@@ -98,7 +98,7 @@ AnnotationFunction = function(fun, fun_name = "", which = c("column", "row"),

 	which = match.arg(which)[1]

-	verbose = ht_global_opt$verbose

+	verbose = ht_opt$verbose

 	anno = new("AnnotationFunction")

@@ -231,7 +231,7 @@ setMethod(f = "draw",

         pushViewport(viewport(width = 0.8, height = 0.8))

     }

-    verbose = ht_global_opt$verbose

+    verbose = ht_opt$verbose

     if(verbose) qqcat("draw annotation generated by @{object@fun_name}\n")

     if(missing(index)) index = seq_len(object@n)

@@ -308,7 +308,7 @@ Heatmap = function(matrix, col, name,

     raster_quality = 2,

     raster_device_param = list()) {

-    verbose = ht_global_opt("verbose")

+    verbose = ht_opt("verbose")

     if(!dev.interactive()) {

         pdf(file = NULL)

@@ -327,26 +327,26 @@ Heatmap = function(matrix, col, name,

     for(opt_name in c("row_names_gp", "column_names_gp", "row_title_gp", "column_title_gp")) {

         opt_name2 = paste0("heatmap_", opt_name)

         if(! opt_name %in% called_args) { # if this argument is not called

-            if(!is.null(ht_global_opt(opt_name2))) {

-                if(verbose) qqcat("re-assign @{opt_name} with `ht_global_opt('@{opt_name2}'')`\n")

-                assign(opt_name, ht_global_opt(opt_name2))

+            if(!is.null(ht_opt(opt_name2))) {

+                if(verbose) qqcat("re-assign @{opt_name} with `ht_opt('@{opt_name2}'')`\n")

+                assign(opt_name, ht_opt(opt_name2))

             }

         }

     }

     if("heatmap_legend_param" %in% called_args) {

         for(opt_name in setdiff(c("title_gp", "title_position", "labels_gp", "grid_width", "grid_height", "grid_border"), names(heatmap_legend_param))) {

-            opt_name2 = paste0("heatmap_legend_", opt_name)

-            if(!is.null(ht_global_opt(opt_name2)))

-                if(verbose) qqcat("re-assign heatmap_legend_param$@{opt_name} with `ht_global_opt('@{opt_name2}'')`\n")

-                heatmap_legend_param[[opt_name]] = ht_global_opt(opt_name2)

+            opt_name2 = paste0("legend_", opt_name)

+            if(!is.null(ht_opt(opt_name2)))

+                if(verbose) qqcat("re-assign heatmap_legend_param$@{opt_name} with `ht_opt('@{opt_name2}'')`\n")

+                heatmap_legend_param[[opt_name]] = ht_opt(opt_name2)

         }

     } else {

         for(opt_name in c("title_gp", "title_position", "labels_gp", "grid_width", "grid_height", "grid_border")) {

-            opt_name2 = paste0("heatmap_legend_", opt_name)

-            if(!is.null(ht_global_opt(opt_name2)))

-                if(verbose) qqcat("re-assign heatmap_legend_param$@{opt_name} with `ht_global_opt('@{opt_name2}'')`\n")

-                heatmap_legend_param[[opt_name]] = ht_global_opt(opt_name2)

+            opt_name2 = paste0("legend_", opt_name)

+            if(!is.null(ht_opt(opt_name2)))

+                if(verbose) qqcat("re-assign heatmap_legend_param$@{opt_name} with `ht_opt('@{opt_name2}'')`\n")

+                heatmap_legend_param[[opt_name]] = ht_opt(opt_name2)

         }

     }

@@ -616,7 +616,7 @@ Heatmap = function(matrix, col, name,

     .Object@row_dend_param$distance = clustering_distance_rows

     .Object@row_dend_param$method = clustering_method_rows

     .Object@row_dend_param$side = match.arg(row_dend_side)[1]

-    .Object@row_dend_param$width = row_dend_width + unit(1, "mm")  # append the gap

+    .Object@row_dend_param$width = row_dend_width + DENDROGRAM_PADDING  # append the gap

     .Object@row_dend_param$show = show_row_dend

     .Object@row_dend_param$gp = check_gp(row_dend_gp)

     .Object@row_dend_param$reorder = row_dend_reorder

@@ -653,7 +653,7 @@ Heatmap = function(matrix, col, name,

     .Object@column_dend_param$distance = clustering_distance_columns

     .Object@column_dend_param$method = clustering_method_columns

     .Object@column_dend_param$side = match.arg(column_dend_side)[1]

-    .Object@column_dend_param$height = column_dend_height + unit(1, "mm")  # append the gap

+    .Object@column_dend_param$height = column_dend_height + DENDROGRAM_PADDING  # append the gap

     .Object@column_dend_param$show = show_column_dend

     .Object@column_dend_param$gp = check_gp(column_dend_gp)

     .Object@column_dend_param$reorder = column_dend_reorder

@@ -671,7 +671,7 @@ Heatmap = function(matrix, col, name,

     if(is.null(top_annotation)) {

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

     } else {

-        .Object@top_annotation_param$height = height(top_annotation) + COLUMN_ANNO_PADDING*2  # append the gap

+        .Object@top_annotation_param$height = height(top_annotation) + COLUMN_ANNO_PADDING  # append the gap

     }

     if(!is.null(top_annotation)) {

         if(length(top_annotation) > 0) {

@@ -691,7 +691,7 @@ Heatmap = function(matrix, col, name,

     if(is.null(bottom_annotation)) {

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

     } else {

-        .Object@bottom_annotation_param$height = height(bottom_annotation) + COLUMN_ANNO_PADDING*2  # append the gap

+        .Object@bottom_annotation_param$height = height(bottom_annotation) + COLUMN_ANNO_PADDING  # append the gap

     }

     if(!is.null(bottom_annotation)) {

         if(length(bottom_annotation) > 0) {

@@ -711,7 +711,7 @@ Heatmap = function(matrix, col, name,

     if(is.null(left_annotation)) {

         .Object@left_annotation_param$width = unit(0, "mm")

     } else {

-        .Object@left_annotation_param$width = width(left_annotation) + ROW_ANNO_PADDING*2  # append the gap

+        .Object@left_annotation_param$width = width(left_annotation) + ROW_ANNO_PADDING  # append the gap

     }

     if(!is.null(left_annotation)) {

         if(length(left_annotation) > 0) {

@@ -731,7 +731,7 @@ Heatmap = function(matrix, col, name,

     if(is.null(right_annotation)) {

         .Object@right_annotation_param$width = unit(0, "mm")

     } else {

-        .Object@right_annotation_param$width = width(right_annotation) + ROW_ANNO_PADDING*2  # append the gap

+        .Object@right_annotation_param$width = width(right_annotation) + ROW_ANNO_PADDING  # append the gap

     }

     if(!is.null(right_annotation)) {

         if(length(right_annotation) > 0) {

@@ -825,7 +825,7 @@ make_cluster = function(object, which = c("row", "column")) {

     verbose = object@heatmap_param$verbose

-    if(ht_global_opt("fast_hclust")) {

+    if(ht_opt("fast_hclust")) {

         hclust = fastcluster::hclust

         if(verbose) qqcat("apply hclust by fastcluster::hclust\n")

     } else {

@@ -1396,12 +1396,23 @@ setMethod(f = "make_layout",

         }

         row_dend_max_height = dend_heights(row_dend_slice) + max(dend_heights(object@row_dend_list))

         object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) {

+            

+            if(row_dend_side == "left") {

+                pushViewport(viewport(x = unit(0, "npc"), width = unit(1, "npc") - DENDROGRAM_PADDING, just = "left"))

+            } else {

+                pushViewport(viewport(x = DENDROGRAM_PADDING, width = unit(1, "npc") - DENDROGRAM_PADDING, just = "left"))

+            }

             for(i in seq_len(nr_slice)) {

-                draw_dend(object, k = i, which = "row", y = slice_y[i], height = slice_height[i], just = "top")

+                draw_dend(object, k = i, which = "row", y = slice_y[i], height = slice_height[i], just = "top",

+                    max_height = row_dend_max_height)

             }

             if(nr_slice > 1) {

-                pushViewport(viewport(xscale = c(0, row_dend_max_height), width = unit(1, "npc") - DENDROGRAM_PADDING*2))

+                if(row_dend_side == "left") {

+                    pushViewport(viewport(xscale = c(0, row_dend_max_height)))

+                } else {

+                    pushViewport(viewport(xscale = c(0, row_dend_max_height)))

+                }

                 p = sapply(object@row_dend_list, function(x) {

                     attr(x, "x")/nobs(x)

                 })

@@ -1413,10 +1424,11 @@ setMethod(f = "make_layout",

                     slice_leaf_pos[i] = slice_leaf_pos[i] - slice_height[i]*p[i]

                 }

                 row_dend_slice = merge(row_dend_slice, object@row_dend_list, only_parent = TRUE)

-                row_dend_slice = adjust_dend_by_x(row_dend_slice, x = slice_leaf_pos)

+                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"))

                 popViewport()

             }

+            upViewport()

         })

     }

@@ -1436,12 +1448,22 @@ setMethod(f = "make_layout",

         }

         column_dend_max_height = dend_heights(column_dend_slice) + max(dend_heights(object@column_dend_list))

         object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) {

+            if(column_dend_side == "top") {

+                pushViewport(viewport(y = DENDROGRAM_PADDING, height = unit(1, "npc") - DENDROGRAM_PADDING, just = "bottom"))

+            } else {

+                pushViewport(viewport(y = unit(0, "npc"), height = unit(1, "npc") - DENDROGRAM_PADDING, just = "bottom"))

+            }

             for(i in seq_len(nc_slice)) {

-                draw_dend(object, k = i, which = "column", x = slice_x[i], width = slice_width[i], just = "left")

+                draw_dend(object, k = i, which = "column", x = slice_x[i], width = slice_width[i], just = "left",

+                    max_height = column_dend_max_height)

             }

             if(nc_slice > 1) {

-                pushViewport(viewport(yscale = c(0, column_dend_max_height), height = unit(1, "npc") - DENDROGRAM_PADDING*2))

+                if(column_dend_side == "top") {

+                    pushViewport(viewport(yscale = c(0, column_dend_max_height)))

+                } else {

+                    pushViewport(viewport(yscale = c(0, column_dend_max_height)))

+                }

                 p = sapply(object@column_dend_list, function(x) {

                     attr(x, "x")/nobs(x)

                 })

@@ -1453,10 +1475,11 @@ setMethod(f = "make_layout",

                     slice_leaf_pos[i] = slice_leaf_pos[i] + slice_width[i]*p[i]

                 }

                 column_dend_slice = merge(column_dend_slice, object@column_dend_list, only_parent = TRUE)

-                column_dend_slice = adjust_dend_by_x(column_dend_slice, x = slice_leaf_pos)

+                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"))

                 popViewport()

             }

+            upViewport()

         })

     }

@@ -1517,8 +1540,9 @@ setMethod(f = "make_layout",

             object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) {

                 for(i in seq_len(nc_slice)) {

-                    draw_annotation(object, k = i, which = "top", x = slice_x[i], 

-                        width = slice_width[i], height = unit(1, "npc"), just = "left")

+                    draw_annotation(object, k = i, which = "top", x = slice_x[i], width = slice_width[i], 

+                        y = COLUMN_ANNO_PADDING, height = unit(1, "npc") - COLUMN_ANNO_PADDING, 

+                        just = c("left", "bottom"))

                 }

             }) 

         }

@@ -1534,8 +1558,9 @@ setMethod(f = "make_layout",

             object@layout$layout_index = rbind(object@layout$layout_index, column_anno_bottom = heatmap_layout_index("column_anno_bottom"))

             object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) {

                 for(i in seq_len(nc_slice)) {

-                    draw_annotation(object, k = i, which = "bottom", x = slice_x[i], 

-                        width = slice_width[i], height = unit(1, "npc"), just = "left")

+                    draw_annotation(object, k = i, which = "bottom", x = slice_x[i], width = slice_width[i], 

+                        y = unit(0, "npc"), height = unit(1, "npc") - COLUMN_ANNO_PADDING, 

+                        just = c("left", "bottom"))

                 }

             })

         }

@@ -1551,8 +1576,9 @@ setMethod(f = "make_layout",

             object@layout$layout_index = rbind(object@layout$layout_index, row_anno_left = heatmap_layout_index("row_anno_left"))

             object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) {

                     for(i in seq_len(nr_slice)) {

-                        draw_annotation(object, k = i, which = "left",  y = slice_y[i], 

-                            height = slice_height[i], width = unit(1, "npc"), just = "top") 

+                        draw_annotation(object, k = i, which = "left",  y = slice_y[i], height = slice_height[i], 

+                            x = unit(0, "npc"), width = unit(1, "npc") - ROW_ANNO_PADDING, 

+                            just = c("left", "top"))

                     }

                 }

             )

@@ -1569,8 +1595,9 @@ setMethod(f = "make_layout",

             object@layout$layout_index = rbind(object@layout$layout_index, row_anno_right = heatmap_layout_index("row_anno_right"))

             object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) {

                 for(i in seq_len(nr_slice)) {

-                    draw_annotation(object, k = i, which = "right", y = slice_y[i], 

-                        height = slice_height[i], width = unit(1, "npc"), just = "top")

+                    draw_annotation(object, k = i, which = "right", y = slice_y[i], height = slice_height[i], 

+                        x = ROW_ANNO_PADDING, width = unit(1, "npc") - ROW_ANNO_PADDING, 

+                        just = c("left", "top"))

                 }

             })

         }

@@ -1895,7 +1922,7 @@ R_binary = function() {

 setMethod(f = "draw_dend",

     signature = "Heatmap",

     definition = function(object,

-    which = c("row", "column"), k = 1, ...) {

+    which = c("row", "column"), k = 1, max_height = NULL, ...) {

     which = match.arg(which)[1]

@@ -1921,19 +1948,20 @@ setMethod(f = "draw_dend",

         return(invisible(NULL))

     }

-    max_height = dend_heights(dend)

+    if(is.null(max_height)) {

+        max_height = dend_heights(dend)

+    }

-    dend_padding = unit(1, "mm")

     if(side %in% c("left", "right")) {

         xscale = c(0, max_height)

         yscale = c(0, nobs(dend))

-        width = unit(1, "npc") - dend_padding*2

+        width = unit(1, "npc")

         height = unit(1, "npc")

         name = paste(object@name, "dend_row", k, sep = "_")

     } else {

         xscale = c(0, nobs(dend))

         yscale = c(0, max_height)

-        height = unit(1, "npc") - dend_padding*2

+        height = unit(1, "npc")

         width = unit(1, "npc")

         name = paste(object@name, "dend_column", k, sep = "_")

     }

@@ -104,7 +104,7 @@ HeatmapAnnotation = function(...,

 	fun_args = names(as.list(environment()))

-	verbose = ht_global_opt$verbose

+	verbose = ht_opt$verbose

 	.Object = new("HeatmapAnnotation")

@@ -266,8 +266,7 @@ setMethod(f = "make_layout",

     show_annotation_legend = TRUE, 

     annotation_legend_list = list(),

-    gap = unit(2, "mm"), 

-    ht_gap = gap, 

+    ht_gap = unit(2, "mm"), 

     main_heatmap = which(sapply(object@ht_list, inherits, "Heatmap"))[1],

     padding = NULL,

@@ -286,10 +285,8 @@ setMethod(f = "make_layout",

     row_dend_reorder = NULL,

     row_dend_gp = NULL,

     row_order = NULL,

-    km = NULL,

-    split = NULL,

-    row_km = km,

-    row_split = split,

+    row_km = NULL,

+    row_split = NULL,

     heatmap_body_height = NULL,

     column_gap = NULL,

@@ -301,11 +298,11 @@ setMethod(f = "make_layout",

     column_dend_reorder = NULL,

     column_dend_gp = NULL,

     column_order = NULL,

-    column_km = km,

+    column_km = NULL,

     column_split = NULL,

     heatmap_body_width = NULL) {

-    verbose = ht_global_opt("verbose")

+    verbose = ht_opt("verbose")

     if(object@layout$initialized) {

         if(verbose) qqcat("heatmap list is already initialized\n")

@@ -1014,33 +1011,96 @@ setMethod(f = "make_layout",

 setMethod(f = "draw",

     signature = "HeatmapList",

     definition = function(object, 

-        padding = NULL, 

-        newpage = TRUE,

-        row_title = character(0), 

-        row_title_side = c("left", "right"), 

-        row_title_gp = gpar(fontsize = 14),

-        column_title = character(0), 

-        column_title_side = c("top", "bottom"), 

-        column_title_gp = gpar(fontsize = 14), 

-        heatmap_legend_side = c("right", "left", "bottom", "top"), 

-        heatmap_legend_offset = unit(0, "mm"),

-        show_heatmap_legend = TRUE, 

-        heatmap_legend_list = list(),

-        annotation_legend_side = c("right", "left", "bottom", "top"), 

-        annotation_legend_offset = unit(0, "mm"),

-        show_annotation_legend = TRUE, 

-        annotation_legend_list = list(),

-        gap = unit(2, "mm"), 

-        main_heatmap = which(sapply(object@ht_list, inherits, "Heatmap"))[1],

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

-        row_sub_title_side = c("original", "left", "right"), ...) {

+    newpage = TRUE,

+

+    row_title = character(0), 

+    row_title_side = c("left", "right"), 

+    row_title_gp = gpar(fontsize = 14),

+    column_title = character(0), 

+    column_title_side = c("top", "bottom"), 

+    column_title_gp = gpar(fontsize = 14), 

+

+    heatmap_legend_side = c("right", "left", "bottom", "top"), 

+    heatmap_legend_offset = unit(0, "mm"),

+    merge_legends = FALSE,

+    show_heatmap_legend = TRUE, 

+    heatmap_legend_list = list(),

+    annotation_legend_side = c("right", "left", "bottom", "top"), 

+    annotation_legend_offset = unit(0, "mm"),

+    show_annotation_legend = TRUE, 

+    annotation_legend_list = list(),

+

+    gap = unit(2, "mm"), 

+    ht_gap = gap, 

+

+    main_heatmap = which(sapply(object@ht_list, inherits, "Heatmap"))[1],

+    padding = NULL,

+

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

+    row_sub_title_side = c("original", "left", "right"),

+    column_dend_side = c("original", "top", "bottom"),

+    column_sub_title_side = c("original", "top", "bottom"),

+    

+    row_gap = NULL,

+    cluster_rows = NULL,

+    clustering_distance_rows = NULL,

+    clustering_method_rows = NULL,

+    row_dend_width = NULL, 

+    show_row_dend = NULL, 

+    row_dend_reorder = NULL,

+    row_dend_gp = NULL,

+    row_order = NULL,

+    km = NULL,

+    split = NULL,

+    row_km = km,

+    row_split = split,

+    heatmap_body_height = NULL,

+

+    column_gap = NULL,

+    cluster_columns = NULL,

+    clustering_distance_columns = NULL,

+    clustering_method_columns = NULL,

+    column_dend_width = NULL, 

+    show_column_dend = NULL, 

+    column_dend_reorder = NULL,

+    column_dend_gp = NULL,

+    column_order = NULL,

+    column_km = NULL,

+    column_split = NULL,

+    heatmap_body_width = NULL,

+

+    ### global setting

+    heatmap_row_names_gp = NULL,

+    heatmap_column_names_gp = NULL,

+    heatmap_row_title_gp = NULL,

+    heatmap_column_title_gp = NULL,

+    legend_title_gp = NULL,

+    legend_title_position = NULL,

+    legend_labels_gp = NULL,

+    legend_grid_height = NULL,

+    legend_grid_width = NULL,

+    legend_grid_border = NULL,

+    fastcluster = NULL,

+    show_vp_border = NULL,

+    anno_simple_row_size = NULL

+    ) {

+

+    direction = object@direction

     l = sapply(object@ht_list, inherits, "Heatmap")

     if(! any(l)) {

-        stop("There should be at least one Heatmap in the heatmap list. You can add a matrix with zero column to the list.")

-    }

-    if(nrow(object@ht_list[[ which(l)[1] ]]@matrix) == 0 && length(l) > 1) {

-        stop("Since you have a zeor-row matrix, only one heatmap (no row annotation) is allowed.")

+        ob = sapply(object@ht_list, nobs)

+        ob = ob[!is.na(ob)]

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

+            stop("There is no heatmap in the list and cannot infer the number of observations in the heatmap annotations, please add a zero row/column matrix by hand.")

+        }

+        if(direction == "horizontal") {

+            nr = ob[1]

+            object = object + Heatmap(matrix(nc = 0, nr = nr))

+        } else {

+            nc = ob[1]

+            object = object %v% Heatmap(matrix(nr = 0, nc = nc))

+        }

     }

     if(newpage) {

@@ -1059,26 +1119,85 @@ setMethod(f = "draw",

     object = make_layout(

         object, 

         row_title = row_title, 

-        row_title_gp = row_title_gp, 

-        row_title_side = row_title_side,

+        row_title_side = row_title_side, 

+        row_title_gp = row_title_gp,

         column_title = column_title, 

         column_title_side = column_title_side, 

-        column_title_gp = column_title_gp,

+        column_title_gp = column_title_gp, 

+

         heatmap_legend_side = heatmap_legend_side, 

+        merge_legends = merge_legends,

         show_heatmap_legend = show_heatmap_legend, 

         heatmap_legend_list = heatmap_legend_list,

         annotation_legend_side = annotation_legend_side, 

-        show_annotation_legend = show_annotation_legend,

-        annotation_legend_list = annotation_legend_list, 

-        gap = gap, 

-        main_heatmap = main_heatmap, 

+        show_annotation_legend = show_annotation_legend, 

+        annotation_legend_list = annotation_legend_list,

+

+        ht_gap = ht_gap, 

+

+        main_heatmap = main_heatmap,

+        padding = padding,

+

         row_dend_side = row_dend_side,

-        row_sub_title_side = row_sub_title_side, 

-        padding = padding, 

-        ...

+        row_sub_title_side = row_sub_title_side,

+        column_dend_side = column_dend_side,

+        column_sub_title_side = column_sub_title_side,

+        

+        row_gap = row_gap,

+        cluster_rows = cluster_rows,

+        clustering_distance_rows = clustering_distance_rows,

+        clustering_method_rows = clustering_method_rows,

+        row_dend_width = row_dend_width, 

+        show_row_dend = show_row_dend, 

+        row_dend_reorder = row_dend_reorder,

+        row_dend_gp = row_dend_gp,

+        row_order = row_order,

+        row_km = row_km,

+        row_split = row_split,

+        heatmap_body_height = heatmap_body_height,

+

+        column_gap = column_gap,

+        cluster_columns = cluster_columns,

+        clustering_distance_columns = clustering_distance_columns,

+        clustering_method_columns = clustering_method_columns,

+        column_dend_width = column_dend_width, 

+        show_column_dend = show_column_dend, 

+        column_dend_reorder = column_dend_reorder,

+        column_dend_gp = column_dend_gp,

+        column_order = column_order,

+        column_km = column_km,

+        column_split = column_split,

+        heatmap_body_width = heatmap_body_width

     )

-    

+    verbose = ht_opt$verbose

+

+    ovl = list()

+    for(opt_nm in c("heatmap_row_names_gp",

+                    "heatmap_column_names_gp",

+                    "heatmap_row_title_gp",

+                    "heatmap_column_title_gp",

+                    "legend_title_gp",

+                    "legend_title_position",

+                    "legend_labels_gp",

+                    "legend_grid_height",

+                    "legend_grid_width",

+                    "legend_grid_border",

+                    "fastcluster",

+                    "show_vp_border",

+                    "anno_simple_row_size")) {

+        v = get(opt_nm, inherits = FALSE)

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

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

+            ht_opt[[opt_nm]] = v

+

+            if(verbose) qqcat("temporarily set the global parameter @{opt_nm}\n")

+        }

+    }

+    if(length(ovl)) {

+        on.exit(ht_opt(ovl))

+    }

+

     padding = object@ht_list_param$padding

     layout = grid.layout(nrow = length(HEATMAP_LIST_LAYOUT_COLUMN_COMPONENT), 

         ncol = length(HEATMAP_LAYOUT_ROW_COMPONENT), 

@@ -1178,7 +1297,7 @@ setMethod(f = "component_width",

                     if(inherits(ht, "Heatmap")) {

                         ht@heatmap_param$width

                     } else {

-                        ht@size

+                        size(ht)

                     }

                 })))

             if(is_abs_unit(width)) {

@@ -1223,7 +1342,7 @@ setMethod(f = "component_height",

                     if(inherits(ht, "Heatmap")) {

                         ht@heatmap_param$height

                     } else {

-                        ht@size

+                        size(ht)

                     }

                 })))

             if(is_abs_unit(height)) {

@@ -1243,7 +1362,7 @@ setMethod(f = "adjust_heatmap_list",

     signature = "HeatmapList",

     definition = function(object) {

-    verbose = ht_global_opt("verbose")

+    verbose = ht_opt("verbose")

     ## this function does mainly two things

     ## 1. calculate viewport/layout for individual heatmaps/annotations

@@ -1257,20 +1376,20 @@ setMethod(f = "adjust_heatmap_list",

     if(direction == "horizontal") {

         # adjust top anntatation, top annotation of all heatmaps should be aligned

-        max_top_anno_height = max(do.call("unit.c", lapply(object@ht_list[ht_index], function(ht) component_height(ht, "column_anno_top"))))

+        max_top_anno_height = max(do.call("unit.c", lapply(object@ht_list[ht_index], function(ht) component_height(ht, "column_anno_top")))) - COLUMN_ANNO_PADDING

         max_top_anno_height = convertHeight(max_top_anno_height, "mm")

-        max_bottom_anno_height = max(do.call("unit.c", lapply(object@ht_list[ht_index], function(ht) component_height(ht, "column_anno_bottom"))))

+        max_bottom_anno_height = max(do.call("unit.c", lapply(object@ht_list[ht_index], function(ht) component_height(ht, "column_anno_bottom")))) - COLUMN_ANNO_PADDING

         max_bottom_anno_height = convertHeight(max_bottom_anno_height, "mm")

         for(i in ht_index) {

             if(has_component(object@ht_list[[i]], "column_anno_top")) {

                 if(verbose) qqcat("adjust height of top annotation of heamtap @{object@ht_list[[i]]@name}\n")

                 object@ht_list[[i]]@top_annotation = resize(object@ht_list[[i]]@top_annotation, height = max_top_anno_height)

-                object@ht_list[[i]] = set_component_height(object@ht_list[[i]], "column_anno_top", object@ht_list[[i]]@top_annotation@height)

+                object@ht_list[[i]] = set_component_height(object@ht_list[[i]], "column_anno_top", object@ht_list[[i]]@top_annotation@height + COLUMN_ANNO_PADDING)

             }

             if(has_component(object@ht_list[[i]], "column_anno_bottom")) {   

                 if(verbose) qqcat("adjust height of bottom annotation of heamtap @{object@ht_list[[i]]@name}\n")

                 object@ht_list[[i]]@bottom_annotation = resize(object@ht_list[[i]]@bottom_annotation, height = max_bottom_anno_height)

-                object@ht_list[[i]] = set_component_height(object@ht_list[[i]], "column_anno_bottom", object@ht_list[[i]]@bottom_annotation@height)

+                object@ht_list[[i]] = set_component_height(object@ht_list[[i]], "column_anno_bottom", object@ht_list[[i]]@bottom_annotation@height + COLUMN_ANNO_PADDING)

             }

         }

@@ -1331,7 +1450,7 @@ setMethod(f = "adjust_heatmap_list",

                     total_null_units_lt = c(total_null_units_lt, list(ht@matrix_param$width))

                 }

             } else {

-                total_fixed_width = total_fixed_width + ht@size

+                total_fixed_width = total_fixed_width + size(ht)

             }

         }

         if(n > 1) {

@@ -1346,7 +1465,7 @@ setMethod(f = "adjust_heatmap_list",

                 if(inherits(ht, "Heatmap")) {

                     ht@heatmap_param$width

                 } else {

-                    ht@size

+                    size(ht)

                 }

             })

         } else {

@@ -1360,7 +1479,7 @@ setMethod(f = "adjust_heatmap_list",

                         sum(component_width(ht, setdiff(names(HEATMAP_LAYOUT_ROW_COMPONENT), "heatmap_body"))) + ht@matrix_param$width[[1]]*unit_per_null

                     }

                 } else {

-                    ht@size

+                    size(ht)

                 }

             })

         }

@@ -1394,20 +1513,20 @@ setMethod(f = "adjust_heatmap_list",

         }

     } else {

         # adjust left anntatation, right annotation of all heatmaps should be aligned

-        max_left_anno_width = max(do.call("unit.c", lapply(object@ht_list[ht_index], function(ht) component_width(ht, "row_anno_left"))))

+        max_left_anno_width = max(do.call("unit.c", lapply(object@ht_list[ht_index], function(ht) component_width(ht, "row_anno_left")))) - ROW_ANNO_PADDING

         max_left_anno_width = convertWidth(max_left_anno_width, "mm")

-        max_right_anno_width = max(do.call("unit.c", lapply(object@ht_list[ht_index], function(ht) component_width(ht, "row_anno_right"))))

+        max_right_anno_width = max(do.call("unit.c", lapply(object@ht_list[ht_index], function(ht) component_width(ht, "row_anno_right")))) - ROW_ANNO_PADDING

         max_right_anno_width = convertWidth(max_right_anno_width, "mm")

         for(i in ht_index) {

             if(has_component(object@ht_list[[i]], "row_anno_left")) {

                 if(verbose) qqcat("adjust width of left annotation of heamtap @{object@ht_list[[i]]@name}\n")

                 object@ht_list[[i]]@left_annotation = resize(object@ht_list[[i]]@left_annotation, width = max_left_anno_width)

-                object@ht_list[[i]] = set_component_width(object@ht_list[[i]], "row_anno_left", object@ht_list[[i]]@left_annotation@width)

+                object@ht_list[[i]] = set_component_width(object@ht_list[[i]], "row_anno_left", object@ht_list[[i]]@left_annotation@width + ROW_ANNO_PADDING)

             }

             if(has_component(object@ht_list[[i]], "row_anno_right")) {   

                 if(verbose) qqcat("adjust width of right annotation of heamtap @{object@ht_list[[i]]@name}\n")

                 object@ht_list[[i]]@right_annotation = resize(object@ht_list[[i]]@right_annotation, width = max_right_anno_width)

-                object@ht_list[[i]] = set_component_width(object@ht_list[[i]], "row_anno_right", object@ht_list[[i]]@right_annotation@width)

+                object@ht_list[[i]] = set_component_width(object@ht_list[[i]], "row_anno_right", object@ht_list[[i]]@right_annotation@width + ROW_ANNO_PADDING)

             }

         }

@@ -1467,7 +1586,7 @@ setMethod(f = "adjust_heatmap_list",

                     total_null_units_lt = c(total_null_units_lt, list(ht@matrix_param$height))

                 }

             } else {

-                total_fixed_height = total_fixed_height + ht@size

+                total_fixed_height = total_fixed_height + size(ht)

             }

         }

         if(n > 1) {

@@ -1482,7 +1601,7 @@ setMethod(f = "adjust_heatmap_list",

                 if(inherits(ht, "Heatmap")) {

                     ht@heatmap_param$height

                 } else {

-                    ht@size

+                    size(ht)

                 }

             })

         } else {

@@ -1496,7 +1615,7 @@ setMethod(f = "adjust_heatmap_list",

                         sum(component_height(ht, setdiff(names(HEATMAP_LAYOUT_COLUMN_COMPONENT), "heatmap_body"))) + ht@matrix_param$height[[1]]*unit_per_null

                     }

                 } else {

-                    ht@size

+                    size(ht)

                 }

             })

         }

@@ -1624,9 +1743,9 @@ setMethod(f = "draw_heatmap_list",

                 draw(ht, internal = TRUE)

             } else if(inherits(ht, "HeatmapAnnotation")) {

                 # calcualte the position of the heatmap body

-                pushViewport(viewport(x = max_bottom_component_width, width = unit(1, "npc") - max_left_component_width - max_right_component_width, just = c("left")))

+                pushViewport(viewport(x = max_left_component_width, width = unit(1, "npc") - max_left_component_width - max_right_component_width, just = c("left")))

                 for(j in seq_len(n_slice)) {

-                    draw(ht, index = ht_main@row_order_list[[j]], x = slice_x[j], width = slice_width[j], just = slice_just[2], k = j, n = n_slice)

+                    draw(ht, index = ht_main@column_order_list[[j]], x = slice_x[j], width = slice_width[j], just = slice_just[1], k = j, n = n_slice)

                 }

                 upViewport()

             }

@@ -1757,18 +1876,18 @@ setMethod(f = "draw_heatmap_legend",

     if(side != annotation_legend_side) {

         y = unit(0.5, "npc")

-        pushViewport(viewport(x = unit(0.5, "npc"), y = y + offset, width = size[1], height = size[2], just = c("center", "center")))

+        pushViewport(viewport(name = "heatmap_legend", x = unit(0.5, "npc"), y = y + offset, width = size[1], height = size[2], just = c("center", "center")))

     } else {

         if(side %in% c("left", "right")) {

             y1 = unit(0.5, "npc") + size[2]*0.5  # top of heatmap legend

             y2 = unit(0.5, "npc") + annotation_legend_size[2]*0.5

             y = max(y1, y2)

-            pushViewport(viewport(x = unit(0.5, "npc"), y = y + offset, width = size[1], height = size[2], just = c("center", "top")))           

+            pushViewport(viewport(name = "heatmap_legend", x = unit(0.5, "npc"), y = y + offset, width = size[1], height = size[2], just = c("center", "top")))           

         } else {

             x1 = unit(0.5, "npc") - size[1]*0.5  # top of heatmap legend

             x2 = unit(0.5, "npc") - annotation_legend_size[1]*0.5

             x = min(x1, x2)

-            pushViewport(viewport(x = x, y = unit(0.5, "npc") + offset, width = size[1], height = size[2], just = c("left", "center")))           

+            pushViewport(viewport(name = "heatmap_legend", x = x, y = unit(0.5, "npc") + offset, width = size[1], height = size[2], just = c("left", "center")))           

         }

     }

     draw_legend(ColorMappingList, ColorMappingParamList, side = side, legend_list = legend_list, padding = padding, ...)

@@ -151,21 +151,21 @@ SingleAnnotation = function(name, value, col, fun,

     .ENV$current_annotation_which = which

     on.exit(.ENV$current_SingleAnnotation_which <- NULL)

-    verbose = ht_global_opt$verbose

+    verbose = ht_opt$verbose

     # re-define some of the argument values according to global settings

     called_args = names(as.list(match.call())[-1])

     if("legend_param" %in% called_args) {

         for(opt_name in setdiff(c("title_gp", "title_position", "labels_gp", "grid_width", "grid_height", "grid_border"), names(legend_param))) {

-            opt_name2 = paste0("annotation_legend_", opt_name)

-            if(!is.null(ht_global_opt(opt_name2)))

-                legend_param[[opt_name]] = ht_global_opt(opt_name2)

+            opt_name2 = paste0("legend_", opt_name)

+            if(!is.null(ht_opt(opt_name2)))

+                legend_param[[opt_name]] = ht_opt(opt_name2)

         }

     } else {

         for(opt_name in c("title_gp", "title_position", "labels_gp", "grid_width", "grid_height", "grid_border")) {

-            opt_name2 = paste0("annotation_legend_", opt_name)

-            if(!is.null(ht_global_opt(opt_name2)))

-                legend_param[[opt_name]] = ht_global_opt(opt_name2)

+            opt_name2 = paste0("legend_", opt_name)

+            if(!is.null(ht_opt(opt_name2)))

+                legend_param[[opt_name]] = ht_opt(opt_name2)

         }

     }

@@ -525,7 +525,7 @@ setMethod(f = "draw",

         test2 = test

     }

-    verbose = ht_global_opt$verbose

+    verbose = ht_opt$verbose

     ## it draws annotation names, create viewports with names

     if(test2) {

@@ -560,6 +560,7 @@ setMethod(f = "draw",

         fun = object@fun

         if(verbose) qqcat("adjust annotation axis\n")

         if(!is.null(fun@var_env$axis)) {

+            axis_ov = fun@var_env$axis

             if(fun@var_env$axis && n > 1) {

                 if(object@which == "row") {

                     if(k == n && fun@var_env$axis_param$side == "bottom") {

@@ -581,6 +582,9 @@ setMethod(f = "draw",

             }

         }

         draw(fun, index = index)

+        if(!is.null(fun@var_env$axis)) {

+            fun@var_env$axis = axis_ov

+        }

     } else {

         if(verbose) qqcat("execute user-defined annotation function\n")

         object@fun(index, k, n)

@@ -71,41 +71,27 @@ ht_global_opt = setGlobalOptions(

 	heatmap_column_title_gp = list(

 		.value = NULL,

 		.class = "gpar"),

-	heatmap_legend_title_gp = list(

+	legend_title_gp = list(

 		.value = NULL,

 		.class = "gpar"),

-	heatmap_legend_title_position = list(

+	legend_title_position = list(

 		.value = NULL,

 		.class = "character"),

-	heatmap_legend_labels_gp = list(

+	legend_labels_gp = list(

 		.value = NULL,

 		.class = "gpar"),

-	heatmap_legend_grid_height = list(

+	legend_grid_height = list(

 		.value = NULL,

 		.class = "unit"),

-	heatmap_legend_grid_width = list(

+	legend_grid_width = list(

 		.value = NULL,

 		.class = "unit"),

-	heatmap_legend_grid_border = list(

+	legend_grid_border = list(

 		.value = NULL),

-	annotation_legend_title_gp = list(

-		.value = NULL,

-		.class = "gpar"),

-	annotation_legend_title_position = list(

-		.value = NULL,

-		.class = "character"),

-	annotation_legend_labels_gp = list(

-		.value = NULL,

-		.class = "gpar"),

-	annotation_legend_grid_height = list(

-		.value = NULL,

-		.class = "unit"),

-	annotation_legend_grid_width = list(

-		.value = NULL,

-		.class = "unit"),

-	annotation_legend_grid_border = list(

+	border = list(

 		.value = NULL),

+

 	fast_hclust = list(

 		.value = FALSE,

 		.class = "logical",

@@ -136,11 +122,11 @@ ht_opt = ht_global_opt

 .ENV$row_pos = NULL

-DENDROGRAM_PADDING = unit(1, "mm")

+DENDROGRAM_PADDING = unit(0.5, "mm")

 DIMNAME_PADDING = unit(1, "mm")

 TITLE_PADDING = unit(2.5, "mm")

-COLUMN_ANNO_PADDING = unit(1, "mm")

-ROW_ANNO_PADDING = unit(1, "mm")

+COLUMN_ANNO_PADDING = unit(0.5, "mm")

+ROW_ANNO_PADDING = unit(0.5, "mm")

@@ -386,7 +386,9 @@ upViewport = function(...) {

     if(ht_global_opt$show_vp_border) {

         grid.rect(gp = gpar(fill = "transparent", col = "black", lty = 3))

         vpname = current.viewport()$name

-        add_vp_name(vpname)

+        if(!grepl("^GRID.VP", vpname)) {

+            add_vp_name(vpname)

+        }

     }

     grid::upViewport(...)

 }

@@ -395,7 +397,9 @@ popViewport = function(...) {

     if(ht_global_opt$show_vp_border) {

         grid.rect(gp = gpar(fill = "transparent", col = "black", lty = 3))

         vpname = current.viewport()$name

-        add_vp_name(vpname)

+        if(!grepl("^GRID.VP", vpname)) {

+            add_vp_name(vpname)

+        }

     }

     grid::popViewport(...)

 }