@@ -42,7 +42,8 @@

 # draw(anno, test = "anno_empty")

 # anno = anno_empty(border = FALSE)

 # draw(anno, test = "anno_empty without border")

-anno_empty = function(which = c("column", "row"), border = TRUE, width = NULL, height = NULL) {

+anno_empty = function(which = c("column", "row"), border = TRUE, zoom = FALSE,

+	width = NULL, height = NULL) {

 	if(is.null(.ENV$current_annotation_which)) {

 		which = match.arg(which)[1]

@@ -52,6 +53,7 @@ anno_empty = function(which = c("column", "row"), border = TRUE, width = NULL, h

 	anno_size = anno_width_and_height(which, width, height, unit(1, "cm"))

+	

 	fun = function(index) {

 		if(border) grid.rect()

 	}

@@ -61,13 +63,14 @@ anno_empty = function(which = c("column", "row"), border = TRUE, width = NULL, h

 		n = NA,

 		fun_name = "anno_empty",

 		which = which,

-		var_import = list(border),

+		var_import = list(border, zoom),

 		subset_rule = list(),

 		subsetable = TRUE,

 		height = anno_size$height,

 		width = anno_size$width,

 		show_name = FALSE

 	)

+	

 	return(anno) 

 }

@@ -156,6 +156,7 @@ Heatmap = setClass("Heatmap",

 # -gap Gap between row slices if the heatmap is split by rows. The value should be a `grid::unit` object.

 # -row_gap Same as ``gap``.

 # -column_gap Gap between column slices.

+# -show_parent_dend_line When heatmap is split, whether to add a dashed line to mark parent dendrogram and children dendrograms?

 # -width Width of the heatmap body.

 # -height Height of the heatmap body.

 # -heatmap_width Width of the whole heatmap (including heatmap components)

@@ -543,17 +544,25 @@ Heatmap = function(matrix, col, name,

     if(missing(cluster_rows) && !missing(row_order)) {

         cluster_rows = FALSE

     }

-    if(inherits(cluster_rows, "dendrogram") || inherits(cluster_rows, "hclust")) {

+    if(is.logical(cluster_rows)) {

+        if(!cluster_rows) {

+            row_dend_width = unit(0, "mm")

+            show_row_dend = FALSE

+        }

+        .Object@row_dend_param$cluster = cluster_rows

+    } else if(inherits(cluster_rows, "dendrogram") || inherits(cluster_rows, "hclust")) {

         .Object@row_dend_param$obj = cluster_rows

         .Object@row_dend_param$cluster = TRUE

     } else if(inherits(cluster_rows, "function")) {

         .Object@row_dend_param$fun = cluster_rows

         .Object@row_dend_param$cluster = TRUE

     } else {

-        .Object@row_dend_param$cluster = cluster_rows

-        if(!cluster_rows) {

-            row_dend_width = unit(0, "mm")

-            show_row_dend = FALSE

+        oe = try(cluster_rows <- as.dendrogram(cluster_rows), silent = TRUE)

+        if(!inherits(oe, "try-error")) {

+            .Object@row_dend_param$obj = cluster_rows

+            .Object@row_dend_param$cluster = TRUE

+        } else {

+            stop_wrap("`cluster_rows` should be a logical value, a clustering function or a clustering object.")

         }

     }

     if(!show_row_dend) {

@@ -580,17 +589,25 @@ Heatmap = function(matrix, col, name,

     if(missing(cluster_columns) && !missing(column_order)) {

         cluster_columns = FALSE

     }

-    if(inherits(cluster_columns, "dendrogram") || inherits(cluster_columns, "hclust")) {

+    if(is.logical(cluster_columns)) {

+        if(!cluster_columns) {

+            column_dend_height = unit(0, "mm")

+            show_column_dend = FALSE

+        }

+        .Object@column_dend_param$cluster = cluster_columns

+    } else if(inherits(cluster_columns, "dendrogram") || inherits(cluster_columns, "hclust")) {

         .Object@column_dend_param$obj = cluster_columns

         .Object@column_dend_param$cluster = TRUE

     } else if(inherits(cluster_columns, "function")) {

         .Object@column_dend_param$fun = cluster_columns

         .Object@column_dend_param$cluster = TRUE

     } else {

-        .Object@column_dend_param$cluster = cluster_columns

-        if(!cluster_columns) {

-            column_dend_height = unit(0, "mm")

-            show_column_dend = FALSE

+        oe = try(cluster_columns <- as.dendrogram(cluster_columns), silent = TRUE)

+        if(!inherits(oe, "try-error")) {

+            .Object@column_dend_param$obj = cluster_columns

+            .Object@column_dend_param$cluster = TRUE

+        } else {

+            stop_wrap("`cluster_columns` should be a logical value, a clustering function or a clustering object.")

         }

     }

     if(!show_column_dend) {

@@ -348,8 +348,22 @@ HeatmapAnnotation = function(...,

 		}

 	}

+

 	n_total_anno = length(anno_list)

+	## check whether anno_list contains zoomed anno_empty

+	if(n_total_anno > 1) {

+		for(i in seq_len(n_total_anno)) {

+			anno = anno_list[[i]]@fun

+			if(identical(anno@fun_name, "anno_empty")) {

+				if(anno@var_env$zoom) {

+					stop_wrap("You set `zoom = TRUE` in `anno_empty()` for the empty annotation. The HeatmapAnnotation object only allows to contain one single annotation if it is a zoomed empty annotation.")

+				}

+			}

+		}

+	}

+

+

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

 	# the nth gap does not really matter

@@ -559,6 +573,7 @@ setMethod(f = "draw",

 	n_anno = length(object@anno_list)

 	anno_size = object@anno_size

 	gap = object@gap

+	vp_param = list(...)

 	if(is.character(test)) {

         test2 = TRUE

@@ -572,7 +587,7 @@ setMethod(f = "draw",

     	if(which == "column") pushViewport(viewport(width = unit(1, "npc") - unit(3, "cm"), height = object@height))

     	if(which == "row") pushViewport(viewport(height = unit(1, "npc") - unit(3, "cm"), width = object@width))

     } else {

-		pushViewport(viewport(...))

+		pushViewport(do.call(viewport, vp_param))

 	}

 	if(missing(index)) {

@@ -1215,3 +1230,15 @@ setMethod(f = "re_size",

 	return(object)

 })

+

+has_zoomed_anno_empty = function(ha) {

+	if(length(ha@anno_list) == 1) {

+		anno = ha@anno_list[[1]]@fun

+		if(identical(anno@fun_name, "anno_empty")) {

+			if(anno@var_env$zoom) {

+				return(TRUE)

+			}

+		}

+	}

+	return(FALSE)

+}

@@ -192,6 +192,8 @@ oncoPrint = function(mat,

 		}

 		alter_fun = alter_fun[unique(c("background", intersect(names(alter_fun), all_type)))]

+		all_type = setdiff(names(alter_fun), "background")

+		arr = arr[, , all_type, drop = FALSE]

 		if(is.null(alter_fun_is_vectorized)) {

 			alter_fun_is_vectorized = guess_alter_fun_is_vectorized(alter_fun)

@@ -30,7 +30,7 @@ Heatmap(matrix, col, name,

     row_dend_side = c("left", "right"),

     row_dend_width = unit(10, "mm"),

     show_row_dend = TRUE,

-    row_dend_reorder = TRUE,

+    row_dend_reorder = is.logical(cluster_rows) || is.function(cluster_rows),

     row_dend_gp = gpar(),

     cluster_columns = TRUE,

     clustering_distance_columns = "euclidean",

@@ -39,7 +39,7 @@ Heatmap(matrix, col, name,

     column_dend_height = unit(10, "mm"),

     show_column_dend = TRUE,

     column_dend_gp = gpar(),

-    column_dend_reorder = TRUE,

+    column_dend_reorder = is.logical(cluster_columns) || is.function(cluster_columns),

     row_order = NULL,

     column_order = NULL,

@@ -71,6 +71,7 @@ Heatmap(matrix, col, name,

     gap = unit(1, "mm"),

     row_gap = unit(1, "mm"),

     column_gap = unit(1, "mm"),

+    show_parent_dend_line = ht_opt$show_parent_dend_line,

     heatmap_width = unit(1, "npc"),

     width = NULL,

@@ -149,6 +150,7 @@ Heatmap(matrix, col, name,

   \item{gap}{Gap between row slices if the heatmap is split by rows. The value should be a \code{\link[grid]{unit}} object.}

   \item{row_gap}{Same as \code{gap}.}

   \item{column_gap}{Gap between column slices.}

+  \item{show_parent_dend_line}{When heatmap is split, whether to add a dashed line to mark parent dendrogram and children dendrograms?}

   \item{width}{Width of the heatmap body.}

   \item{height}{Height of the heatmap body.}

   \item{heatmap_width}{Width of the whole heatmap (including heatmap components)}

@@ -56,7 +56,7 @@ HeatmapAnnotation(...,

 }

 \details{

-For arguments \code{border}, \code{annotation_name_offset}, \code{annotation_name_side}, \code{annotation_name_rot},

+For arguments \code{show_legend}, \code{border}, \code{annotation_name_offset}, \code{annotation_name_side}, \code{annotation_name_rot},

 \code{show_annotation_name}, they can be set as named vectors to modify values for some of the annotations,

 e.g. assuming you have an annotation with name \code{foo}, you can specify \code{border = c(foo = TRUE)} in \code{\link{HeatmapAnnotation}}.

@@ -84,7 +84,8 @@ Draw a list of heatmaps

     heatmap_border = NULL,

     annotation_border = NULL,

     fastcluster = NULL,

-    anno_simple_size = NULL)

+    anno_simple_size = NULL,

+    show_parent_dend_line = NULL)

 }

 \arguments{

@@ -157,6 +158,7 @@ Draw a list of heatmaps

   \item{annotation_border}{this set the value in \code{\link{ht_opt}} and reset back after the plot is done}

   \item{fastcluster}{this set the value in \code{\link{ht_opt}} and reset back after the plot is done}

   \item{anno_simple_size}{this set the value in \code{\link{ht_opt}} and reset back after the plot is done}

+  \item{show_parent_dend_line}{this set the value in \code{\link{ht_opt}} and reset back after the plot is done}

 }

 \details{

@@ -65,6 +65,7 @@ Other parameters:

 \describe{

   \item{fast_hclust}{whether use \code{\link[fastcluster]{hclust}} to speed up clustering?}

+  \item{show_parent_dend_line}{when heatmap is split, whether to add a dashed line to mark parent dendrogram and children dendrograms?}

 }

 You can get or set option values by the traditional way (like \code{\link[base]{options}}) or by \code{$} operator: