@@ -6,4 +6,5 @@ check.bat

 ^\.Rproj\.user$

 .travis.yml

 vignettes_old

+revdep/

@@ -1,8 +1,8 @@

 Package: ComplexHeatmap

 Type: Package

 Title: Make Complex Heatmaps

-Version: 1.99.3

-Date: 2018-11-28

+Version: 1.99.4

+Date: 2018-12-7

 Author: Zuguang Gu

 Maintainer: Zuguang Gu <z.gu@dkfz.de>

 Depends: R (>= 3.1.2), methods, grid, graphics, stats, grDevices

@@ -1,3 +1,9 @@

+CHANGES in VERSION 1.99.4

+

+* anno_mark() is now calculated in multiple slices.

+

+========================

+

 CHANGES in VERSION 1.99.1

 * add `cluster_row_slices` and `cluster_column_slices` arguments in `Heatmap()`.

@@ -2676,6 +2676,9 @@ anno_mark = function(at, labels, which = c("column", "row"),

 		width = unit(1, "npc")

 	}

+	.pos = NULL

+	.scale = NULL

+

 	# a map between row index and positions

 	# pos_map = 

 	row_fun = function(index) {

@@ -2690,27 +2693,35 @@ anno_mark = function(at, labels, which = c("column", "row"),

 		labels_gp = subset_gp(labels_gp, labels2index[labels])

 		link_gp = subset_gp(link_gp, labels2index[labels])

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

+		if(is.null(.scale)) {

+			.scale = c(0.5, n+0.5)

+		}

+		pushViewport(viewport(xscale = c(0, 1), yscale = .scale))

 		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 - extend[1], n+0.5 + extend[2])))

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

+		if(is.null(.pos)) {

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

+			pos = n-i2+1 # position of rows

+		} else {

+			pos = .pos[rev(which(index %in% at))]

+		}

+		h1 = pos - text_height*0.5

+		h2 = pos + text_height*0.5

+		pos_adjusted = rev(smartAlign(h1, h2, c(.scale[1] - extend[1], .scale[2] + extend[2])))

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

 		n2 = length(labels)

 		if(side == "right") {

 			grid.text(labels, rep(link_width, n2), h, default.units = "native", gp = labels_gp, just = "left")

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

-			grid.segments(unit(rep(0, n2), "npc"), n-i2+1, rep(link_width*(1/3), n2), n-i2+1, default.units = "native", gp = link_gp)

-			grid.segments(rep(link_width*(1/3), n2), n-i2+1, rep(link_width*(2/3), n2), h, default.units = "native", gp = link_gp)

+			grid.segments(unit(rep(0, n2), "npc"), pos, rep(link_width*(1/3), n2), pos, default.units = "native", gp = link_gp)

+			grid.segments(rep(link_width*(1/3), n2), pos, rep(link_width*(2/3), n2), h, default.units = "native", gp = link_gp)

 			grid.segments(rep(link_width*(2/3), n2), h, rep(link_width, n2), h, default.units = "native", gp = link_gp)

 		} else {

 			grid.text(labels, unit(1, "npc")-rep(link_width, n2), h, default.units = "native", gp = labels_gp, just = "right")

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

-			grid.segments(unit(rep(1, n2), "npc"), n-i2+1, unit(1, "npc")-rep(link_width*(1/3), n2), n-i2+1, default.units = "native", gp = link_gp)

-			grid.segments(unit(1, "npc")-rep(link_width*(1/3), n2), n-i2+1, unit(1, "npc")-rep(link_width*(2/3), n2), h, default.units = "native", gp = link_gp)

+			grid.segments(unit(rep(1, n2), "npc"), pos, unit(1, "npc")-rep(link_width*(1/3), n2), pos, default.units = "native", gp = link_gp)

+			grid.segments(unit(1, "npc")-rep(link_width*(1/3), n2), pos, unit(1, "npc")-rep(link_width*(2/3), n2), h, default.units = "native", gp = link_gp)

 			grid.segments(unit(1, "npc")-rep(link_width*(2/3), n2), h, unit(1, "npc")-rep(link_width, n2), h, default.units = "native", gp = link_gp)

 		}

 		upViewport()

@@ -2720,38 +2731,43 @@ anno_mark = function(at, labels, which = c("column", "row"),

 		# adjust at and labels

 		at = intersect(index, at)

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

+			return(NULL)

+		}

 		labels = at2labels[as.character(at)]

 		labels_gp = subset_gp(labels_gp, labels2index[labels])

-		lines_gp = subset_gp(lines_gp, labels2index[labels])

+		link_gp = subset_gp(link_gp, labels2index[labels])

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

+		if(is.null(.scale)) {

+			.scale = c(0.5, n+0.5)

+		}

+		pushViewport(viewport(yscale = c(0, 1), xscale = .scale))

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

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

-		i2 = which(index %in% at)

-		h1 = i2 - text_height*0.5

-		h2 = i2 + text_height*0.5

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

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

-		if(is.null(link_width)) {

-			if(convertHeight(unit(1, "npc") - max_text_width(labels, gp = labels_gp), "mm", valueOnly = TRUE) < 0) {

-				link_width = unit(0.5, "npc")

-			} else {

-				link_width = unit(1, "npc") - max_text_width(labels, gp = labels_gp)

-			}

+		if(is.null(.pos)) {

+			i2 = which(index %in% at)

+			pos = i2 # position of rows

+		} else {

+			pos = .pos[which(index %in% at)]

 		}

+		h1 = pos - text_height*0.5

+		h2 = pos + text_height*0.5

+		pos_adjusted = smartAlign(h1, h2, c(.scale[1] - extend[1], .scale[2] + extend[2]))

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

+

 		n2 = length(labels)

 		if(side == "top") {

 			grid.text(labels, h, rep(link_width, n2), default.units = "native", gp = labels_gp, rot = 90, just = "left")

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

-			grid.segments(i2, unit(rep(0, n2), "npc"), i2, rep(link_width*(1/3), n2), default.units = "native", gp = link_gp)

-			grid.segments(i2, rep(link_width*(1/3), n2), h, rep(link_width*(2/3), n2), default.units = "native", gp = link_gp)

+			grid.segments(pos, unit(rep(0, n2), "npc"), pos, rep(link_width*(1/3), n2), default.units = "native", gp = link_gp)

+			grid.segments(pos, rep(link_width*(1/3), n2), h, rep(link_width*(2/3), n2), default.units = "native", gp = link_gp)

 			grid.segments(h, rep(link_width*(2/3), n2), h, rep(link_width, n), default.units = "native", gp = link_gp)

 		} else {

 			grid.text(labels, h, rep(max_text_width(labels, gp = labels_gp), n2), default.units = "native", gp = labels_gp, rot = 90, just = "right")

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

-			grid.segments(i2, unit(rep(1, n2), "npc"), i2, unit(1, "npc")-rep(link_width*(1/3), n2), default.units = "native", gp = link_gp)

-			grid.segments(i2, unit(1, "npc")-rep(link_width*(1/3), n2), h, unit(1, "npc")-rep(link_width*(2/3), n2), default.units = "native", gp = link_gp)

+			grid.segments(pos, unit(rep(1, n2), "npc"), pos, unit(1, "npc")-rep(link_width*(1/3), n2), default.units = "native", gp = link_gp)

+			grid.segments(pos, unit(1, "npc")-rep(link_width*(1/3), n2), h, unit(1, "npc")-rep(link_width*(2/3), n2), default.units = "native", gp = link_gp)

 			grid.segments(h, unit(1, "npc")-rep(link_width*(2/3), n2), h, unit(1, "npc")-rep(link_width, n2), default.units = "native", gp = link_gp)

 		}

 		upViewport()

@@ -2770,7 +2786,7 @@ anno_mark = function(at, labels, which = c("column", "row"),

 		width = width,

 		height = height,

 		n = -1,

-		var_import = list(at, labels2index, at2labels, link_gp, labels_gp, padding, 

+		var_import = list(at, labels2index, at2labels, link_gp, labels_gp, padding, .pos, .scale,

 			side, link_width, extend),

 		show_name = FALSE

 	)

@@ -602,6 +602,12 @@ Heatmap = function(matrix, col, name,

         if(is.character(row_order)) {

             row_order = structure(seq_len(nrow(matrix)), names = rownames(matrix))[row_order]

         }

+        if(any(is.na(row_order))) {

+            stop_wrap("`row_order` should not contain NA values.")

+        }

+        if(length(row_order) != nrow(matrix)) {

+            stop_wrap("length of `row_order` should be same as the number of marix rows.")

+        }

         .Object@row_order = row_order

     }

     .Object@row_dend_param$cluster_slices = cluster_row_slices

@@ -647,6 +653,12 @@ Heatmap = function(matrix, col, name,

         if(is.character(column_order)) {

             column_order = structure(seq_len(ncol(matrix)), names = colnames(matrix))[column_order]

         }

+        if(any(is.na(column_order))) {

+            stop_wrap("`column_order` should not contain NA values.")

+        }

+        if(length(column_order) != ncol(matrix)) {

+            stop_wrap("length of `column_order` should be same as the number of marix columns")

+        }

         .Object@column_order = column_order

     }

     .Object@column_dend_param$cluster_slices = cluster_column_slices

@@ -500,7 +500,73 @@ setMethod(f = "draw_annotation",

         n = length(object@row_order_list)

     }

+    ## deal with the special anno_mark

+    anno_mark_param = list()

+    if(which %in% c("left", "right")) {

+        slice_y = object@layout$slice$y

+        n_slice = length(slice_y)

+        slice_height = object@layout$slice$height

+

+        if(n_slice > 1) {

+            all_anno_type = anno_type(annotation)

+            if("anno_mark" %in% all_anno_type) {

+                ## only make the anno_mark annotation

+                ro_lt = object@row_order_list

+                # calcualte the position of each row with taking "gaps" into account

+                .scale = c(0, 1)

+

+                .pos = NULL

+                for(i in seq_along(ro_lt)) {

+                    # assume slices are align to top `slice_just` contains "top"

+                    .pos1 = slice_y[i] - (seq_along(ro_lt[[i]]) - 0.5)/length(ro_lt[[i]]) * slice_height[i]

+                    .pos1 = convertY(.pos1, "native", valueOnly = TRUE)

+                    .pos = c(.pos, .pos1)

+                }

+

+                anno_mark_param$.scale = .scale

+                anno_mark_param$.pos = .pos

+                anno_mark_param$index = unlist(ro_lt)

+                

+                anno_mark_param$vp_height = convertHeight(unit(1, "npc"), "cm")

+                anno_mark_param$vp_width = unit(1, "npc")

+                anno_mark_param$vp_just = "top"

+                anno_mark_param$vp_x = unit(0.5, "npc")

+                anno_mark_param$vp_y = unit(1, "npc")

+            }

+        }

+    } else {

+        slice_x = object@layout$slice$x

+        n_slice = length(slice_x)

+        slice_width = object@layout$slice$width

+

+        if(n_slice > 1) {

+            all_anno_type = anno_type(annotation)

+            if("anno_mark" %in% all_anno_type) {

+                ## only make the anno_mark annotation

+                co_lt = object@column_order_list

+                .scale = c(0, 1)

+

+                .pos = NULL

+                for(i in seq_along(co_lt)) {

+                    .pos1 = slice_x[i] + (seq_along(co_lt[[i]]) - 0.5)/length(co_lt[[i]]) * slice_width[i]

+                    .pos1 = convertX(.pos1, "native", valueOnly = TRUE)

+                    .pos = c(.pos, .pos1)

+                }

+

+                anno_mark_param$.scale = .scale

+                anno_mark_param$.pos = .pos

+                anno_mark_param$index = unlist(co_lt)

+                

+                anno_mark_param$vp_height = unit(1, "npc")

+                anno_mark_param$vp_width = convertWidth(unit(1, "npc"), "cm")

+                anno_mark_param$vp_just = "left"

+                anno_mark_param$vp_x = unit(0, "npc")

+                anno_mark_param$vp_y = unit(0.5, "npc")

+            }

+        }

+    }

+

     pushViewport(viewport(...))

-    draw(annotation, index = index, k = k, n = n)

+    draw(annotation, index = index, k = k, n = n, anno_mark_param = anno_mark_param)

     upViewport()

 })

@@ -553,6 +553,8 @@ setMethod(f = "get_legend_param_list",

 # -n Total number of slices.

 # -... Pass to `grid::viewport` which contains all the annotations.

 # -test Is it in test mode? The value can be logical or a text which is plotted as the title of plot.

+# -anno_mark_param It contains specific parameters for drawing `anno_mark` and pass to the

+#     `draw,SingleAnnotation-method`.

 #

 # == value

 # No value is returned.

@@ -563,7 +565,7 @@ setMethod(f = "get_legend_param_list",

 setMethod(f = "draw",

 	signature = "HeatmapAnnotation",

 	definition = function(object, index, k = 1, n = 1, ..., 

-		test = FALSE) {

+		test = FALSE, anno_mark_param = list()) {

 	which = object@which

 	n_anno = length(object@anno_list)

@@ -609,21 +611,23 @@ setMethod(f = "draw",

 		for(i in seq_len(n_anno)) {

 			pushViewport(viewport(y = sum(anno_size[seq(i, n_anno)]) + sum(gap[seq(i, n_anno)]) - gap[n_anno], 

 				height = anno_size[i], just = c("center", "top")))

-			oe = try(draw(object@anno_list[[i]], index, k, n))

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

-				cat("Error when drawing annotation '", object@anno_list[[i]]@name, "'\n", sep = "")

-				stop_wrap(oe)

-			}

+			draw(object@anno_list[[i]], index, k, n, anno_mark_param = anno_mark_param)

+			# oe = try(draw(object@anno_list[[i]], index, k, n))

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

+			# 	cat("Error when drawing annotation '", object@anno_list[[i]]@name, "'\n", sep = "")

+			# 	stop_wrap(oe)

+			# }

 			upViewport()

 		}

 	} else if(which == "row") {

 		for(i in seq_len(n_anno)) {

 			pushViewport(viewport(x = sum(anno_size[seq_len(i)]) + sum(gap[seq_len(i)]) - gap[i], width = anno_size[i], just = c("right", "center")))

-			oe = try(draw(object@anno_list[[i]], index, k, n))

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

-				cat("Error when drawing annotation '", object@anno_list[[i]]@name, "'\n", sep = "")

-				stop_wrap(oe)

-			}

+			draw(object@anno_list[[i]], index, k, n, anno_mark_param = anno_mark_param)

+			# oe = try(draw(object@anno_list[[i]], index, k, n))

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

+			# 	cat("Error when drawing annotation '", object@anno_list[[i]]@name, "'\n", sep = "")

+			# 	stop_wrap(oe)

+			# }

 			upViewport()

 		}

 	}

@@ -913,6 +917,10 @@ names.HeatmapAnnotation = function(x) {

 	return(x)

 }

+anno_type = function(ha) {

+	sapply(ha@anno_list, function(x) x@fun@fun_name)

+}

+

 # == title

 # Subset the HeatmapAnnotation object

@@ -596,16 +596,47 @@ setMethod(f = "draw_heatmap_list",

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

                 draw(ht, internal = TRUE)

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

+                # if the HeatmapAnnotation contains anno_mark() and it is split into more than one slices

+                anno_mark_param = list()

+                if(n_slice > 1) {

+                    all_anno_type = anno_type(ht)

+                    if("anno_mark" %in% all_anno_type) {

+                        ## only make the anno_mark annotation

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

+                        ro_lt = ht_main@row_order_list

+                        # calcualte the position of each row with taking "gaps" into account

+                        .scale = c(0, 1)

+

+                        .pos = NULL

+                        for(i in seq_along(ro_lt)) {

+                            # assume slices are align to top `slice_just` contains "top"

+                            .pos1 = slice_y[i] - (seq_along(ro_lt[[i]]) - 0.5)/length(ro_lt[[i]]) * slice_height[i]

+                            .pos1 = convertY(.pos1, "native", valueOnly = TRUE)

+                            .pos = c(.pos, .pos1)

+                        }

+

+                        anno_mark_param$.scale = .scale

+                        anno_mark_param$.pos = .pos

+                        anno_mark_param$index = unlist(ro_lt)

+                        

+                        anno_mark_param$vp_height = convertHeight(unit(1, "npc"), "cm")

+                        anno_mark_param$vp_width = unit(1, "npc")

+                        anno_mark_param$vp_just = "top"

+                        anno_mark_param$vp_x = unit(0.5, "npc")

+                        anno_mark_param$vp_y = unit(1, "npc")

+                        popViewport()

+                    }

+                }

+

                 # calcualte the position of the heatmap body

                 pushViewport(viewport(y = max_bottom_component_height, height = unit(1, "npc") - max_top_component_height - max_bottom_component_height, just = c("bottom")))

                 for(j in seq_len(n_slice)) {

-                    draw(ht, index = ht_main@row_order_list[[j]], y = slice_y[j], height = slice_height[j], just = slice_just[2], k = j, n = n_slice)

+                    draw(ht, index = ht_main@row_order_list[[j]], y = slice_y[j], height = slice_height[j], just = slice_just[2], k = j, n = n_slice, anno_mark_param = anno_mark_param)

                 }

                 upViewport()

             }

             upViewport()

         }

-

         upViewport()

     } else {

         heatmap_height = object@layout$heatmap_height

@@ -653,10 +684,41 @@ setMethod(f = "draw_heatmap_list",

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

                 draw(ht, internal = TRUE)

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

+                # if the HeatmapAnnotation contains anno_mark() and it is split into more than one slices

+                anno_mark_param = list()

+                if(n_slice > 1) {

+                    all_anno_type = anno_type(ht)

+                    if("anno_mark" %in% all_anno_type) {

+                        ## only make the anno_mark annotation

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

+                        co_lt = ht_main@column_order_list

+                        .scale = c(0, 1)

+

+                        .pos = NULL

+                        for(i in seq_along(co_lt)) {

+                            # assume slices are align to left, `slice_just` contains "left"

+                            .pos1 = slice_x[i] + (seq_along(co_lt[[i]]) - 0.5)/length(co_lt[[i]]) * slice_width[i]

+                            .pos1 = convertX(.pos1, "native", valueOnly = TRUE)

+                            .pos = c(.pos, .pos1)

+                        }

+

+                        anno_mark_param$.scale = .scale

+                        anno_mark_param$.pos = .pos

+                        anno_mark_param$index = unlist(co_lt)

+                        

+                        anno_mark_param$vp_height = unit(1, "npc")

+                        anno_mark_param$vp_width = convertWidth(unit(1, "npc"), "cm")

+                        anno_mark_param$vp_just = "left"

+                        anno_mark_param$vp_x = unit(0, "npc")

+                        anno_mark_param$vp_y = unit(0.5, "npc")

+                        popViewport()

+                    }

+                }

+

                 # calcualte the position of the heatmap body

                 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@column_order_list[[j]], x = slice_x[j], width = slice_width[j], just = slice_just[1], 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, anno_mark_param = anno_mark_param)

                 }

                 upViewport()

             }

@@ -226,6 +226,9 @@ setMethod(f = "make_layout",

                 if(length(row_split) > 1 && length(row_split) != ht_nr) {

                     stop_wrap("`row_split` should have same length as nrow of the main matrix.")

                 }

+                if(length(row_split) == 1 && !object@ht_list[[i_main]]@row_dend_param$cluster) {

+                    stop_wrap("Since there is no row clustering for the main heatmap, `row_split` is not allowed to set as a single number.")

+                }

             }

         }

         if(!is.null(row_km)) {

@@ -296,6 +299,12 @@ setMethod(f = "make_layout",

             if(verbose) qqcat("set row_dend_reorder to main heatmap\n")

         }

         if(!is.null(row_order)) {

+            if(any(is.na(row_order))) {

+                stop_wrap("`row_order` should not contain NA values.")

+            }

+            if(length(row_order) != nrow(object@ht_list[[i_main]]@matrix)) {

+                stop_wrap("length of `row_order` should be same as the number of main marix rows.")

+            }

             if(is.character(row_order)) {

                 row_order = structure(seq_len(nrow(object@ht_list[[i_main]]@matrix)), names = rownames(object@ht_list[[i_main]]@matrix))[row_order]

             }

@@ -345,6 +354,9 @@ setMethod(f = "make_layout",

                 if(length(column_split) > 1 && length(column_split) != ht_nr) {

                     stop_wrap("`column_split` should have same length as ncol of the main matrix.")

                 }

+                if(length(column_split) == 1 && !object@ht_list[[i_main]]@column_dend_param$cluster) {

+                    stop_wrap("Since there is no column clustering for the main heatmap, `column_split` is not allowed to set as a single number.")

+                }

             }

         }

         if(!is.null(column_km)) {

@@ -415,6 +427,12 @@ setMethod(f = "make_layout",

             if(verbose) qqcat("set column_dend_reorder to main heatmap\n")

         }

         if(!is.null(column_order)) {

+            if(any(is.na(column_order))) {

+                stop_wrap("`column_order` should not contain NA values.")

+            }

+            if(length(column_order) != ncol(object@ht_list[[i_main]]@matrix)) {

+                stop_wrap("length of `column_order` should be same as the number of main marix columns.")

+            }

             if(is.character(column_order)) {

                 column_order = structure(seq_len(ncol(object@ht_list[[i_main]]@matrix)), names = colnames(object@ht_list[[i_main]]@matrix))[column_order]

             }

@@ -529,6 +529,7 @@ SingleAnnotation = function(name, value, col, fun,

 # -n Total number of slices. ``k`` and ``n`` are used to adjust annotation names. E.g.

 #    if ``k`` is 2 and ``n`` is 3, the annotation names are not drawn.

 # -test Is it in test mode? The value can be logical or a text which is plotted as the title of plot.

+# -anno_mark_param It contains specific parameters for drawing `anno_mark`.

 #

 # == value

 # No value is returned.

@@ -538,7 +539,23 @@ SingleAnnotation = function(name, value, col, fun,

 #

 setMethod(f = "draw",

 	signature = "SingleAnnotation",

-	definition = function(object, index, k = 1, n = 1, test = FALSE) {

+	definition = function(object, index, k = 1, n = 1, test = FALSE,

+        anno_mark_param = list()) {

+

+    ## make the special anno_mark when the anotation is split

+    if(object@fun@fun_name == "anno_mark" && length(anno_mark_param) > 0) {

+        if(k > 1) {

+            return(invisible(NULL))

+        } else {

+            ## change values for .pos and .scale for anno_mark

+            object@fun@var_env$.pos = anno_mark_param$.pos

+            object@fun@var_env$.scale = anno_mark_param$.scale

+            pushViewport(viewport(x = anno_mark_param$vp_x, y = anno_mark_param$vp_y, width = anno_mark_param$vp_width, height = anno_mark_param$vp_height, just = anno_mark_param$vp_just))

+            draw(object@fun, index = anno_mark_param$index)

+            upViewport()

+            return(invisible(NULL))

+        }

+    }

     if(is.character(test)) {

         test2 = TRUE

@@ -8,7 +8,7 @@ Draw the Heatmap Annotations

 }

 \usage{

 \S4method{draw}{HeatmapAnnotation}(object, index, k = 1, n = 1, ...,

-    test = FALSE)

+    test = FALSE, anno_mark_param = list())

 }

 \arguments{

@@ -18,6 +18,7 @@ Draw the Heatmap Annotations

   \item{n}{Total number of slices.}

   \item{...}{Pass to \code{\link[grid]{viewport}} which contains all the annotations.}

   \item{test}{Is it in test mode? The value can be logical or a text which is plotted as the title of plot.}

+  \item{anno_mark_param}{It contains specific parameters for drawing \code{\link{anno_mark}} and pass to the \code{\link{draw,SingleAnnotation-method}}.}

 }

 \value{

@@ -7,7 +7,8 @@ Draw the Single Annotation

 Draw the Single Annotation

 }

 \usage{

-\S4method{draw}{SingleAnnotation}(object, index, k = 1, n = 1, test = FALSE)

+\S4method{draw}{SingleAnnotation}(object, index, k = 1, n = 1, test = FALSE,

+    anno_mark_param = list())

 }

 \arguments{

@@ -16,6 +17,7 @@ Draw the Single Annotation

   \item{k}{The index of the slice.}

   \item{n}{Total number of slices. \code{k} and \code{n} are used to adjust annotation names. E.g. if \code{k} is 2 and \code{n} is 3, the annotation names are not drawn.}

   \item{test}{Is it in test mode? The value can be logical or a text which is plotted as the title of plot.}

+  \item{anno_mark_param}{It contains specific parameters for drawing \code{\link{anno_mark}}.}

 }

 \value{

@@ -101,3 +101,43 @@ draw(ha, 1:10, test = TRUE)

 ha = rowAnnotation(fun = fun, width = unit(4, "cm"))

 draw(ha, 1:10, test = TRUE)

+

+## test anno_mark

+m = matrix(rnorm(1000), nrow = 100)

+ha1 = rowAnnotation(foo = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10]))

+Heatmap(m, name = "mat", cluster_rows = FALSE, right_annotation = ha1)

+Heatmap(m, name = "mat", cluster_rows = FALSE) + ha1

+

+split = rep("a", 100); split[c(1:4, 20, 60, 98:100)] = "b"

+Heatmap(m, name = "mat", cluster_rows = FALSE, right_annotation = ha1, row_split = split, gap = unit(1, "cm"))

+Heatmap(m, name = "mat", cluster_rows = FALSE, row_split = split, gap = unit(1, "cm")) + ha1

+

+# ha has two annotations

+ha2 = rowAnnotation(foo = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10]), bar = 1:100)

+Heatmap(m, name = "mat", cluster_rows = FALSE, right_annotation = ha2)

+Heatmap(m, name = "mat", cluster_rows = FALSE) + ha2

+

+Heatmap(m, name = "mat", cluster_rows = FALSE, right_annotation = ha2, row_split = split, gap = unit(1, "cm"))

+Heatmap(m, name = "mat", cluster_rows = FALSE, row_split = split, gap = unit(1, "cm")) + ha2

+

+

+## test anno_mark as column annotation

+m = matrix(rnorm(1000), ncol = 100)

+ha1 = columnAnnotation(foo = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10]))

+Heatmap(m, name = "mat", cluster_columns = FALSE, top_annotation = ha1)

+ha1 %v% Heatmap(m, name = "mat", cluster_columns = FALSE)

+

+split = rep("a", 100); split[c(1:4, 20, 60, 98:100)] = "b"

+Heatmap(m, name = "mat", cluster_columns = FALSE, top_annotation = ha1, column_split = split, column_gap = unit(1, "cm"))

+ha1 %v% Heatmap(m, name = "mat", cluster_columns = FALSE, column_split = split, gap = unit(1, "cm"))

+

+# ha has two annotations

+ha2 = HeatmapAnnotation(foo = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10]), bar = 1:100)

+Heatmap(m, name = "mat", cluster_columns = FALSE, top_annotation = ha2)

+ha2 %v% Heatmap(m, name = "mat", cluster_columns = FALSE)

+

+Heatmap(m, name = "mat", cluster_columns = FALSE, top_annotation = ha2, column_split = split, column_gap = unit(1, "cm"))

+ha2 %v% Heatmap(m, name = "mat", cluster_columns = FALSE, column_split = split, column_gap = unit(1, "cm"))

+

+

+