@@ -97,8 +97,8 @@ exportMethods(set_component_height)

 import(grDevices)

 import(graphics)

 import(grid)

-import(stats)

 import(methods)

+import(stats)

 importFrom("GetoptLong", qq)

 importFrom("GetoptLong", qq.options)

 importFrom("GetoptLong", qqcat)

@@ -1,6 +1,15 @@

 CHANGES in VERSION 1.15.1

 * random colors are generated by new `rand_color()` function in circlize package.

+* add `density_param` in `densityHeatmap()` function

+* annotations with duplicated names have no legends any more

+* re-implement `grid.xaxis()` to draw axis labels rotated 90 degrees

+* grids in discrete legend are arranged by rows if ncol > 1

+* raster image is generated in a independent R session

+* empty string in annotation or heatmap is mapped to NA

+* annotation and heatmap legends can be merged into one column. 

+

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

 CHANGES in VERSION 1.13.2

deleted file mode 100755

@@ -1,3 +0,0 @@

-[Dolphin]

-Timestamp=2015,6,15,11,33,52

-ViewMode=2

@@ -180,6 +180,7 @@ setMethod(f = "map_to_colors",

 	x2 = vector(length = length(x))

 	if(object@type == "discrete") {

+		x[grepl("^\\s*$", x)] = NA

 		lna = is.na(x)

 		if(is.numeric(x)) x = as.character(x)

@@ -214,7 +215,7 @@ setMethod(f = "map_to_colors",

 # -color_bar if the mapping is continuous, whether show the legend as discrete color bar or continuous color bar

 # -grid_height height of each legend grid.

 # -grid_width width of each legend grid.

-# -grid_border color for legend grid borders.

+# -border color for legend grid borders.

 # -at break values of the legend

 # -labels labels corresponding to break values

 # -labels_gp graphcial parameters for legend labels

@@ -247,7 +248,7 @@ setMethod(f = "color_mapping_legend",

 	color_bar = c("discrete", "continuous"),

 	grid_height = unit(4, "mm"),

 	grid_width = unit(4, "mm"),

-	grid_border = NULL,

+	border = NULL,

 	at = object@levels,

 	labels = at,

 	labels_gp = gpar(fontsize = 10),

@@ -290,13 +291,13 @@ setMethod(f = "color_mapping_legend",

 			labels = rev(labels)

 		}

 		gf = Legend(at = at, labels = labels, title = title, title_gp = title_gp, grid_height = grid_height,

-			grid_width = grid_width, border = grid_border, labels_gp = labels_gp, nrow = nrow, ncol = ncol,

+			grid_width = grid_width, border = border, labels_gp = labels_gp, nrow = nrow, ncol = ncol,

 			legend_gp = gpar(fill = map_to_colors(object, at)), title_position = title_position)

 	} else {

 		gf = Legend(at = at, labels = labels, col_fun = object@col_fun, title = title, title_gp = title_gp, grid_height = grid_height,

-			grid_width = grid_width, border = grid_border, labels_gp = labels_gp, direction = legend_direction,

+			grid_width = grid_width, border = border, labels_gp = labels_gp, direction = legend_direction,

 			legend_width = legend_width, legend_height = legend_height, title_position = title_position)

 	}

@@ -202,7 +202,8 @@ Heatmap = setClass("Heatmap",

 #        is appended to a list of heatmaps.

 # -show_heatmap_legend whether show heatmap legend?

 # -heatmap_legend_param a list contains parameters for the heatmap legend. See `color_mapping_legend,ColorMapping-method` for all available parameters.

-# -use_raster whether render the heatmap body as a raster image. It helps to reduce file size when the matrix is huge.

+# -use_raster whether render the heatmap body as a raster image. It helps to reduce file size when the matrix is huge. Note if ``cell_fun``

+#       is set, ``use_raster`` is enforced to be ``FALSE``.

 # -raster_device graphic device which is used to generate the raster image

 # -raster_quality a value set to larger than 1 will improve the quality of the raster image.

 # -raster_device_param a list of further parameters for the selected graphic device

@@ -230,7 +231,7 @@ Heatmap = function(matrix, col, name,

     na_col = "grey", 

     color_space = "LAB",

     rect_gp = gpar(col = NA), 

-    cell_fun = function(j, i, x, y, width, height, fill) NULL,

+    cell_fun = NULL,

     row_title = character(0), 

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

     row_title_gp = gpar(fontsize = 14), 

@@ -1289,6 +1290,11 @@ setMethod(f = "draw_heatmap_body",

     y = (rev(seq_len(nr)) - 0.5) / nr

     expand_index = expand.grid(seq_len(nr), seq_len(nc))

+    cell_fun = object@matrix_param$cell_fun

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

+        use_raster = FALSE

+    }

+        

     if(use_raster) {

         # write the image into a temporary file and read it back

         device_info = switch(raster_device,

@@ -1314,37 +1320,68 @@ setMethod(f = "draw_heatmap_body",

         temp_image = tempfile(pattern = paste0(".heatmap_body_", object@name, "_", k, "_"), tmpdir = ".", fileext = paste0(".", device_info[2]))

         #getFromNamespace(raster_device, ns = device_info[1])(temp_image, width = heatmap_width*raster_quality, height = heatmap_height*raster_quality)

         device_fun = getFromNamespace(raster_device, ns = device_info[1])

-        do.call("device_fun", c(list(filename = temp_image, width = heatmap_width*raster_quality, height = heatmap_height*raster_quality), raster_device_param))

-    }

+        

+        ############################################

+        ## make the heatmap body in a another process

+        temp_R_data = tempfile(pattern = paste0(".heatmap_body_", object@name, "_", k, "_"), tmpdir = ".", fileext = paste0(".RData"))

+        temp_R_file = tempfile(pattern = paste0(".heatmap_body_", object@name, "_", k, "_"), tmpdir = ".", fileext = paste0(".R"))

+        save(device_fun, device_info, temp_image, heatmap_width, raster_quality, heatmap_height, raster_device_param,

+            gp, x, expand_index, nc, nr, col_matrix, row_order, column_order, y,

+            file = temp_R_data)

+        R_cmd = qq("

+        library(@{device_info[1]})

+        library(grid)

+        load('@{temp_R_data}')

+        do.call('device_fun', c(list(filename = temp_image, width = heatmap_width*raster_quality, height = heatmap_height*raster_quality), raster_device_param))

+        grid.rect(x[expand_index[[2]]], y[expand_index[[1]]], width = unit(1/nc, 'npc'), height = unit(1/nr, 'npc'), gp = do.call('gpar', c(list(fill = col_matrix), gp)))

+        dev.off()

+        q(save = 'no')

+        ", code.pattern = "@\\{CODE\\}")

+        writeLines(R_cmd, con = temp_R_file)

+        oe = try(system(qq("\"@{R_binary()}\" --vanilla < \"@{temp_R_file}\"", code.pattern = "@\\{CODE\\}"), ignore.stdout = TRUE))

+        ############################################

+        file.remove(temp_image)

+        file.remove(temp_R_data)

+        file.remove(temp_R_file)

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

+            stop(oe)

+        }

+        image = getFromNamespace(device_info[3], ns = device_info[2])(temp_image)

+        image = as.raster(image)

+        grid.raster(image, width = unit(1, "npc"), height = unit(1, "npc"))

-    if(any(names(gp) %in% c("type"))) {

-        if(gp$type == "none") {

+    } else {

+        if(any(names(gp) %in% c("type"))) {

+            if(gp$type == "none") {

+            } else {

+                grid.rect(x[expand_index[[2]]], y[expand_index[[1]]], width = unit(1/nc, "npc"), height = unit(1/nr, "npc"), gp = do.call("gpar", c(list(fill = col_matrix), gp)))

+            }

         } else {

             grid.rect(x[expand_index[[2]]], y[expand_index[[1]]], width = unit(1/nc, "npc"), height = unit(1/nr, "npc"), gp = do.call("gpar", c(list(fill = col_matrix), gp)))

         }

-    } else {

-        grid.rect(x[expand_index[[2]]], y[expand_index[[1]]], width = unit(1/nc, "npc"), height = unit(1/nr, "npc"), gp = do.call("gpar", c(list(fill = col_matrix), gp)))

-    }

-    cell_fun = object@matrix_param$cell_fun

-    for(i in row_order) {

-        for(j in column_order) {

-            cell_fun(j, i, unit(x[which(column_order == j)], "npc"), unit(y[which(row_order == i)], "npc"), unit(1/nc, "npc"), unit(1/nr, "npc"), col_matrix[which(row_order == i), which(column_order == j)])

+        if(is.function(cell_fun)) {

+            for(i in row_order) {

+                for(j in column_order) {

+                    cell_fun(j, i, unit(x[which(column_order == j)], "npc"), unit(y[which(row_order == i)], "npc"), unit(1/nc, "npc"), unit(1/nr, "npc"), col_matrix[which(row_order == i), which(column_order == j)])

+                }

+            }

         }

     }

-    if(use_raster) {

-        dev.off()

-        image = getFromNamespace(device_info[3], ns = device_info[2])(temp_image)

-        image = as.raster(image)

-        grid.raster(image, width = unit(1, "npc"), height = unit(1, "npc"))

-        file.remove(temp_image)

-    }

-

     upViewport()

 })

+is_windows = function() {

+    tolower(.Platform$OS.type) == "windows"

+}

+

+R_binary = function() {

+    R_exe = ifelse(is_windows(), "R.exe", "R")

+    return(file.path(R.home("bin"), R_exe))

+}

+

 # == title

 # Draw dendrogram on row or column

 #

@@ -245,9 +245,21 @@ HeatmapAnnotation = function(df, name, col, na_col = "grey",

 			} else if(is.atomic(anno_arg_list[[ag]])) {

 			    if(is.null(simple_length)) {

-			    	simple_length = length(anno_arg_list[[ag]])

-			    } else if(length(anno_arg_list[[ag]]) != simple_length) {

-			    	stop("length of simple annotations differ.")

+			    	if(is.matrix(anno_arg_list[[ag]])) {

+			    		simple_length = nrow(anno_arg_list[[ag]])

+			    	} else {

+			    		simple_length = length(anno_arg_list[[ag]])

+			    	}

+			    } else{

+			    	if(is.matrix(anno_arg_list[[ag]])) {

+			    		if(nrow(anno_arg_list[[ag]]) != simple_length) {

+			    			stop("length of simple annotations differ.")

+			    		}

+			    	} else {

+			    		if(length(anno_arg_list[[ag]]) != simple_length) {

+			    			stop("length of simple annotations differ.")

+			    		}

+			    	}

 			    }

 				if(missing(col)) {

 			        anno_list = c(anno_list, list(SingleAnnotation(name = ag, value = anno_arg_list[[ag]], na_col = na_col, which = which, 

@@ -304,7 +316,15 @@ HeatmapAnnotation = function(df, name, col, na_col = "grey",

 	if(length(anno_size) == 1) {

 		if(!is.unit(anno_size)) {

-			anno_size = rep(anno_size, n_total_anno)

+			anno_size = sapply(anno_list, function(x) {

+				if(is_simple_annotation(x)) {

+					return(1)

+				} else if(is_matrix_annotation(x)) {

+					return(attr(x@is_anno_matrix, "k"))

+				} else {

+					return(2)

+				}

+			})

 		}

 	}

@@ -183,6 +183,7 @@ setMethod(f = "add_heatmap",

 # -column_title_side will the title be put on the top or bottom of the heatmap.

 # -column_title_gp graphic parameters for drawing text.

 # -heatmap_legend_side side of the heatmap legend.

+# -merge_legends whether put heatmap legends and annotation legends in a same column

 # -show_heatmap_legend whether show heatmap legend.

 # -heatmap_legend_list a list of self-defined legend, should be wrapped into `grid::grob` objects.

 # -annotation_legend_side side of annotation legend.

@@ -226,6 +227,7 @@ setMethod(f = "make_layout",

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

     column_title_gp = gpar(fontsize = 14), 

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

+    merge_legends = FALSE,

     show_heatmap_legend = TRUE, 

     heatmap_legend_list = list(),

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

@@ -283,6 +285,8 @@ setMethod(f = "make_layout",

     }

     object@ht_list_param$gap = gap

+    object@ht_list_param$merge_legends = merge_legends

+

     for(i in seq_len(n)) {

         # if the zero-column matrix is the first one

         if(inherits(object@ht_list[[i]], "Heatmap")) {

@@ -445,7 +449,8 @@ setMethod(f = "make_layout",

     }

     object@ht_list_param$gap = gap

     object@ht_list_param$main_heatmap = i_main

-    

+    object@ht_list_param$merge_legends = merge_legends

+

     n = length(object@ht_list)

     ## orders of other heatmaps should be changed

@@ -591,9 +596,15 @@ setMethod(f = "make_layout",

     for(i in seq_along(object@ht_list)) {

         ht = object@ht_list[[i]]

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

+            if(merge_legends && !is.null(ht@top_annotation)) {

+                ColorMappingList = c(ColorMappingList, get_color_mapping_list(ht@top_annotation))

+            }

             if(ht@heatmap_param$show_heatmap_legend) {

                 ColorMappingList = c(ColorMappingList, ht@matrix_color_mapping)

             }

+            if(merge_legends && !is.null(ht@bottom_annotation)) {

+                ColorMappingList = c(ColorMappingList, get_color_mapping_list(ht@bottom_annotation))

+            }

         }

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

             ColorMappingList = c(ColorMappingList, get_color_mapping_list(ht))

@@ -641,16 +652,20 @@ setMethod(f = "make_layout",

     ## annotation legend to top, bottom, left and right

     # default values

     ColorMappingList = list()

-    for(i in seq_along(object@ht_list)) {

-        ht = object@ht_list[[i]]

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

-            if(!is.null(ht@top_annotation)) {

-                ColorMappingList = c(ColorMappingList, get_color_mapping_list(ht@top_annotation))

-            }

-            if(!is.null(ht@bottom_annotation)) {

-                ColorMappingList = c(ColorMappingList, get_color_mapping_list(ht@bottom_annotation))

+    if(!merge_legends) {

+        for(i in seq_along(object@ht_list)) {

+            ht = object@ht_list[[i]]

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

+                if(!is.null(ht@top_annotation)) {

+                    ColorMappingList = c(ColorMappingList, get_color_mapping_list(ht@top_annotation))

+                }

+                if(!is.null(ht@bottom_annotation)) {

+                    ColorMappingList = c(ColorMappingList, get_color_mapping_list(ht@bottom_annotation))

+                }

             }

         }

+    } else {

+        annotation_legend_list = list()

     }

     if(length(ColorMappingList) == 0 && length(annotation_legend_list) == 0) {

         show_annotation_legend = FALSE

@@ -1173,11 +1188,20 @@ setMethod(f = "draw_heatmap_legend",

     ColorMappingList = list()

     ColorMappingParamList = list()

     for(i in seq_along(object@ht_list)) {

+        ht = object@ht_list[[i]]

         if(inherits(object@ht_list[[i]], "Heatmap")) {

+            if(object@ht_list_param$merge_legends && !is.null(ht@top_annotation)) {

+                ColorMappingList = c.list(ColorMappingList, list = get_color_mapping_list(ht@top_annotation))

+                ColorMappingParamList = c.list(ColorMappingParamList, list = get_color_mapping_param_list(ht@top_annotation))

+            }

             if(object@ht_list[[i]]@heatmap_param$show_heatmap_legend) {

                 ColorMappingList = c.list(ColorMappingList, object@ht_list[[i]]@matrix_color_mapping)

                 ColorMappingParamList = c.list(ColorMappingParamList, object@ht_list[[i]]@matrix_color_mapping_param)

             }

+            if(object@ht_list_param$merge_legends && !is.null(ht@bottom_annotation)) {

+                ColorMappingList = c.list(ColorMappingList, list = get_color_mapping_list(ht@bottom_annotation))

+                ColorMappingParamList = c.list(ColorMappingParamList, list = get_color_mapping_param_list(ht@bottom_annotation))

+            }

         } else if(inherits(object@ht_list[[i]], "HeatmapAnnotation")) {

             ColorMappingList = c.list(ColorMappingList, list = get_color_mapping_list(object@ht_list[[i]]))

             ColorMappingParamList = c.list(ColorMappingParamList, list = get_color_mapping_param_list(object@ht_list[[i]]))

@@ -1298,11 +1322,21 @@ setMethod(f = "heatmap_legend_size",

     ColorMappingList = list()

     ColorMappingParamList = list()

     for(i in seq_along(object@ht_list)) {

+        ht = object@ht_list[[i]]

         if(inherits(object@ht_list[[i]], "Heatmap")) {

+            if(object@ht_list_param$merge_legends && !is.null(ht@top_annotation)) {

+                ColorMappingList = c.list(ColorMappingList, list = get_color_mapping_list(ht@top_annotation))

+                ColorMappingParamList = c.list(ColorMappingParamList, list = get_color_mapping_param_list(ht@top_annotation))

+            }

             if(object@ht_list[[i]]@heatmap_param$show_heatmap_legend) {

                 ColorMappingList = c.list(ColorMappingList, object@ht_list[[i]]@matrix_color_mapping)

                 ColorMappingParamList = c.list(ColorMappingParamList, object@ht_list[[i]]@matrix_color_mapping_param)

             }

+            if(object@ht_list_param$merge_legends && !is.null(ht@bottom_annotation)) {

+                ColorMappingList = c.list(ColorMappingList, list = get_color_mapping_list(ht@bottom_annotation))

+                ColorMappingParamList = c.list(ColorMappingParamList, list = get_color_mapping_param_list(ht@bottom_annotation))

+            }

+            

         } else if(inherits(object@ht_list[[i]], "HeatmapAnnotation")) {

             ColorMappingList = c.list(ColorMappingList, list = get_color_mapping_list(object@ht_list[[i]]))

             ColorMappingParamList = c.list(ColorMappingParamList, list = get_color_mapping_param_list(object@ht_list[[i]]))

@@ -1369,6 +1403,12 @@ draw_legend = function(ColorMappingList, ColorMappingParamList, side = c("right"

     side = match.arg(side)[1]

+    # remove legends which are duplicated by testing the names

+    legend_names = sapply(ColorMappingList, function(x) x@name)

+    l = !duplicated(legend_names)

+    ColorMappingList = ColorMappingList[l]

+    ColorMappingParamList = ColorMappingParamList[l]

+

     n = length(ColorMappingList)

     if(n == 0 && length(legend_list) == 0) {

         return(unit(c(0, 0), "null"))

@@ -139,6 +139,7 @@ Legend = function(at, labels = at, nrow = NULL, ncol = 1, col_fun,

 	return(gf)

 }

+# grids are arranged by rows

 discrete_legend_body = function(at, labels = at, nrow = NULL, ncol = 1,

 	grid_height = unit(4, "mm"), grid_width = unit(4, "mm"), gap = unit(2, "mm"),

 	labels_gp = gpar(fontsize = 10),

@@ -156,14 +157,18 @@ discrete_legend_body = function(at, labels = at, nrow = NULL, ncol = 1,

 		nrow = 1

 		ncol = 1

 	}

+	ncol = ifelse(ncol > n_labels, n_labels, ncol)

+

+	labels_mat = matrix(c(labels, rep("", nrow*ncol - n_labels)), nrow = nrow, ncol = ncol, byrow = TRUE)

+	index_mat = matrix(1:(nrow*ncol), nrow = nrow, ncol = ncol, byrow = TRUE)

+

 	labels_padding_left = unit(1, "mm")

 	labels_max_width = NULL

 	for(i in 1:ncol) {

-		index = seq(nrow*(i-1)+1, min(c(nrow*i, n_labels)))

 		if(i == 1) {

-			labels_max_width = max(do.call("unit.c", lapply(labels[index], function(x) {

+			labels_max_width = max(do.call("unit.c", lapply(labels_mat[, i], function(x) {

 					g = grobWidth(textGrob(x, gp = labels_gp))

 					if(i < ncol) {

 						g = g + gap

@@ -171,7 +176,7 @@ discrete_legend_body = function(at, labels = at, nrow = NULL, ncol = 1,

 					g

 				})))

 		} else {

-			labels_max_width = unit.c(labels_max_width, max(do.call("unit.c", lapply(labels[index], function(x) {

+			labels_max_width = unit.c(labels_max_width, max(do.call("unit.c", lapply(labels_mat[, i], function(x) {

 					g = grobWidth(textGrob(x, gp = labels_gp))

 					if(i < ncol) {

 						g = g + gap

@@ -191,7 +196,7 @@ discrete_legend_body = function(at, labels = at, nrow = NULL, ncol = 1,

 	# legend grid

 	for(i in 1:ncol) {

-		index = seq(nrow*(i-1)+1, min(c(nrow*i, n_labels)))

+		index = index_mat[, i][labels_mat[, i] != ""]

 		ni = length(index)

 		x = unit(rep(0, ni), "npc")

 		y = (0:(ni-1))*(grid_height)

@@ -35,7 +35,8 @@ SingleAnnotation = setClass("SingleAnnotation",

 		show_legend = "logical",

 		which = "character",

 		name_to_data_vp = "logical",

-		name_param = "list"

+		name_param = "list",

+        is_anno_matrix = "logical"

 	),

 	prototype = list(

 		color_mapping = NULL,

@@ -137,14 +138,37 @@ SingleAnnotation = function(name, value, col, fun,

         stop("`name_rot` can only take values in c(0, 90, 180, 270)")

     }

-    

+    .Object@is_anno_matrix = FALSE

+    use_mat_column_names = FALSE

+    if(!missing(value)) {

+        if(is.logical(value)) {

+            value = as.character(value)

+        }

+        if(is.factor(value)) {

+            value = as.vector(value)

+        }

+        if(is.matrix(value)) {

+            .Object@is_anno_matrix = TRUE

+            attr(.Object@is_anno_matrix, "column_names") = colnames(value)

+            attr(.Object@is_anno_matrix, "k") = ncol(value)

+            use_mat_column_names = TRUE

+            use_mat_nc = ncol(value)

+        }

+    }

+

     if(which == "column") {

     	if(!name_side %in% c("left", "right")) {

     		stop("`name_side` should be 'left' or 'right' when it is a column annotation.")

     	}

     	if(name_side == "left") {

-    		name_x = unit(0, "npc") - name_offset

-    		name_y = unit(0.5, "npc")

+    		

+            if(use_mat_column_names) {

+                name_x = unit(rep(0, use_mat_nc), "npc") - name_offset

+                name_y = unit((use_mat_nc - seq_len(use_mat_nc) + 0.5)/use_mat_nc, "npc")

+            } else {

+                name_x = unit(0, "npc") - name_offset

+                name_y = unit(0.5, "npc")

+            }

             if(name_rot == 0) {

                 name_just = "right"

             } else if(name_rot == 90) {

@@ -155,8 +179,13 @@ SingleAnnotation = function(name, value, col, fun,

                 name_just = "top"

             }

     	} else {

-    		name_x = unit(1, "npc") + name_offset

-    		name_y = unit(0.5, "npc")

+            if(use_mat_column_names) {

+                name_x = unit(rep(1, use_mat_nc), "npc") + name_offset

+                name_y = unit((use_mat_nc - seq_len(use_mat_nc) + 0.5)/use_mat_nc, "npc")

+            } else {

+        		name_x = unit(1, "npc") + name_offset

+        		name_y = unit(0.5, "npc")

+            }

             if(name_rot == 0) {

                 name_just = "left"

             } else if(name_rot == 90) {

@@ -172,8 +201,13 @@ SingleAnnotation = function(name, value, col, fun,

     		stop("`name_side` should be 'left' or 'right' when it is a column annotation.")

     	}

     	if(name_side == "top") {

-    		name_x = unit(0.5, "npc")

-    		name_y = unit(1, "npc") + name_offset

+            if(use_mat_column_names) {

+                name_x = unit((seq_len(use_mat_nc) - 0.5)/use_mat_nc, "npc")

+                name_y = unit(rep(1, use_mat_nc), "npc") + name_offset

+            } else {

+        		name_x = unit(0.5, "npc")

+        		name_y = unit(1, "npc") + name_offset

+            }

             if(name_rot == 0) {

                 name_just = "bottom"

             } else if(name_rot == 90) {

@@ -184,8 +218,13 @@ SingleAnnotation = function(name, value, col, fun,

                 name_just = "right"

             }

     	} else {

-    		name_x = unit(0.5, "npc")

-    		name_y = unit(0, "npc") - name_offset

+            if(use_mat_column_names) {

+                name_x = unit((seq_len(use_mat_nc) - 0.5)/use_mat_nc, "npc")

+                name_y = unit(rep(0, use_mat_nc), "npc") - name_offset

+            } else {

+        		name_x = unit(0.5, "npc")

+        		name_y = unit(0, "npc") - name_offset

+            }

             if(name_rot == 0) {

                 name_just = "top"

             } else if(name_rot == 90) {

@@ -209,20 +248,10 @@ SingleAnnotation = function(name, value, col, fun,

     	stop("You should not set `fill`.")

     }

-    if(!missing(value)) {

-	    if(is.logical(value)) {

-	    	value = as.character(value)

-	    }

-	    if(is.factor(value)) {

-            value = as.vector(value)

-        }

-	}

-

     if(missing(fun)) {

     	if(missing(col)) {

     		col = default_col(value)

     	}

-        

     	if(is.atomic(col)) {

     	    if(is.null(names(col))) {

                 if(is.factor(value)) {

@@ -250,17 +279,31 @@ SingleAnnotation = function(name, value, col, fun,

 	        .Object@fun = function(index) {

 	        	n = length(index)

 				x = (seq_len(n) - 0.5) / n

-				fill = map_to_colors(color_mapping, value[index])

-				#l = which(!is.na(value[index]))

-				grid.rect(x, y = 0.5, width = 1/n, height = 1, gp = do.call("gpar", c(list(fill = fill), gp)))

+                if(is.matrix(value)) {

+                    nc = ncol(value)

+                    for(i in seq_len(nc)) {

+                        fill = map_to_colors(color_mapping, value[index, i])

+                        grid.rect(x, y = (nc-i +0.5)/nc, width = 1/n, height = 1/nc, gp = do.call("gpar", c(list(fill = fill), gp)))

+                    }

+                } else {

+    				fill = map_to_colors(color_mapping, value[index])

+    				grid.rect(x, y = 0.5, width = 1/n, height = 1, gp = do.call("gpar", c(list(fill = fill), gp)))

+                }

 			}

 		} else {

 			.Object@fun = function(index, k = NULL, N = NULL) {

 				n = length(index)

 				y = (n - seq_len(n) + 0.5) / n

-				fill = map_to_colors(color_mapping, value[index])

-				#l = which(!is.na(value[index]))

-				grid.rect(x = 0.5, y, height = 1/n, width = 1, gp = do.call("gpar", c(list(fill = fill), gp)))

+                if(is.matrix(value)) {

+                    nc = ncol(value)

+                    for(i in seq_len(nc)) {

+                        fill = map_to_colors(color_mapping, value[index, i])

+                        grid.rect(x = (i-0.5)/nc, y, height = 1/n, width = 1/nc, gp = do.call("gpar", c(list(fill = fill), gp)))

+                    }

+                } else {

+    				fill = map_to_colors(color_mapping, value[index])

+    				grid.rect(x = 0.5, y, height = 1/n, width = 1, gp = do.call("gpar", c(list(fill = fill), gp)))

+                }

 			}

 		}

@@ -342,8 +385,19 @@ setMethod(f = "draw",

 	}

 	# add annotation name

 	if(object@name_param$show) {

-		grid.text(object@name, x = object@name_param$x, y = object@name_param$y, just = object@name_param$just, 

-			rot = object@name_param$rot, gp = object@name_param$gp)

+        if(is_matrix_annotation(object)) {

+            if(!is.null(attr(object@is_anno_matrix, "column_names"))) {

+                anno_mat_column_names = attr(object@is_anno_matrix, "column_names")

+                grid.text(anno_mat_column_names, x = object@name_param$x, y = object@name_param$y, just = object@name_param$just, 

+                    rot = object@name_param$rot, gp = object@name_param$gp)

+            } else {

+                grid.text(object@name, x = object@name_param$x, y = object@name_param$y, just = object@name_param$just, 

+                    rot = object@name_param$rot, gp = object@name_param$gp)

+            }

+        } else {

+    		grid.text(object@name, x = object@name_param$x, y = object@name_param$y, just = object@name_param$just, 

+    			rot = object@name_param$rot, gp = object@name_param$gp)

+        }

 	}

 	upViewport()

@@ -364,7 +418,7 @@ setMethod(f = "draw",

 setMethod(f = "show",

 	signature = "SingleAnnotation",

 	definition = function(object) {

-	if(is.null(object@color_mapping)) {

+	if(is_fun_annotation(object)) {

 		cat("An annotation with self-defined function\n")

 		cat("name:", object@name, "\n")

 		cat("position:", object@which, "\n")

@@ -373,5 +427,21 @@ setMethod(f = "show",

 		cat("name:", object@name, "\n")

 		cat("position:", object@which, "\n")

 		cat("show legend:", object@show_legend, "\n")

+        if(is_matrix_annotation(object)) {

+            cat("a matrix with", attr(object@is_anno_matrix, "k"), "columns\n")

+        }

 	}

 })

+

+

+is_simple_annotation = function(single_anno) {

+    !is_fun_annotation(single_anno) && !is_matrix_annotation(single_anno)

+}

+

+is_matrix_annotation = function(single_anno) {

+    single_anno@is_anno_matrix

+}

+

+is_fun_annotation = function(single_anno) {

+    is.null(single_anno@color_mapping)

+}

@@ -1229,3 +1229,24 @@ row_anno_link = function(...) {

 column_anno_link = function(...) {

 	anno_link(..., which = "column")

 }

+

+

+grid.xaxis = function(main = TRUE, at = NULL, label = NULL, gp = gpar()) {

+	if(is.null(at)) {

+		at = grid.pretty(current.viewport()$xscale)

+		label = at

+	}

+	if(is.null(label)) {

+		label = at

+	}

+	n = length(at)

+	if(main) {

+		grid.lines(at[c(1, n)], unit(c(0, 0), "native"), gp = gp, default.units = "native")

+		grid.segments(at, unit(rep(-0.5, n), "lines"), at, unit(rep(0, n), "npc"), gp = gp, default.units = "native")

+		grid.text(label, at, unit(rep(-1, n), "lines"), rot = 90, just = "right", gp = gp, default.units = "native")

+	} else {

+		grid.lines(at[c(1, n)], unit(c(1, 1), "native"), gp = gp, default.units = "native")

+		grid.segments(at, unit(1, "npc") + unit(rep(0.5, n), "lines"), at, unit(rep(1, n), "npc"), gp = gp, default.units = "native")

+		grid.text(label, at, unit(1, "npc") + unit(rep(1, n), "lines"), rot = 90, just = "left", gp = gp, default.units = "native")

+	}

+}

@@ -5,6 +5,7 @@

 # == param

 # -data  a matrix or a list. If it is a matrix, density will be calculated by columns.

 # -col a list of colors that density values are mapped to.

+# -density_param parameters send to `stats::density`, ``na.rm`` is enforced to ``TRUE``.

 # -color_space the color space in which colors are interpolated. Pass to `circlize::colorRamp2`.

 # -anno annotation for the matrix columns or the list. The value should be a vector or a data frame 

 #       and colors for annotations are randomly assigned. If you want to customize the annotation colors,

@@ -33,6 +34,9 @@

 # in each column (or each vector in the list) through a heatmap. It is useful if you have huge number 

 # of columns in ``data`` to visualize.

 #

+# The density matrix is generated with 500 rows ranging between the maximun and minimal values in all densities.

+# The density values in each row are linearly intepolated between the two density values at the two nearest bounds.

+#

 # == value

 # No value is returned.

 #

@@ -54,6 +58,7 @@

 #

 densityHeatmap = function(data, 

 	col = rev(brewer.pal(11, "Spectral")),

+	density_param = list(na.rm = TRUE),

 	color_space = "LAB", 

 	anno = NULL, 

 	ylab = deparse(substitute(data)), 

@@ -74,12 +79,14 @@ densityHeatmap = function(data,

 	column_order = NULL,

 	...) {

+	density_param$na.rm = TRUE

+

 	if(is.matrix(data)) {

-		density_list = apply(data, 2, density, na.rm = TRUE)

+		density_list = apply(data, 2, function(x) do.call(density, c(list(x = x), density_param)))

 		quantile_list = apply(data, 2, quantile, na.rm = TRUE)

 		mean_value = apply(data, 2, mean, na.rm = TRUE)

 	} else if(is.data.frame(data) || is.list(data)) {

-		density_list = lapply(data, density, na.rm = TRUE)

+		density_list = lapply(data, function(x) do.call(density, c(list(x = x), density_param)))

 		quantile_list = sapply(data, quantile, na.rm = TRUE)

 		mean_value = sapply(data, mean, na.rm = TRUE)

 	} else {

@@ -11,7 +11,7 @@ Heatmap(matrix, col, name,

     na_col = "grey",

     color_space = "LAB",

     rect_gp = gpar(col = NA),

-    cell_fun = function(j, i, x, y, width, height, fill) NULL,

+    cell_fun = NULL,

     row_title = character(0),

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

     row_title_gp = gpar(fontsize = 14),

@@ -138,7 +138,7 @@ Heatmap(matrix, col, name,

   \item{width}{the width of the single heatmap, should be a fixed \code{\link[grid]{unit}} object. It is used for the layout when the heatmap is appended to a list of heatmaps.}

   \item{show_heatmap_legend}{whether show heatmap legend?}

   \item{heatmap_legend_param}{a list contains parameters for the heatmap legend. See \code{\link{color_mapping_legend,ColorMapping-method}} for all available parameters.}

-  \item{use_raster}{whether render the heatmap body as a raster image. It helps to reduce file size when the matrix is huge.}

+  \item{use_raster}{whether render the heatmap body as a raster image. It helps to reduce file size when the matrix is huge. Note if \code{cell_fun} is set, \code{use_raster} is enforced to be \code{FALSE}.}

   \item{raster_device}{graphic device which is used to generate the raster image}

   \item{raster_quality}{a value set to larger than 1 will improve the quality of the raster image.}

   \item{raster_device_param}{a list of further parameters for the selected graphic device}

@@ -16,7 +16,7 @@ Draw legend based on color mapping

     color_bar = c("discrete", "continuous"),

     grid_height = unit(4, "mm"),

     grid_width = unit(4, "mm"),

-    grid_border = NULL,

+    border = NULL,

     at = object@levels,

     labels = at,

     labels_gp = gpar(fontsize = 10),

@@ -36,7 +36,7 @@ Draw legend based on color mapping

   \item{color_bar}{if the mapping is continuous, whether show the legend as discrete color bar or continuous color bar}

   \item{grid_height}{height of each legend grid.}

   \item{grid_width}{width of each legend grid.}

-  \item{grid_border}{color for legend grid borders.}

+  \item{border}{color for legend grid borders.}

   \item{at}{break values of the legend}

   \item{labels}{labels corresponding to break values}

   \item{labels_gp}{graphcial parameters for legend labels}

@@ -9,6 +9,7 @@ Use colors to represent density distribution

 \usage{

 densityHeatmap(data,

     col = rev(brewer.pal(11, "Spectral")),

+    density_param = list(na.rm = TRUE),

     color_space = "LAB",

     anno = NULL,

     ylab = deparse(substitute(data)),

@@ -33,6 +34,7 @@ densityHeatmap(data,

   \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns.}

   \item{col}{a list of colors that density values are mapped to.}

+  \item{density_param}{parameters send to \code{\link[stats]{density}}, \code{na.rm} is enforced to \code{TRUE}.}

   \item{color_space}{the color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}

   \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame  and colors for annotations are randomly assigned. If you want to customize the annotation colors, use a \code{\link{HeatmapAnnotation-class}} object directly.}

   \item{ylab}{label on y-axis in the plot}

@@ -59,6 +61,9 @@ To visualize data distribution in a matrix or in a list, sometimes we use boxplo

 Here we use colors to map the density values and visualize distribution of values

 in each column (or each vector in the list) through a heatmap. It is useful if you have huge number 

 of columns in \code{data} to visualize.

+

+The density matrix is generated with 500 rows ranging between the maximun and minimal values in all densities.

+The density values in each row are linearly intepolated between the two density values at the two nearest bounds.

 }

 \value{

 No value is returned.

@@ -14,6 +14,7 @@ Make layout for the complete plot

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

     column_title_gp = gpar(fontsize = 14),

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

+    merge_legends = FALSE,

     show_heatmap_legend = TRUE,

     heatmap_legend_list = list(),

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

@@ -45,6 +46,7 @@ Make layout for the complete plot

   \item{column_title_side}{will the title be put on the top or bottom of the heatmap.}

   \item{column_title_gp}{graphic parameters for drawing text.}

   \item{heatmap_legend_side}{side of the heatmap legend.}

+  \item{merge_legends}{whether put heatmap legends and annotation legends in a same column}

   \item{show_heatmap_legend}{whether show heatmap legend.}

   \item{heatmap_legend_list}{a list of self-defined legend, should be wrapped into \code{\link[grid]{grob}} objects.}

   \item{annotation_legend_side}{side of annotation legend.}