@@ -1,7 +1,7 @@

 Package: ComplexHeatmap

 Type: Package

 Title: Making Complex Heatmaps

-Version: 1.11.4

+Version: 1.11.5

 Date: 2016-6-7

 Author: Zuguang Gu

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

@@ -1,3 +1,9 @@

+CHANGES in VERSION 1.11.5

+

+* `gap` in `HeatmapAnnotation` has been adjusted

+

+=============================

+

 CHANGES in VERSION 1.11.2

 * `grid.dendrogram()`: do not draw dendrogram if the height is zero

@@ -199,14 +199,11 @@ HeatmapAnnotation = function(df, name, col, na_col = "grey",

 		}

 	}

-	if(which == "column") {

-		anno_list = rev(anno_list)

-	}

-

 	n_anno = length(anno_list)

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

+	# the nth gap does not really matter

     if(length(gap) == 1) {

     	.Object@gap = rep(gap, n_anno)

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

@@ -214,6 +211,7 @@ HeatmapAnnotation = function(df, name, col, na_col = "grey",

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

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

     } else {

+    	gap[n_anno] = unit(0, "mm")

     	.Object@gap = gap

     }

@@ -231,8 +229,6 @@ HeatmapAnnotation = function(df, name, col, na_col = "grey",

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

 	}

-	if(which == "column") anno_size = anno_size[rev(seq_len(n_anno))]

-

 	names(anno_list) = sapply(anno_list, function(x) x@name)

     .Object@anno_list = anno_list

     .Object@anno_size = anno_size

@@ -391,18 +387,30 @@ setMethod(f = "draw",

 	gap = object@gap

 	pushViewport(viewport(...))

-	for(i in seq_len(n_anno)) {

-		if(which == "column") {

-			if(align_to == "bottom") {

-				pushViewport(viewport(y = sum(anno_size[seq_len(i)]) + sum(gap[seq_len(i)]) - gap[i], height = anno_size[i], just = c("center", "top")))

-			} else {

-				pushViewport(viewport(y = unit(1, "npc") - (sum(anno_size[seq(i, n_anno)]) + sum(gap[seq(i, n_anno)]) - gap[n_anno + 1 - i]), height = anno_size[i], just = c("center", "bottom")))

+	if(which == "column") {

+		if(align_to == "bottom") { # put on top of the heatmap

+			# start from the last annoation which is put on bottom

+			for(i in rev(seq_len(n_anno))) {

+				pushViewport(viewport(y = sum(anno_size[seq(n_anno - i + 1, n_anno))]) + sum(gap[seq(n_anno - i + 1, n_anno)]) + gap[n_anno], 

+					height = anno_size[i], just = c("center", "top"))

+				draw(object@anno_list[[i]], index, k, n)

+				upViewport()

 			}

-		} else {

+		} else { # put on bottom of the heatmap

+			# start for the first annotation which is put on the top

+			for(i in seq_len(n_anno)) {

+				pushViewport(viewport(y = unit(1, "npc") - (sum(anno_size[seq_len(i)]) + sum(gap[seq_len(i)]) - gap[i]), 

+					height = anno_size[i], just = c("center", "bottom"))

+				draw(object@anno_list[[i]], index, k, n)

+				upViewport()

+			}

+		}

+	} else if(which == "row") {

+		for(i in seq_len(n_anno)) {

 			pushViewport(viewport(x = sum(anno_size[seq_len(i)]) + sum(gap[seq_len(i)]) - gap[i], width = anno_size[i], just = c("right", "center")))

+			draw(object@anno_list[[i]], index, k, n)

+			upViewport()

 		}

-		draw(object@anno_list[[i]], index, k, n)

-		upViewport()

 	}

 	upViewport()

 })