Heatmap(anno_gene, name = "anno_gene", column_names_gp = gpar(fontsize = 8)) +

+	Heatmap(gene_type, name = "gene type", col = brewer.pal(length(unique(gene_type)), "Set1"), column_names_gp = gpar(fontsize = 8)) +

+	Heatmap(anno_gene, name = "anno_gene", col = brewer.pal(length(unique(anno_gene)), "Set2"), column_names_gp = gpar(fontsize = 8)) +

 	Heatmap(dist, name = "dist_tss", col = colorRamp2(c(0, 10000), c("black", "white")), column_names_gp = gpar(fontsize = 8)) +

 	Heatmap(anno_enhancer, name = "anno_enhancer", col = colorRamp2(c(0, 1), c("white", "orange")), cluster_columns = FALSE, column_names_gp = gpar(fontsize = 8), column_title = "Enhancer", column_title_gp = gpar(fontsize = 10))

@@ -52,5 +52,19 @@ Boston_scaled = apply(Boston, 2, scale)

 Heatmap(Boston_scaled, cluster_columns = boston.pv$hclust, heatmap_legend_title = "Boston")

 ```

+## Change styles of legend

+

+By default, for both discrete and continuous colors, the legend is represented as a discrete color bar.

+But continuous colors can also be set to continuous color bar. You can change the legend style both

+for heatmap legend and simple annotation legend.

+

+```{r}

+mat = matrix(rnorm(100), 10)

+ha = HeatmapAnnotation(df = data.frame(value = runif(10)), 

+	col = list(value = colorRamp2(c(0, 1), c("white", "red"))),

+	color_bar = "continuous")

+Heatmap(mat, heatmap_legend_title = "mat", heatmap_legend_color_bar = "continuous", 

+	top_annotation = ha)

+```