@@ -132,6 +132,7 @@ export("anno_points")

 export("anno_simple")

 export("anno_summary")

 export("anno_text")

+export("anno_zoom")

 export("annotation_axis_grob")

 export("cluster_within_group")

 export("columnAnnotation")

@@ -147,6 +148,7 @@ export("decorate_row_names")

 export("decorate_row_title")

 export("decorate_title")

 export("default_axis_param")

+export("default_get_type")

 export("dend_heights")

 export("dend_xy")

 export("dendrogramGrob")

@@ -1,8 +1,9 @@

+

 CHANGES in VERSION 1.99.4

 * anno_mark() is now calculated in multiple slices.

-* oncoPrint(): automatically split the alteration type if the separator is one of

-  ";:,|".

+* oncoPrint(): automatically split the alteration type if the separator is one of ";:,|".

+* add anno_zoom()

 ========================

@@ -2619,6 +2619,7 @@ row_anno_text = function(...) {

 # -labels_gp Graphic settings for the labels.

 # -padding Padding between neighbouring labels in the plot.

 # -link_width Width of the segments.

+# -link_height Similar as ``link_width``, used for column annotation.

 # -extend By default, the region for the labels has the same width (if it is a column annotation) or

 #         same height (if it is a row annotation) as the heatmap. The size can be extended by this options.

 #         The value can be a proportion number or  a `grid::unit` object. The length can be either one or two.

@@ -2645,7 +2646,8 @@ row_anno_text = function(...) {

 anno_mark = function(at, labels, which = c("column", "row"), 

 	side = ifelse(which == "column", "top", "right"),

 	lines_gp = gpar(), labels_gp = gpar(), padding = 0.5, 

-	link_width = unit(5, "mm"), link_gp = lines_gp, 

+	link_width = unit(5, "mm"), link_height = link_width,

+	link_gp = lines_gp, 

 	extend = unit(0, "mm")) {

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

@@ -2707,7 +2709,7 @@ anno_mark = function(at, labels, which = c("column", "row"),

 		}

 		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])))

+		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)

@@ -2758,17 +2760,17 @@ anno_mark = function(at, labels, which = c("column", "row"),

 		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(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)

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

+			link_height = link_height - unit(1, "mm")

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

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

+			grid.segments(h, rep(link_height*(2/3), n2), h, rep(link_height, 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(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)

+			link_height = link_height - unit(1, "mm")

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

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

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

 		}

 		upViewport()

 	}

@@ -2787,7 +2789,7 @@ anno_mark = function(at, labels, which = c("column", "row"),

 		height = height,

 		n = -1,

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

-			side, link_width, extend),

+			side, link_width, link_height, extend),

 		show_name = FALSE

 	)

@@ -3092,3 +3094,393 @@ anno_block = function(gp = gpar(), labels = NULL, labels_gp = gpar(), labels_rot

 	)

 	return(anno) 

 }

+

+# == title

+# Zoom annotation

+#

+# == param

+# -align_to

+# -panel_fun

+# -which Whether it is a column annotation or a row annotation?

+# -side Side of the boxes If it is a column annotation, valid values are "top" and "bottom";

+#       If it is a row annotation, valid values are "left" and "right".

+# -size

+# -gap

+# -link_gp Graphic settings for the segments.

+# -link_width Width of the segments.

+# -link_height Similar as ``link_width``, used for column annotation.

+# -extend By default, the region for the labels has the same width (if it is a column annotation) or

+#         same height (if it is a row annotation) as the heatmap. The size can be extended by this options.

+#         The value can be a proportion number or  a `grid::unit` object. The length can be either one or two.

+# -width Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.

+# -height Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.

+#

+# == details

+#

+anno_zoom = function(align_to, panel_fun = function(index, nm = NULL) { grid.rect() }, 

+	which = c("column", "row"), side = ifelse(which == "column", "top", "right"),

+	size = NULL, gap = unit(1, "mm"), 

+	link_width = unit(5, "mm"), link_height = link_width, link_gp = gpar(),

+	extend = unit(0, "mm"), width = NULL, height = NULL) {

+	

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

+		which = match.arg(which)[1]

+	} else {

+		which = .ENV$current_annotation_which

+	}

+

+	anno_size = anno_width_and_height(which, width, height, unit(2, "cm") + link_width)

+

+	# align_to should be

+	# 1. a vector of class labels that the length should be same as the nrow of the matrix

+	# 2. a list of numeric indices

+

+	if(is.list(align_to)) {

+		if(!any(sapply(align_to, is.numeric))) {

+			stop_wrap(paste0("`at` should be numeric ", which, " index corresponding to the matrix."))

+		}

+	}

+

+	.pos = NULL # position of the rows

+

+	if(length(as.list(formals(panel_fun))) == 1) {

+ 		formals(panel_fun) = alist(index = , nm = NULL)

+	}

+

+	if(length(extend) == 1) extend = rep(extend, 2)

+	if(length(extend) > 2) extend = extend[1:2]

+	if(!inherits(extend, "unit")) extend = unit(extend, "npc")

+

+	# anno_zoom is always executed in one-slice mode (which means mulitple slices

+	# are treated as one big slilce)

+	row_fun = function(index) {

+		n = length(index)

+		if(is.atomic(align_to)) {

+			if(length(setdiff(align_to, index)) == 0 && !any(duplicated(align_to))) {

+				align_to = list(align_to)

+			} else {

+				if(length(align_to) != n) {

+					stop_wrap("If `align_to` is a vector with group labels, the length should be the same as the number of rows in the heatmap.")

+				}

+				lnm = as.character(unique(align_to[index]))

+				align_to = as.list(tapply(seq_along(align_to), align_to, function(x) x))

+				align_to = align_to[lnm]

+			}

+		}

+

+		nrl = sapply(align_to, length)

+		align_to_df = lapply(align_to, function(x) {

+			ind = which(index %in% x)

+			n = length(ind)

+			s = NULL

+			e = NULL

+			s[1] = ind[1]

+			if(n > 1) {

+				ind2 = which(ind[2:n] - ind[1:(n-1)] > 1)

+				if(length(ind2)) s = c(s, ind[ ind2 + 1 ])

+				k = length(s)

+				e[k] = ind[length(ind)]

+				if(length(ind2)) e[1:(k-1)] = ind[1:(n-1)][ ind2 ]

+			} else {

+				e = ind[1]

+			}

+			data.frame(s = s, e = e)

+		})

+

+		# pos is from top to bottom

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

+			pos = (n:1 - 0.5)/n # position of rows

+		} else {

+			pos = .pos

+		}

+

+		.scale = c(0, 1)

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

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

+		

+		# the position of boxes initially are put evenly

+		# add the gap

+		n_boxes = length(align_to)

+		if(length(gap) == 1) gap = rep(gap, n_boxes)

+		if(is.null(size)) size = nrl

+		if(length(size) != length(align_to)) {

+			stop_wrap("Length of `size` should be the same as the number of groups of indices.")

+		}

+		if(!inherits(size, "unit")) {

+			size_is_unit = FALSE

+			if(n_boxes == 1) {

+				h = data.frame(bottom = .scale[1] - extend[1], top = .scale[2] + extend[2])

+			} else {

+				gap = convertHeight(gap, "native", valueOnly = TRUE)

+				box_height = size/sum(size) * (1 + sum(extend) - sum(gap[1:(n_boxes-1)]))

+				h = data.frame(

+						top = cumsum(box_height) + cumsum(gap) - gap[length(gap)] - extend[1]

+					)

+				h$bottom = h$top - box_height

+				h = 1 - h[, 2:1]

+				colnames(h) = c("top", "bottom")

+			}

+		} else {

+			size_is_unit = TRUE

+			box_height = size

+			box_height2 = box_height # box_height2 adds the gap

+			for(i in 1:n_boxes) {

+				if(i == 1 || i == n_boxes) {

+					if(n_boxes > 1) {

+						box_height2[i] = box_height2[i] + gap[i]*0.5

+					}

+				} else {

+					box_height2[i] = box_height2[i] + gap[i]

+				}

+			}

+			box_height2 = convertHeight(box_height2, "native", valueOnly = TRUE)

+			# the original positions of boxes

+			mean_pos = sapply(align_to, function(ind) mean(pos[ind]))

+			h1 = mean_pos - box_height2*0.5

+			h2 = mean_pos + box_height2*0.5

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

+			colnames(h) = c("bottom", "top")

+			h = h[nrow(h):1, , drop = FALSE]

+

+			# recalcualte h to remove gaps

+			gap_height = convertHeight(gap, "native", valueOnly = TRUE)

+			if(n_boxes > 1) {

+				for(i in 1:n_boxes) {

+					if(i == 1) {

+						h[i, "bottom"] = h[i, "bottom"] + gap_height[i]/2

+					} else if(i == n_boxes) {

+						h[i, "top"] = h[i, "top"] - gap_height[i]/2

+					} else {

+						h[i, "bottom"] = h[i, "bottom"] + gap_height[i]/2

+						h[i, "top"] = h[i, "top"] - gap_height[i]/2

+					}

+				}

+			}

+		}

+		popViewport()

+

+		# draw boxes

+		if(side == "right") {

+			pushViewport(viewport(x = link_width, just = "left", width = anno_size$width - link_width))

+		} else {

+			pushViewport(viewport(x = 0, just = "left", width = anno_size$width - link_width))

+		}

+		for(i in 1:n_boxes) {

+			current_vp_name = current.viewport()$name

+			pushViewport(viewport(y = (h[i, "top"] + h[i, "bottom"])/2, height = h[i, "top"] - h[i, "bottom"], 

+				default.units = "native"))

+			if(is.function(panel_fun)) panel_fun(align_to[[i]], names(align_to)[i])

+			popViewport()

+

+			if(current.viewport()$name != current_vp_name) {

+				stop_wrap("If you push viewports `panel_fun`, you need to pop all them out.")

+			}

+		}

+		popViewport()

+		# draw the links

+		link_gp = recycle_gp(link_gp, n_boxes)

+		if(side == "right") {

+			pushViewport(viewport(x = unit(0, "npc"), just = "left", width = link_width))

+		} else {

+			pushViewport(viewport(x = unit(1, "npc"), just = "right", width = link_width))

+		}

+		for(i in 1:n_boxes) {

+			df = align_to_df[[i]]

+			for(j in 1:nrow(df)) {

+				# draw each polygon

+				if(side == "right") {

+					grid.polygon(unit.c(unit(c(0, 0), "npc"), rep(link_width, 2)),

+						c(pos[df[j, 2]] - 0.5/n, pos[df[j, 1]] + 0.5/n, h[i, "top"], h[i, "bottom"]),

+						default.units = "native", gp = subset_gp(link_gp, i))

+				} else {

+					grid.polygon(unit.c(rep(link_width, 2), unit(c(0, 0), "npc")),

+						c(pos[df[j, 2]] - 0.5/n, pos[df[j, 1]] + 0.5/n, h[i, "top"], h[i, "bottom"]),

+						default.units = "native", gp = subset_gp(link_gp, i))

+				}

+			}

+		}

+ 

+		popViewport()

+		

+	}

+

+	column_fun = function(index) {

+		n = length(index)

+		

+		if(is.atomic(align_to)) {

+			if(length(setdiff(align_to, index)) == 0 && !any(duplicated(align_to))) {

+				align_to = list(align_to)

+			} else {

+				if(length(align_to) != n) {

+					stop_wrap("If `align_to` is a vector with group labels, the length should be the same as the number of columns in the heatmap.")

+				}

+				lnm = as.character(unique(align_to[index]))

+				align_to = as.list(tapply(seq_along(align_to), align_to, function(x) x))

+				align_to = align_to[lnm]

+			}

+		}

+		nrl = sapply(align_to, length)

+		align_to_df = lapply(align_to, function(x) {

+			ind = which(index %in% x)

+			n = length(ind)

+			s = NULL

+			e = NULL

+			s[1] = ind[1]

+			if(n > 1) {

+				ind2 = which(ind[2:n] - ind[1:(n-1)] > 1)

+				if(length(ind2)) s = c(s, ind[ ind2 + 1 ])

+				k = length(s)

+				e[k] = ind[length(ind)]

+				if(length(ind2)) e[1:(k-1)] = ind[1:(n-1)][ ind2 ]

+			} else {

+				e = ind[1]

+			}

+			data.frame(s = s, e = e)

+		})

+

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

+			pos = (1:n - 0.5)/n 

+		} else {

+			pos = .pos

+		}

+

+		.scale = c(0, 1)

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

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

+		

+		# the position of boxes initially are put evenly

+		# add the gap

+		n_boxes = length(align_to)

+		if(length(gap) == 1) gap = rep(gap, n_boxes)

+		if(is.null(size)) size = nrl

+		if(length(size) != length(align_to)) {

+			stop_wrap("Length of `size` should be the same as the number of groups of indices.")

+		}

+		if(!inherits(size, "unit")) {

+			size_is_unit = FALSE

+			if(n_boxes == 1) {

+				h = data.frame(left = .scale[1] - extend[1], right = .scale[2] + extend[2])

+			} else {

+				gap = convertWidth(gap, "native", valueOnly = TRUE)

+				box_width = size/sum(size) * (1 + sum(extend) - sum(gap[1:(n_boxes-1)]))

+				h = data.frame(

+						right = cumsum(box_width) + cumsum(gap) - gap[length(gap)] - extend[1]

+					)

+				h$left = h$right - box_width

+			}

+		} else {

+			size_is_unit = TRUE

+			box_width = size

+			box_width2 = box_width

+			for(i in 1:n_boxes) {

+				if(i == 1 || i == n_boxes) {

+					if(n_boxes > 1) {

+						box_width2[i] = box_width2[i] + gap[i]*0.5

+					}

+				} else {

+					box_width2[i] = box_width2[i] + gap[i]

+				}

+			}

+			box_width2 = convertWidth(box_width2, "native", valueOnly = TRUE)

+			# the original positions of boxes

+			mean_pos = sapply(align_to, function(ind) mean(pos[ind]))

+			h1 = mean_pos - box_width2*0.5

+			h2 = mean_pos + box_width2*0.5

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

+			colnames(h) = c("left", "right")

+

+			# recalcualte h to remove gaps

+			gap_width = convertWidth(gap, "native", valueOnly = TRUE)

+			if(n_boxes > 1) {

+				for(i in 1:n_boxes) {

+					if(i == 1) {

+						h[i, "left"] = h[i, "left"] + gap_width[i]/2

+					} else if(i == n_boxes) {

+						h[i, "right"] = h[i, "right"] - gap_width[i]/2

+					} else {

+						h[i, "left"] = h[i, "left"] + gap_width[i]/2

+						h[i, "right"] = h[i, "right"] - gap_width[i]/2

+					}

+				}

+			}

+		}

+		popViewport()

+

+		# draw boxes

+		if(side == "top") {

+			pushViewport(viewport(y = link_height, just = "bottom", height = anno_size$height - link_height))

+		} else {

+			pushViewport(viewport(y = 0, just = "bottom", height = anno_size$height - link_height))

+		}

+		for(i in 1:n_boxes) {

+			current_vp_name = current.viewport()$name

+			pushViewport(viewport(x = (h[i, "right"] + h[i, "left"])/2, width = h[i, "right"] - h[i, "left"], 

+				default.units = "native"))

+			if(is.function(panel_fun)) panel_fun(align_to[[i]], names(align_to)[i])

+			popViewport()

+

+			if(current.viewport()$name != current_vp_name) {

+				stop_wrap("If you push viewports `panel_fun`, you need to pop all them out.")

+			}

+		}

+		popViewport()

+		# draw the links

+		link_gp = recycle_gp(link_gp, n_boxes)

+		if(side == "top") {

+			pushViewport(viewport(y = unit(0, "npc"), just = "bottom", height = link_height))

+		} else {

+			pushViewport(viewport(y = unit(1, "npc"), just = "top", height = link_height))

+		}

+		for(i in 1:n_boxes) {

+			df = align_to_df[[i]]

+			for(j in 1:nrow(df)) {

+				# draw each polygon

+				if(side == "top") {

+					grid.polygon(

+						c(pos[df[j, 2]] + 0.5/n, pos[df[j, 1]] - 0.5/n, h[i, "left"], h[i, "right"]),

+						unit.c(unit(c(0, 0), "npc"), rep(link_width, 2)),

+						default.units = "native", gp = subset_gp(link_gp, i))

+				} else {

+					grid.polygon(

+						c(pos[df[j, 2]] + 0.5/n, pos[df[j, 1]] - 0.5/n, h[i, "left"], h[i, "right"]),

+						unit.c(rep(link_width, 2), unit(c(0, 0), "npc")),

+						default.units = "native", gp = subset_gp(link_gp, i))

+				}

+			}

+		}

+		popViewport()

+		

+	}

+

+	if(which == "row") {

+		fun = row_fun

+	} else if(which == "column") {

+		fun = column_fun

+	}

+	

+	anno = AnnotationFunction(

+		fun = fun,

+		fun_name = "anno_zoom",

+		which = which,

+		height = anno_size$height,

+		width = anno_size$width,

+		n = -1,

+		var_import = list(align_to, .pos, gap, size, panel_fun, side, anno_size, extend,

+			link_width, link_height, link_gp),

+		show_name = FALSE

+	)

+

+	anno@subset_rule$align_to = function(x, i) {

+		if(is.atomic(x)) {

+			x[i]

+		} else {

+			x = lapply(x, function(x) intersect(x, i))

+			x = x[sapply(x, length) > 0]

+		}

+	}

+

+	anno@subsetable = TRUE

+	return(anno)

+}

+

+

@@ -509,7 +509,7 @@ setMethod(f = "draw_annotation",

         if(n_slice > 1) {

             all_anno_type = anno_type(annotation)

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

+            if(any(c("anno_zoom", "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

@@ -541,7 +541,7 @@ setMethod(f = "draw_annotation",

         if(n_slice > 1) {

             all_anno_type = anno_type(annotation)

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

+            if(any(c("anno_zoom", "anno_mark") %in% all_anno_type)) {

                 ## only make the anno_mark annotation

                 co_lt = object@column_order_list

                 .scale = c(0, 1)

@@ -600,7 +600,7 @@ setMethod(f = "draw_heatmap_list",

                 anno_mark_param = list()

                 if(n_slice > 1) {

                     all_anno_type = anno_type(ht)

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

+                    if(any(c("anno_zoom", "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

@@ -688,7 +688,7 @@ setMethod(f = "draw_heatmap_list",

                 anno_mark_param = list()

                 if(n_slice > 1) {

                     all_anno_type = anno_type(ht)

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

+                    if(any(c("anno_zoom", "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

@@ -543,7 +543,7 @@ setMethod(f = "draw",

         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(object@fun@fun_name %in% c("anno_mark", "anno_zoom") && length(anno_mark_param) > 0) {

         if(k > 1) {

             return(invisible(NULL))

         } else {

@@ -9,7 +9,7 @@

 #      When the value is a list, the names of the list represent alteration types.

 #      You can use `unify_mat_list` to make all matrix having same row names and column names.

 # -get_type If different alterations are encoded in the matrix as complex strings, this self-defined function

-#           determines how to extract them. It only works when ``mat`` is a matrix.

+#           determines how to extract them. It only works when ``mat`` is a matrix. The default value is `default_get_type`.

 # -alter_fun A single function or a list of functions which defines how to add graphics for different alterations.

 # -alter_fun_is_vectorized Whether ``alter_fun`` is implemented vectorized. Internally the function will guess.

 # -col A vector of color for which names correspond to alteration types.

@@ -51,10 +51,7 @@

 # Zuguang Gu <z.gu@dkfz.de>

 #

 oncoPrint = function(mat, 

-	get_type = function(x) {

-		x = strsplit(x, "\\s*[;:,|]\\s*")[[1]]

-		x[!x %in% c("na", "NA")]

-	},

+	get_type = default_get_type,

 	alter_fun, 

 	alter_fun_is_vectorized = NULL,

 	col, 

@@ -611,3 +608,13 @@ guess_alter_fun_is_vectorized = function(alter_fun) {

 	}

 }

+# == title

+# Default get_type for oncoPrint()

+#

+# == param

+# -x A strings which encode multiple altertations.

+#

+default_get_type = function(x) {

+	x = strsplit(x, "\\s*[;:,|]\\s*")[[1]]

+	x[!x %in% c("na", "NA")]

+}

@@ -10,7 +10,8 @@ Link annotation with labels

 anno_mark(at, labels, which = c("column", "row"),

     side = ifelse(which == "column", "top", "right"),

     lines_gp = gpar(), labels_gp = gpar(), padding = 0.5,

-    link_width = unit(5, "mm"), link_gp = lines_gp,

+    link_width = unit(5, "mm"), link_height = link_width,

+    link_gp = lines_gp,

     extend = unit(0, "mm"))

 }

 \arguments{

@@ -24,6 +25,7 @@ anno_mark(at, labels, which = c("column", "row"),

   \item{labels_gp}{Graphic settings for the labels.}

   \item{padding}{Padding between neighbouring labels in the plot.}

   \item{link_width}{Width of the segments.}

+  \item{link_height}{Similar as \code{link_width}, used for column annotation.}

   \item{extend}{By default, the region for the labels has the same width (if it is a column annotation) or same height (if it is a row annotation) as the heatmap. The size can be extended by this options. The value can be a proportion number or  a \code{\link[grid]{unit}} object. The length can be either one or two.}

 }

new file mode 100644

@@ -0,0 +1,39 @@

+\name{anno_zoom}

+\alias{anno_zoom}

+\title{

+Zoom annotation

+}

+\description{

+Zoom annotation

+}

+\usage{

+anno_zoom(align_to, panel_fun = function(index, nm = NULL) { grid.rect() },

+    which = c("column", "row"), side = ifelse(which == "column", "top", "right"),

+    size = NULL, gap = unit(1, "mm"),

+    link_width = unit(5, "mm"), link_height = link_width, link_gp = gpar(),

+    extend = unit(0, "mm"), width = NULL, height = NULL)

+}

+\arguments{

+

+  \item{align_to}{-align_to}

+  \item{panel_fun}{-panel_fun}

+  \item{which}{Whether it is a column annotation or a row annotation?}

+  \item{side}{Side of the boxes If it is a column annotation, valid values are "top" and "bottom"; If it is a row annotation, valid values are "left" and "right".}

+  \item{size}{-size}

+  \item{gap}{-gap}

+  \item{link_gp}{Graphic settings for the segments.}

+  \item{link_width}{Width of the segments.}

+  \item{link_height}{Similar as \code{link_width}, used for column annotation.}

+  \item{extend}{By default, the region for the labels has the same width (if it is a column annotation) or same height (if it is a row annotation) as the heatmap. The size can be extended by this options. The value can be a proportion number or  a \code{\link[grid]{unit}} object. The length can be either one or two.}

+  \item{width}{Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.}

+  \item{height}{Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.}

+

+}

+\details{

+

+}

+\examples{

+# There is no example

+NULL

+

+}

new file mode 100644

@@ -0,0 +1,20 @@

+\name{default_get_type}

+\alias{default_get_type}

+\title{

+Default get_type for oncoPrint()

+}

+\description{

+Default get_type for oncoPrint()

+}

+\usage{

+default_get_type(x)

+}

+\arguments{

+

+  \item{x}{A strings which encode multiple altertations.}

+

+}

+\examples{

+# There is no example

+NULL

+}

@@ -8,7 +8,7 @@ Make oncoPrint

 }

 \usage{

 oncoPrint(mat,

-    get_type = function(x) strsplit(x, "\\\\s*[;:,|]\\\\s*")[[1]],

+    get_type = default_get_type,

     alter_fun,

     alter_fun_is_vectorized = NULL,

     col,

@@ -45,7 +45,7 @@ oncoPrint(mat,

 \arguments{

   \item{mat}{The value should be a character matrix which encodes mulitple alterations  or a list of matrices for which every matrix contains binary value representing whether the alteration is present or absent.  When the value is a list, the names of the list represent alteration types. You can use \code{\link{unify_mat_list}} to make all matrix having same row names and column names.}

-  \item{get_type}{If different alterations are encoded in the matrix as complex strings, this self-defined function determines how to extract them. It only works when \code{mat} is a matrix.}

+  \item{get_type}{If different alterations are encoded in the matrix as complex strings, this self-defined function determines how to extract them. It only works when \code{mat} is a matrix. The default value is \code{\link{default_get_type}}.}

   \item{alter_fun}{A single function or a list of functions which defines how to add graphics for different alterations.}

   \item{alter_fun_is_vectorized}{Whether \code{alter_fun} is implemented vectorized. Internally the function will guess.}

   \item{col}{A vector of color for which names correspond to alteration types.}

@@ -358,9 +358,72 @@ anno = anno_block(gp = gpar(fill = 1:4), labels = letters[1:4], labels_gp = gpar

 draw(anno, index = 1:10, k = 2, n = 4, test = "anno_block")

+### anno_zoom

+fa = sort(sample(letters[1:3], 100, replace = TRUE, prob = c(1, 2, 3)))

+panel_fun = function(index, nm) {

+	grid.rect()

+	grid.text(nm)

+}

+anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun)

+draw(anno, index = 1:100, test = "anno_zoom")

+

+anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,

+	gap = unit(1, "cm"))

+draw(anno, index = 1:100, test = "anno_zoom, set gap")

+

+anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,

+	size = 1:3)

+draw(anno, index = 1:100, test = "anno_zoom, size set as relative values")

+

+anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,

+	size = 1:3, extend = unit(1, "cm"))

+draw(anno, index = 1:100, test = "anno_zoom, extend")

+

+anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,

+	size = unit(1:3, "cm"))

+draw(anno, index = 1:100, test = "anno_zoom, size set as absolute values")

+

+anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,

+	size = unit(c(2, 20, 40), "cm"))

+draw(anno, index = 1:100, test = "anno_zoom, big size")

+

+

+anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,

+	size = unit(1:3, "cm"), side = "left")

+draw(anno, index = 1:100, test = "anno_zoom, side")

+

+

+anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,

+	size = unit(1:3, "cm"), link_gp = gpar(fill = 1:3))

+draw(anno, index = 1:100, test = "anno_zoom, link_gp")

+

+anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,

+	size = unit(1:3, "cm"), link_gp = gpar(fill = 1:3),

+	link_width = unit(2, "cm"), width = unit(4, "cm"))

+draw(anno, index = 1:100, test = "anno_zoom, width")

+

+anno = anno_zoom(align_to = list(a = 1:10, b = 30:45, c = 70:90), 

+	which = "row", panel_fun = panel_fun, size = unit(1:3, "cm"))

+draw(anno, index = 1:100, test = "anno_zoom, a list of indices")

+

+anno = anno_zoom(align_to = fa, which = "column", panel_fun = panel_fun,

+	size = unit(1:3, "cm"))

+draw(anno, index = 1:100, test = "anno_zoom, column annotation")

+

+

+m = matrix(rnorm(100*10), nrow = 100)

+hc = hclust(dist(m))

+fa2 = cutree(hc, k = 4)

+anno = anno_zoom(align_to = fa2, which = "row", panel_fun = panel_fun)

+draw(anno, index = hc$order, test = "anno_zoom, column annotation")

+anno = anno_zoom(align_to = fa2, which = "column", panel_fun = panel_fun)

+draw(anno, index = hc$order, test = "anno_zoom, column annotation")

+anno = anno_zoom(align_to = fa2, which = "row", panel_fun = panel_fun)

+Heatmap(m, cluster_rows = hc, right_annotation = rowAnnotation(foo = anno))

+Heatmap(m, cluster_rows = hc, right_annotation = rowAnnotation(foo = anno), row_split = 2)