@@ -243,7 +243,7 @@ HeatmapAnnotation = function(...,

     an = names(anno_value_list)

     show_annotation_name = recycle_param(show_annotation_name, 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)

+    if(inherits(annotation_name_offset, "unit")) annotation_name_offset = to_unit_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)) {

@@ -156,7 +156,7 @@ densityHeatmap = function(data,

 	bb = grid.pretty(c(min_x, max_x))

 	ht = Heatmap(mat, col = col, name = "density", 

-		column_title = column_title,

+		column_title = title,

 		column_title_gp = title_gp,

 		cluster_rows = FALSE, 

 		cluster_columns = cluster_columns,

@@ -362,10 +362,10 @@ oncoPrint = function(mat,

 			left_annotation = left_annotation[l_non_empty_row, ]

 		}

 		if(pct_side == "left") {

-			left_annotation = c(left_annotation, pct_ha)

+			left_annotation = c(left_annotation, pct_ha, gap = unit(1, "mm"))

 		}

 		if(row_names_side == "left") {

-			left_annotation = c(left_annotation, rn_ha)

+			left_annotation = c(left_annotation, rn_ha, gap = unit(1, "mm"))

 		}

 	}

@@ -381,10 +381,10 @@ oncoPrint = function(mat,

 			right_annotation = right_annotation[l_non_empty_row, ]

 		}

 		if(pct_side == "right") {

-			if(!is.null(pct_ha)) right_annotation = c(pct_ha, right_annotation)

+			if(!is.null(pct_ha)) right_annotation = c(pct_ha, right_annotation, gap = unit(1, "mm"))

 		}

 		if(row_names_side == "right") {

-			if(!is.null(rn_ha)) right_annotation = c(rn_ha, right_annotation)

+			if(!is.null(rn_ha)) right_annotation = c(rn_ha, right_annotation, gap = unit(1, "mm"))

 		}

 	}

 	if(remove_empty_columns) {

@@ -163,7 +163,7 @@ get_dist = function(matrix, method) {

         } else if(nargs == 3) {

             dst = dist2(matrix, method)

         } else {

-            stop_wrap("Since your distance method is a funciton, it can only accept one or two arguments.")

+            stop_wrap("Since your distance method is a function, it can only accept one or two arguments.")

         }

     } else if(method %in% c("euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski")) {

         # if(any(is.na(matrix))) {

@@ -532,7 +532,7 @@ recycle_param = function(x, all_names, default, as.list = FALSE) {

         }

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

         if(as.list) {

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

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

         }

         return(x)

     } else {

@@ -543,7 +543,7 @@ recycle_param = function(x, all_names, default, as.list = FALSE) {

         if(is.null(nm)) {

             if(length(x) == 1) {

                 if(as.list) {

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

+                    x = rep(list(x), n)

                 } else {

                     x = rep(x, n)

                 }

@@ -551,7 +551,7 @@ recycle_param = function(x, all_names, default, as.list = FALSE) {

                 if(length(x) > n) {

                     x = x[1:n]

                     if(as.list) {

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

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

                     }

                 } else {

                     if(as.list) {

@@ -18,9 +18,9 @@ HeatmapAnnotation(...,

     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,

@@ -16,9 +16,9 @@ SingleAnnotation(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)

 }

@@ -32,8 +32,22 @@ For retrieving orders and dendrograms from a list of heatmaps. See https://joker

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

+For complex annotations generated by `anno_*()` functions, width or height should be set inside 

+the `anno_*()` function, such as `anno_points(..., height = ...)`. The size of simple annotations

+is controlled by `anno_simple_size`. The `width`/`height` and `annotation_width`/`annotation_height`

+are used to adjust the size for multiple annotations which are put in one `HeatmapAnnotation` object.

+See https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#multiple-annotations

+

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

+In the annotation functions `anno_*()`, the argument `axis_param` can be used to set the axes. The value

+should be a list and the default settings for axis can be get by:

+

+```{r, eval = FALSE}

+default_axis_param("column")

+default_axis_param("row")

+```

+

 ### How to control the style of legends?

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