@@ -2599,13 +2599,12 @@ anno_mark = function(at, labels, which = c("column", "row"),

 		link_gp = subset_gp(link_gp, labels2index[labels])

 		pushViewport(viewport(xscale = c(0, 1), yscale = c(0.5, n+0.5)))

-		# go to the parent viewport

-

+		if(inherits(extend, "unit")) extend = convertHeight(extend, "native", valueOnly = TRUE)

 		text_height = convertHeight(grobHeight(textGrob(labels, gp = labels_gp))*(1+padding), "native", valueOnly = TRUE)

 		i2 = rev(which(index %in% at))

 		h1 = n-i2+1 - text_height*0.5

 		h2 = n-i2+1 + text_height*0.5

-		pos = rev(smartAlign(h1, h2, c(0.5, n+0.5)))

+		pos = rev(smartAlign(h1, h2, c(0.5 - extend[1], n+0.5 + extend[2])))

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

 		n2 = length(labels)

@@ -1073,21 +1073,22 @@ make_cluster = function(object, which = c("row", "column")) {

         if(which == "row") {

             km.fit = kmeans(mat, centers = km)

             cl = km.fit$cluster

-            meanmat = lapply(unique(cl), function(i) {

+            meanmat = lapply(sort(unique(cl)), function(i) {

                 colMeans(mat[cl == i, , drop = FALSE])

             })

         } else {

             km.fit = kmeans(t(mat), centers = km)

             cl = km.fit$cluster

-            meanmat = lapply(unique(cl), function(i) {

+            meanmat = lapply(sort(unique(cl)), function(i) {

                 rowMeans(mat[, cl == i, drop = FALSE])

             })

         }

-        

-        meanmat = as.matrix(as.data.frame(meanmat))

+

+        meanmat = do.call("cbind", meanmat)

         hc = hclust(dist(t(meanmat)))

         weight = colMeans(meanmat)

-        hc = as.hclust(reorder(as.dendrogram(hc), -weight, mean))

+        hc = as.hclust(reorder(as.dendrogram(hc), weight, mean))

+

         cl2 = numeric(length(cl))

         for(i in seq_along(hc$order)) {

             cl2[cl == hc$order[i]] = i

@@ -101,9 +101,9 @@ HeatmapAnnotation = function(...,

 	show_annotation_name = TRUE,

 	annotation_name_gp = gpar(),

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

+	annotation_name_offset = NULL,

 	annotation_name_side = ifelse(which == "column", "right", "bottom"),

-	annotation_name_rot = ifelse(which == "column", 0, 90),

+	annotation_name_rot = NULL,

 	annotation_height = NULL, 

 	annotation_width = NULL, 

@@ -242,9 +242,10 @@ HeatmapAnnotation = function(...,

     an = names(anno_value_list)

     show_annotation_name = recycle_param(show_annotation_name, an, TRUE)

-    annotation_name_offset = recycle_param(annotation_name_offset, an, TRUE)

-    annotation_name_side = recycle_param(annotation_name_side, an, TRUE)

-    annotation_name_rot = recycle_param(annotation_name_rot, an, TRUE)

+    annotation_name_side = recycle_param(annotation_name_side, an, ifelse(which == "column", "right", "bottom"))

+    if(inherits(annotation_name_offset, "unit")) annotation_name_offset = unit_to_str(annotation_name_offset)

+    annotation_name_offset = recycle_param(annotation_name_offset, an, NULL, as.list = TRUE)

+    annotation_name_rot = recycle_param(annotation_name_rot, an, NULL, as.list = TRUE)

     if(missing(border)) {

     	if(!is.null(ht_opt$annotation_border)) border = ht_opt$annotation_border

     }

@@ -296,16 +297,11 @@ HeatmapAnnotation = function(...,

 		arg_list = list(name = ag, which = which,

 				show_name = show_annotation_name[i_anno], 

 				name_gp = subset_gp(annotation_name_gp, i_anno), 

-	        	name_offset = annotation_name_offset[i_anno], 

+	        	name_offset = annotation_name_offset[[i_anno]], 

 	        	name_side = annotation_name_side[i_anno], 

-	        	name_rot = annotation_name_rot[i_anno],

+	        	name_rot = annotation_name_rot[[i_anno]],

 	        	border = border[i_anno])

-		# if(!is_name_offset_called) {

-		# 	arg_list$name_rot = NULL

-		# }

-		# if(!is_name_rot_called) {

-		# 	arg_list$name_offset = NULL

-		# }

+

 		if(inherits(anno_value_list[[ag]], c("function", "AnnotationFunction"))) {

 			arg_list$fun = anno_value_list[[ag]]

 			if(inherits(anno_value_list[[ag]], "function")) {

@@ -149,9 +149,9 @@ SingleAnnotation = function(name, value, col, fun,

 	legend_param = list(),

 	show_name = TRUE, 

 	name_gp = gpar(fontsize = 12),

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

+	name_offset = NULL,

 	name_side = ifelse(which == "column", "right", "bottom"),

-    name_rot = ifelse(which == "column", 0, 90),

+    name_rot = NULL,

     anno_simple_size = ht_opt$anno_simple_size,

     width = NULL, height = NULL) {

@@ -188,8 +188,10 @@ SingleAnnotation = function(name, value, col, fun,

     }

     .Object@name = name

-    if(!name_rot %in% c(0, 90, 180, 270)) {

-        stop_wrap(qq("@{name}: `name_rot` can only take values in c(0, 90, 180, 270)"))

+    if(!is.null(name_rot)) {

+        if(!name_rot %in% c(0, 90, 180, 270)) {

+            stop_wrap(qq("@{name}: `name_rot` can only take values in c(0, 90, 180, 270)"))

+        }

     }

     if(verbose) qqcat("create a SingleAnnotation with name '@{name}'\n")

@@ -224,8 +226,9 @@ SingleAnnotation = function(name, value, col, fun,

         }

     }

-    is_name_offset_called = !missing(name_offset)

-    is_name_rot_called = !missing(name_rot)

+    # if SingleAnnotation is called by HeatmapAnnotation, following two variables are all TRUE

+    is_name_offset_called = !is.null(name_offset)

+    is_name_rot_called = !is.null(name_rot)

     anno_fun_extend = unit(c(0, 0, 0, 0), "mm")

     if(!missing(fun)) {

         if(inherits(fun, "AnnotationFunction")) {

@@ -240,6 +243,15 @@ SingleAnnotation = function(name, value, col, fun,

         }

     }

+    if(!is.null(name_offset)) {

+        if(is.character(name_offset)) {

+            name_offset = to_unit(name_offset)

+        }

+    } else {

+        name_offset = unit(1, "mm")

+    }

+    name_rot = ifelse(which == "column", 0, 90)

+

     anno_name = name

     if(which == "column") {

         if(verbose) qqcat("@{name}: it is a column annotation\n")

@@ -326,15 +326,25 @@ oncoPrint = function(mat,

 	}

 	if(show_pct) {

-		pct_ha = rowAnnotation(pct = anno_text(pct, just = "right", location = unit(1, "npc"), gp = pct_gp),

-				show_annotation_name = FALSE)

+		if(pct_side == "left") {

+			pct_ha = rowAnnotation(pct = anno_text(pct, just = "right", location = unit(1, "npc"), gp = pct_gp, width = max_text_width(pct, gp = pct_gp) + unit(1, "mm")),

+					show_annotation_name = FALSE)

+		} else {

+			pct_ha = rowAnnotation(pct = anno_text(pct, just = "left", location = unit(0, "npc"), gp = pct_gp, width = max_text_width(pct, gp = pct_gp) + unit(1, "mm")),

+					show_annotation_name = FALSE)

+		}

 		names(pct_ha) = paste0("pct_", random_str())

 	} else {

 		pct_ha = NULL

 	}

 	if(show_row_names) {

-		rn_ha = rowAnnotation(rownames = anno_text(row_labels, gp = pct_gp, just = "left", location = unit(0, "npc")),

-			show_annotation_name = FALSE)

+		if(row_names_side == "right") {

+			rn_ha = rowAnnotation(rownames = anno_text(row_labels, gp = row_names_gp, just = "left", location = unit(0, "npc"), width = max_text_width(pct, gp = row_names_gp) + unit(1, "mm")),

+				show_annotation_name = FALSE)

+		} else {

+			rn_ha = rowAnnotation(rownames = anno_text(row_labels, gp = row_names_gp, just = "right", location = unit(1, "npc"), width = max_text_width(pct, gp = row_names_gp) + unit(1, "mm")),

+				show_annotation_name = FALSE)

+		}

 		names(rn_ha) = paste0("rownames_", random_str())

 	} else {

 		rn_ha = NULL

@@ -522,9 +522,18 @@ normalize_graphic_param_to_mat = function(x, nc, nr, name) {

     }

 }

-recycle_param = function(x, all_names, default) {

+recycle_param = function(x, all_names, default, as.list = FALSE) {

     n = length(all_names)

-    if(length(x) == n) {

+    if(length(x) == 0) {

+        if(as.list) {

+            rep(list(default), n)

+        } else {

+            rep(default, n)

+        }

+    } else if(length(x) == n) {

+        if(as.list) {

+            x = lapply(1:n, x[i])

+        }

         return(x)

     } else {

         nm = names(x)

@@ -533,18 +542,39 @@ recycle_param = function(x, all_names, default) {

         }

         if(is.null(nm)) {

             if(length(x) == 1) {

-                x = rep(x, n)

+                if(as.list) {

+                    x = lapply(1:n , function(x) x)

+                } else {

+                    x = rep(x, n)

+                }

             } else {

                 if(length(x) > n) {

                     x = x[1:n]

+                    if(as.list) {

+                        x = lapply(1:n, x[i])

+                    }

                 } else {

-                    x = c(x, rep(default, n - length(x)))

+                    if(as.list) {

+                        x = c(lapply(seq_along(x), function(i) x[i], 

+                              rep(list(default), n - length(x))))

+                    } else {

+                        x = c(x, rep(default, n - length(x)))

+                    }

                 }

             }

         } else {

-            x2 = structure(rep(default, n), names = all_names)

-            x2[intersect(nm, all_names)] = x[intersect(nm, all_names)]

-            x = x2

+            if(as.list) {

+                x2 = rep(list(default), n)

+                names(x2) = all_names

+                for(cn in intersect(nm, all_names)) {

+                    x2[[cn]] = x[cn]

+                }

+                x = x2

+            } else {

+                x2 = structure(rep(default, n), names = all_names)

+                x2[intersect(nm, all_names)] = x[intersect(nm, all_names)]

+                x = x2

+            }

         }

         return(x)

     }

@@ -777,3 +807,17 @@ random_str = function() {

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

 }

+

+

+to_unit_str = function(unit) {

+    as.character(unit)

+}

+

+to_unit = function(str) {

+    d = gsub("[^\\d]+$", "", str, perl = TRUE)

+    u = gsub("[\\d.]", "", str, perl = TRUE)

+    unit(as.numeric(d), u)

+}

+

+

+

@@ -22,7 +22,7 @@ h1, h2, h3, h4, h5 {

 ### There is no plot comming out after running Heatmap() function.

-In this case, you need to use `draw()` function explicitly. See https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#plot-the-heatmap.

+In this case, you need to use `draw()` function explicitly. See https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#plot-the-heatmap and https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#plot-the-heamtap-list.

 ### Retrieve orders and dendrograms.

@@ -30,6 +30,10 @@ For retrieving orders and dendrograms from a single heatmap. See https://jokergo

 For retrieving orders and dendrograms from a list of heatmaps. See https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#get-orders-and-dendrograms-from-a-list-of-heatmaps.

+### How should I control the height or width of the heatmap annotations?

+

+### How should I control the axes of the annotations?

+

 ### How to control the style of legends?

 The style of legends can be controlled by `heatmap_legend_param` in `Heatmap()`, or