@@ -13,7 +13,7 @@ Suggests: testthat (>= 0.3), knitr, markdown, cluster, MASS, pvclust,

     dendextend (>= 1.0.1), grImport, grImport2, rsvg, glue

 VignetteBuilder: knitr

 Description: Complex heatmaps are efficient to visualize associations 

-    between different sources of data sets and reveal potential structures. 

+    between different sources of data sets and reveal potential patterns. 

     Here the ComplexHeatmap package provides a highly flexible way to arrange 

     multiple heatmaps and supports various annotation graphics.

 biocViews: Software, Visualization, Sequencing

@@ -213,7 +213,7 @@ Heatmap = function(matrix, col, name,

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

     row_dend_width = unit(10, "mm"), 

     show_row_dend = TRUE, 

-    row_dend_reorder = is.logical(cluster_rows),

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

     row_dend_gp = gpar(), 

     cluster_columns = TRUE, 

     clustering_distance_columns = "euclidean", 

@@ -222,7 +222,7 @@ Heatmap = function(matrix, col, name,

     column_dend_height = unit(10, "mm"), 

     show_column_dend = TRUE, 

     column_dend_gp = gpar(), 

-    column_dend_reorder = is.logical(cluster_columns),

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

     row_order = NULL, 

     column_order = NULL,

@@ -254,6 +254,7 @@ Heatmap = function(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,

@@ -759,6 +760,7 @@ Heatmap = function(matrix, col, name,

     .Object@heatmap_param$verbose = verbose

     .Object@heatmap_param$post_fun = post_fun

     .Object@heatmap_param$calling_env = parent.frame()

+    .Object@heatmap_param$show_parent_dend_line = show_parent_dend_line

     if(nrow(matrix) == 0) {

         .Object@matrix_param$height = unit(0, "mm")

@@ -954,7 +956,7 @@ make_cluster = function(object, which = c("row", "column")) {

                 for(i in seq_along(dend_list)) {

                     if(length(order_list[[i]]) > 1) {

                         sub_ind = sort(order_list[[i]])

-                        dend_list[[i]] = reorder(dend_list[[i]], reorder[sub_ind])

+                        dend_list[[i]] = reorder(dend_list[[i]], reorder[sub_ind], mean)

                         # the order of object@row_dend_list[[i]] is the order corresponding to the big dendrogram

                         order_list[[i]] = order.dendrogram(dend_list[[i]])

                     }

@@ -1068,7 +1070,7 @@ make_cluster = function(object, which = c("row", "column")) {

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

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

         weight = colMeans(meanmat)

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

+        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

@@ -1209,7 +1211,7 @@ make_cluster = function(object, which = c("row", "column")) {

             for(i in seq_along(dend_list)) {

                 if(length(order_list[[i]]) > 1) {

                     sub_ind = sort(order_list[[i]])

-                    dend_list[[i]] = reorder(dend_list[[i]], reorder[sub_ind])

+                    dend_list[[i]] = reorder(dend_list[[i]], reorder[sub_ind], mean)

                     order_list[[i]] = sub_ind[ order.dendrogram(dend_list[[i]]) ]

                 }

             }

@@ -201,19 +201,19 @@ setMethod(f = "make_layout",

                 }

                 row_dend_slice = adjust_dend_by_x(row_dend_slice, slice_leaf_pos)

                 grid.dendrogram(row_dend_slice, facing = ifelse(row_dend_side == "left", "right", "left"), gp = object@row_dend_param$gp)

-                if(!object@row_dend_param$split_by_cutree) {

+                if(!object@row_dend_param$split_by_cutree && object@heatmap_param$show_parent_dend_line) {

                     dh = dend_heights(object@row_dend_list)

                     if(row_dend_side == "left") {

                         grid.segments(unit(row_dend_max_height - max(dh), "native") - unit(0.5, "mm"), 

-                            slice_leaf_pos[1] + unit(5, "mm"), 

+                            min(unit.c(slice_leaf_pos[1] + unit(5, "mm"), unit(1, "npc"))), 

                             unit(row_dend_max_height - max(dh), "native") - unit(0.5, "mm"), 

-                            slice_leaf_pos[length(slice_leaf_pos)] - unit(5, "mm"),

+                            max(unit.c(slice_leaf_pos[length(slice_leaf_pos)] - unit(5, "mm"), unit(0, "npc"))),

                             gp = gpar(lty = 3, col = "#666666"))

                     } else {

                         grid.segments(unit(max(dh), "native") + unit(0.5, "mm"), 

-                            slice_leaf_pos[1] + unit(5, "mm"), 

+                            min(unit.c(slice_leaf_pos[1] + unit(5, "mm"), unit(1, "npc"))), 

                             unit(max(dh), "native") + unit(0.5, "mm"), 

-                            slice_leaf_pos[length(slice_leaf_pos)] - unit(5, "mm"),

+                            max(unit.c(slice_leaf_pos[length(slice_leaf_pos)] - unit(5, "mm"), unit(0, "npc"))),

                             gp = gpar(lty = 3, col = "#666666"))

                     }

                 }

@@ -274,18 +274,18 @@ setMethod(f = "make_layout",

                 }

                 column_dend_slice = adjust_dend_by_x(column_dend_slice, slice_leaf_pos)

                 grid.dendrogram(column_dend_slice, facing = ifelse(column_dend_side == "top", "bottom", "top"), gp = object@column_dend_param$gp)

-                if(!object@column_dend_param$split_by_cutree) {

+                if(!object@column_dend_param$split_by_cutree && object@heatmap_param$show_parent_dend_line) {

                     dh = dend_heights(object@column_dend_list)

                     if(row_dend_side == "bottom") {

-                        grid.segments(slice_leaf_pos[1] - unit(5, "mm"), 

+                        grid.segments(max(unit.c(slice_leaf_pos[1] - unit(5, "mm"), unit(0, "npc"))), 

                             unit(column_dend_max_height - max(dh), "native") - unit(0.5, "mm"), 

-                            slice_leaf_pos[length(slice_leaf_pos)] + unit(5, "mm"),

+                            min(unit.c(slice_leaf_pos[length(slice_leaf_pos)] + unit(5, "mm"), unit(1, "npc"))),

                             unit(column_dend_max_height - max(dh), "native") - unit(0.5, "mm"), 

                             gp = gpar(lty = 3, col = "#666666"))

                     } else {

-                        grid.segments(slice_leaf_pos[1] - unit(5, "mm"), 

+                        grid.segments(max(unit.c(slice_leaf_pos[1] - unit(5, "mm"), unit(0, "npc"))), 

                             unit(max(dh), "native") + unit(0.5, "mm"), 

-                            slice_leaf_pos[length(slice_leaf_pos)] + unit(5, "mm"),

+                            min(unit.c(slice_leaf_pos[length(slice_leaf_pos)] + unit(5, "mm"), unit(1, "npc"))),

                             unit(max(dh), "native") + unit(0.5, "mm"), 

                             gp = gpar(lty = 3, col = "#666666"))

                     }

@@ -238,6 +238,7 @@ setMethod(f = "add_heatmap",

 # -annotation_border  this set the value in `ht_opt` and reset back after the plot is done

 # -fastcluster this set the value in `ht_opt` and reset back after the plot is done

 # -anno_simple_size  this set the value in `ht_opt` and reset back after the plot is done

+# -show_parent_dend_line this set the value in `ht_opt` and reset back after the plot is done

 #

 # == detail

 # The function first calls `make_layout,HeatmapList-method` to calculate

@@ -333,7 +334,8 @@ setMethod(f = "draw",

     heatmap_border = NULL,

     annotation_border = NULL,

     fastcluster = NULL,

-    anno_simple_size = NULL

+    anno_simple_size = NULL,

+    show_parent_dend_line = NULL

     ) {

     verbose = ht_opt$verbose

@@ -352,7 +354,8 @@ setMethod(f = "draw",

                     "heatmap_border",

                     "annotation_border",

                     "fastcluster",

-                    "anno_simple_size")) {

+                    "anno_simple_size",

+                    "show_parent_dend_line")) {

         v = get(opt_nm, inherits = FALSE)

         if(!is.null(v)) {

             ovl[[opt_nm]] = ht_opt[[opt_nm]]

@@ -486,15 +489,15 @@ setMethod(f = "draw",

     ht_list_height = sum(component_height(object)) + padding[1] + padding[3]

     if(is_abs_unit(ht_list_width)) {

-        ht_list_width = unit(ceiling(convertWidth(ht_list_width, "mm", valueOnly = TRUE)), "mm")

-        qqcat("Since all heatmaps/annotations have absolute units, the total width of the plot is @{ht_list_width}\n")

+        ht_list_width = unit(convertWidth(ht_list_width, "mm", valueOnly = TRUE), "mm")

+        # qqcat("Since all heatmaps/annotations have absolute units, the total width of the plot is @{ht_list_width}\n")

         w = ht_list_width

     } else {

         w = unit(1, "npc")

     }

     if(is_abs_unit(ht_list_height)) {

-        ht_list_height = unit(ceiling(convertHeight(ht_list_height, "mm", valueOnly = TRUE)), "mm")

-        qqcat("Since all heatmaps/annotations have absolute units, the total height of the plot is @{ht_list_height}\n")

+        ht_list_height = unit(convertHeight(ht_list_height, "mm", valueOnly = TRUE), "mm")

+        # qqcat("Since all heatmaps/annotations have absolute units, the total height of the plot is @{ht_list_height}\n")

         h = ht_list_height

     } else {

         h = unit(1, "npc")

@@ -504,14 +507,13 @@ setMethod(f = "draw",

         ncol = length(HEATMAP_LAYOUT_ROW_COMPONENT), 

         widths = component_width(object), 

         heights = component_height(object))

-    

     pushViewport(viewport(name = "global", width = w, height = h))

     pushViewport(viewport(layout = layout, name = "global_layout", x = padding[2], y = padding[1], width = unit(1, "npc") - padding[2] - padding[4],

         height = unit(1, "npc") - padding[1] - padding[3], just = c("left", "bottom")))

     ht_layout_index = object@layout$layout_index

     ht_graphic_fun_list = object@layout$graphic_fun_list

-    

+

     for(j in seq_len(nrow(ht_layout_index))) {

         pushViewport(viewport(layout.pos.row = ht_layout_index[j, 1], layout.pos.col = ht_layout_index[j, 2]))

         ht_graphic_fun_list[[j]](object)

@@ -48,6 +48,7 @@

 # Other parameters:

 #

 # -fast_hclust whether use `fastcluster::hclust` to speed up clustering?

+# -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 `base::options`) or by ``$`` operator:

 #

@@ -109,6 +110,8 @@ ht_opt = setGlobalOptions(

 		.class = "logical",

 		.length = 1

 	),

+	show_parent_dend_line = TRUE,

+

 	verbose = list(

 		.value = FALSE,

 		.class = "logical",

@@ -462,8 +462,17 @@ popViewport = function(...) {

 dev.off2 = function () {

     i1 = dev.prev()

     i2 = dev.cur()

-    if (i1 > 1)

+

+    if (i1 == 2) {

         dev.set(i1)

+    } else if(i1 > 2) {

+        i11 = dev.prev(i1)

+        if(names(i11) == "RStudioGD") {

+            dev.set(i11)

+        } else {

+            dev.set(i1)

+        }

+    }

     dev.off(i2)

 }