@@ -99,6 +99,7 @@ exportMethods(set_component_height)

 import(grDevices)

 import(graphics)

 import(grid)

+import(methods)

 import(stats)

 importFrom("GetoptLong", qq)

 importFrom("GetoptLong", qq.options)

@@ -110,12 +111,5 @@ importFrom("circlize", rand_color)

 importFrom("circlize", smartAlign)

 importFrom("colorspace", diverge_hcl)

 importFrom("colorspace", rainbow_hcl)

-importFrom("dendextend", "labels<-")

-importFrom("dendextend", get_branches_heights)

-importFrom("dendextend", nnodes)

-importFrom("methods", "new", "show")

-importFrom("methods", setClass)

-importFrom("methods", setGeneric)

-importFrom("methods", setMethod)

 importFrom("utils", "getFromNamespace")

@@ -1,4 +1,3 @@

-<<<<<<< HEAD

 CHANGES in VERSION 1.15.1

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

@@ -23,12 +22,6 @@ CHANGES in VERSION 1.15.1

 CHANGES in VERSION 1.13.2

 * add `packLegend()`

-=======

-CHANGES in VERSION 1.13.2

-

-* add `packLegend()`

-* Legend() supports to add txt labels on grids

->>>>>>> bioc/master

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

deleted file mode 100755

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

-[Dolphin]

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

-ViewMode=2

@@ -1,5 +1,4 @@

-<<<<<<< HEAD

 setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))

 setGeneric('get_color_mapping_param_list', function(object, ...) standardGeneric('get_color_mapping_param_list'))

@@ -42,49 +41,10 @@ setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_he

 setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))

-=======

-setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))

-

-setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))

-

-setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))

-

-setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))

-

-setGeneric('column_order', function(object, ...) standardGeneric('column_order'))

-

-setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))

-

-setGeneric('component_height', function(object, ...) standardGeneric('component_height'))

-

-setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))

-

-setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))

-

-setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))

-

-setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))

-

-setGeneric('prepare', function(object, ...) standardGeneric('prepare'))

-

-setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))

-

-setGeneric('get_color_mapping_param_list', function(object, ...) standardGeneric('get_color_mapping_param_list'))

-

-setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))

-

-setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))

-

-setGeneric('draw', function(object, ...) standardGeneric('draw'))

-

-setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))

-

->>>>>>> bioc/master

 setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))

 setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))

-<<<<<<< HEAD

 setGeneric('prepare', function(object, ...) standardGeneric('prepare'))

 setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))

@@ -92,18 +52,3 @@ setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))

 setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))

 setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))

-=======

-setGeneric('component_width', function(object, ...) standardGeneric('component_width'))

-

-setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))

-

-setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))

-

-setGeneric('row_order', function(object, ...) standardGeneric('row_order'))

-

-setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))

-

-setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))

-

-setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))

->>>>>>> bioc/master

@@ -180,10 +180,7 @@ setMethod(f = "map_to_colors",

 	x2 = vector(length = length(x))

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

-<<<<<<< HEAD

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

-=======

->>>>>>> bioc/master

 		lna = is.na(x)

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

@@ -215,17 +212,10 @@ setMethod(f = "map_to_colors",

 # -title title of the legend, by default it is the name of the legend

 # -title_gp graphical parameters for legend title

 # -title_position position of the title

-<<<<<<< HEAD

 # -color_bar a string of "continous" or "discrete". 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.

 # -border color for legend grid borders.

-=======

-# -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.

->>>>>>> bioc/master

 # -at break values of the legend

 # -labels labels corresponding to break values

 # -labels_gp graphcial parameters for legend labels

@@ -255,17 +245,10 @@ setMethod(f = "color_mapping_legend",

 	title = object@name,

 	title_gp = gpar(fontsize = 10, fontface = "bold"),

 	title_position = c("topleft", "topcenter", "leftcenter", "lefttop"),

-<<<<<<< HEAD

 	color_bar = object@type,

 	grid_height = unit(4, "mm"),

 	grid_width = unit(4, "mm"),

 	border = NULL,

-=======

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

-	grid_height = unit(4, "mm"),

-	grid_width = unit(4, "mm"),

-	grid_border = NULL,

->>>>>>> bioc/master

 	at = object@levels,

 	labels = at,

 	labels_gp = gpar(fontsize = 10),

@@ -285,17 +268,10 @@ setMethod(f = "color_mapping_legend",

 	title_gp = check_gp(title_gp)

 	labels_gp = check_gp(labels_gp)

-<<<<<<< HEAD

 	# color_bar = match.arg(color_bar)

 	if(object@type == "discrete" && color_bar == "continuous") {

 		stop("'color_bar' can only be set to 'discrete' only if the color mapping is discrete")

-=======

-	color_bar = match.arg(color_bar)

-

-	if(object@type == "discrete" && color_bar == "continuous") {

-		stop("'color_bar' can only be set to 'continuous' only if the color mapping is continuous")

->>>>>>> bioc/master

 	}

 	# get labels

@@ -315,21 +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,

-<<<<<<< HEAD

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

-=======

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

->>>>>>> bioc/master

 			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,

-<<<<<<< HEAD

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

-=======

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

->>>>>>> bioc/master

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

 	}

@@ -191,11 +191,7 @@ Heatmap = setClass("Heatmap",

 # -bottom_annotation_height total height of the column annotations on the bottom.

 # -km do k-means clustering on rows. If the value is larger than 1, the heatmap will be split by rows according to the k-means clustering.

 #     For each row-clusters, hierarchical clustering is still applied with parameters above.

-<<<<<<< HEAD

 # -km_title row title for each cluster when ``km`` is set. It must a text with format of ".*\%i.*" where "\%i" is replaced by the index of the cluster.

-=======

-# -km_title row title for each cluster when ``km`` is set. It must a text with format of "*\%i*" where "\%i" is replaced by the index of the cluster.

->>>>>>> bioc/master

 # -split a vector or a data frame by which the rows are split. But if ``cluster_rows`` is a clustering object, ``split`` can be a single number

 #        indicating rows are to be split according to the split on the tree.

 # -gap gap between row-slices if the heatmap is split by rows, should be `grid::unit` object. If it is a vector, the order corresponds

@@ -206,12 +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.

-<<<<<<< HEAD

 # -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``.

-=======

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

->>>>>>> bioc/master

 # -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

@@ -239,11 +231,7 @@ Heatmap = function(matrix, col, name,

     na_col = "grey", 

     color_space = "LAB",

     rect_gp = gpar(col = NA), 

-<<<<<<< HEAD

     cell_fun = NULL,

-=======

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

->>>>>>> bioc/master

     row_title = character(0), 

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

     row_title_gp = gpar(fontsize = 14), 

@@ -282,19 +270,11 @@ Heatmap = function(matrix, col, name,

     column_order = NULL,

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

     show_row_names = TRUE, 

-<<<<<<< HEAD

     row_names_max_width = default_row_names_max_width(), 

     row_names_gp = gpar(fontsize = 12), 

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

     show_column_names = TRUE, 

     column_names_max_height = default_column_names_max_height(), 

-=======

-    row_names_max_width = unit(4, "cm"), 

-    row_names_gp = gpar(fontsize = 12), 

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

-    show_column_names = TRUE, 

-    column_names_max_height = unit(4, "cm"), 

->>>>>>> bioc/master

     column_names_gp = gpar(fontsize = 12),

     top_annotation = new("HeatmapAnnotation"),

     top_annotation_height = top_annotation@size,

@@ -307,17 +287,10 @@ Heatmap = function(matrix, col, name,

     combined_name_fun = function(x) paste(x, collapse = "/"),

     width = NULL, 

     show_heatmap_legend = TRUE,

-<<<<<<< HEAD

     heatmap_legend_param = list(title = name),

     use_raster = FALSE, 

     raster_device = c("png", "jpeg", "tiff", "CairoPNG", "CairoJPEG", "CairoTIFF"),

     raster_quality = 2,

-=======

-    heatmap_legend_param = list(title = name, color_bar = "discrete"),

-    use_raster = FALSE, 

-    raster_device = c("png", "jpeg", "tiff", "CairoPNG", "CairoJPEG", "CairoTIFF"),

-    raster_quality = 1,

->>>>>>> bioc/master

     raster_device_param = list()) {

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

@@ -528,12 +501,9 @@ Heatmap = function(matrix, col, name,

     .Object@row_names_param$side = match.arg(row_names_side)[1]

     .Object@row_names_param$show = show_row_names

     .Object@row_names_param$gp = check_gp(row_names_gp)

-<<<<<<< HEAD

     default_row_names_max_width = function() {

         min(unit.c(unit(6, "cm")), max_text_width(rownames(matrix), gp = .Object@row_names_param$gp))

     }

-=======

->>>>>>> bioc/master

     .Object@row_names_param$max_width = row_names_max_width + unit(2, "mm")

     if(is.null(colnames(matrix))) {

@@ -542,12 +512,9 @@ Heatmap = function(matrix, col, name,

     .Object@column_names_param$side = match.arg(column_names_side)[1]

     .Object@column_names_param$show = show_column_names

     .Object@column_names_param$gp = check_gp(column_names_gp)

-<<<<<<< HEAD

     default_column_names_max_height = function() {

         min(unit.c(unit(6, "cm")), max_text_width(colnames(matrix), gp = .Object@column_names_param$gp))

     }

-=======

->>>>>>> bioc/master

     .Object@column_names_param$max_height = column_names_max_height + unit(2, "mm")

     if(inherits(cluster_rows, "dendrogram") || inherits(cluster_rows, "hclust")) {

@@ -1329,14 +1296,11 @@ setMethod(f = "draw_heatmap_body",

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

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

-<<<<<<< HEAD

     cell_fun = object@matrix_param$cell_fun

     if(!is.null(cell_fun)) {

         use_raster = FALSE

     }

-=======

->>>>>>> bioc/master

     if(use_raster) {

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

         device_info = switch(raster_device,

@@ -1359,7 +1323,6 @@ setMethod(f = "draw_heatmap_body",

         if(heatmap_width <= 0 || heatmap_height <= 0) {

             stop("The width or height of the raster image is zero, maybe you forget to turn off the previous graphic device or it was corrupted. Run `dev.off()` to close it.")

         }

-<<<<<<< HEAD

         tmp_dir = "."

         # dir.create(tmp_dir, showWarnings = FALSE)

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

@@ -1415,43 +1378,10 @@ 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))

-    }

-

-    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)))

-    }

-

-    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(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)

-    }

-

->>>>>>> bioc/master

     upViewport()

 })

-<<<<<<< HEAD

 is_windows = function() {

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

 }

@@ -1461,8 +1391,6 @@ R_binary = function() {

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

 }

-=======

->>>>>>> bioc/master

 # == title

 # Draw dendrogram on row or column

 #

@@ -1517,11 +1445,7 @@ setMethod(f = "draw_dend",

     dend = as.dendrogram(hc)

     n = length(labels(dend))

-<<<<<<< HEAD

     if(nobs(dend) <= 1) {

-=======

-    if(nnodes(dend) <= 1) {

->>>>>>> bioc/master

         return(invisible(NULL))

     }

@@ -245,7 +245,6 @@ HeatmapAnnotation = function(df, name, col, na_col = "grey",

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

 			    if(is.null(simple_length)) {

-<<<<<<< HEAD

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

 			    		simple_length = nrow(anno_arg_list[[ag]])

 			    	} else {

@@ -261,11 +260,6 @@ HeatmapAnnotation = function(df, name, col, na_col = "grey",

 			    			stop("length of simple annotations differ.")

 			    		}

 			    	}

-=======

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

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

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

->>>>>>> bioc/master

 			    }

 				if(missing(col)) {

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

@@ -322,7 +316,6 @@ HeatmapAnnotation = function(df, name, col, na_col = "grey",

 	if(length(anno_size) == 1) {

 		if(!is.unit(anno_size)) {

-<<<<<<< HEAD

 			anno_size = sapply(anno_list, function(x) {

 				if(is_simple_annotation(x)) {

 					return(1)

@@ -332,9 +325,6 @@ HeatmapAnnotation = function(df, name, col, na_col = "grey",

 					return(2)

 				}

 			})

-=======

-			anno_size = rep(anno_size, n_total_anno)

->>>>>>> bioc/master

 		}

 	}

@@ -154,22 +154,15 @@ setMethod(f = "add_heatmap",

     ht_name = names(object@ht_list)

     which_duplicated = duplicated(ht_name)

     if(any(which_duplicated)) {

-<<<<<<< HEAD

         warning(paste0("Heatmap/row annotation names are duplicated: ", paste(ht_name[which_duplicated], collapse = ", ")))

-=======

-        warning(paste0("Heatmap/row annotaiton names are duplicated: ", paste(ht_name[which_duplicated], collapse = ", ")))

->>>>>>> bioc/master

     }

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

     nr = sapply(object@ht_list[l], function(ht) nrow(ht@matrix))

     if(length(unique(nr)) > 1) {

-<<<<<<< HEAD

         cat("`nrow` of all heatmaps:\n")

         print(nr)

-=======

->>>>>>> bioc/master

         stop("`nrow` of all heatmaps should be the same.")

         for(i in l) {

             cat(object@ht_list[[i]]@name, ":", nrow(object@ht_list[[i]]@matrix), "\n")

@@ -192,10 +185,7 @@ 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.

-<<<<<<< HEAD

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

-=======

->>>>>>> bioc/master

 # -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.

@@ -216,10 +206,7 @@ setMethod(f = "add_heatmap",

 # -row_order same setting as in `Heatmap`, if it is specified, ``row_order`` in main heatmap is ignored.

 # -km same setting as in `Heatmap`, if it is specified, ``km`` in main heatmap is ignored.

 # -split same setting as in `Heatmap`, if it is specified, ``split`` in main heatmap is ignored.

-<<<<<<< HEAD

 # -combined_name_fun same setting as in `Heatmap`, if it is specified, ``combined_name_fun`` in main heatmap is ignored.

-=======

->>>>>>> bioc/master

 #

 # == detail

 # It sets the size of each component of the heatmap list and adjusts graphic parameters for each heatmap if necessary.

@@ -243,10 +230,7 @@ setMethod(f = "make_layout",

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

     column_title_gp = gpar(fontsize = 14), 

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

-<<<<<<< HEAD

     merge_legends = FALSE,

-=======

->>>>>>> bioc/master

     show_heatmap_legend = TRUE, 

     heatmap_legend_list = list(),

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

@@ -266,12 +250,8 @@ setMethod(f = "make_layout",

     row_dend_gp = NULL,

     row_order = NULL,

     km = NULL,

-<<<<<<< HEAD

     split = NULL,

     combined_name_fun = NULL) {

-=======

-    split = NULL) {

->>>>>>> bioc/master

     if(object@layout$initialized) {

         return(object)

@@ -309,11 +289,8 @@ setMethod(f = "make_layout",

     }

     object@ht_list_param$gap = gap

-<<<<<<< HEAD

     object@ht_list_param$merge_legends = merge_legends

-=======

->>>>>>> bioc/master

     for(i in seq_len(n)) {

         # if the zero-column matrix is the first one

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

@@ -333,12 +310,9 @@ setMethod(f = "make_layout",

     if(!is.null(km)) {

         object@ht_list[[i_main]]@matrix_param$km = km

     }

-<<<<<<< HEAD

     if(!missing(combined_name_fun)) {

         object@ht_list[[i_main]]@matrix_param$combined_name_fun = combined_name_fun

     }

-=======

->>>>>>> bioc/master

     if(!is.null(cluster_rows)) {

@@ -482,12 +456,8 @@ setMethod(f = "make_layout",

     }

     object@ht_list_param$gap = gap

     object@ht_list_param$main_heatmap = i_main

-<<<<<<< HEAD

     object@ht_list_param$merge_legends = merge_legends

-=======

-    

->>>>>>> bioc/master

     n = length(object@ht_list)

     ## orders of other heatmaps should be changed

@@ -633,7 +603,6 @@ setMethod(f = "make_layout",

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

         ht = object@ht_list[[i]]

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

-<<<<<<< HEAD

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

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

             }

@@ -643,11 +612,6 @@ setMethod(f = "make_layout",

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

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

             }

-=======

-            if(ht@heatmap_param$show_heatmap_legend) {

-                ColorMappingList = c(ColorMappingList, ht@matrix_color_mapping)

-            }

->>>>>>> bioc/master

         }

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

             ColorMappingList = c(ColorMappingList, get_color_mapping_list(ht))

@@ -695,7 +659,6 @@ setMethod(f = "make_layout",

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

     # default values

     ColorMappingList = list()

-<<<<<<< HEAD

     if(!merge_legends) {

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

             ht = object@ht_list[[i]]

@@ -710,18 +673,6 @@ setMethod(f = "make_layout",

         }

     } else {

         annotation_legend_list = 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))

-            }

-        }

->>>>>>> bioc/master

     }

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

         show_annotation_legend = FALSE

@@ -1244,27 +1195,20 @@ setMethod(f = "draw_heatmap_legend",

     ColorMappingList = list()

     ColorMappingParamList = list()

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

-<<<<<<< HEAD

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

->>>>>>> bioc/master

             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)

             }

-<<<<<<< HEAD

             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))

             }

-=======

->>>>>>> bioc/master

         } 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]]))

@@ -1385,28 +1329,21 @@ setMethod(f = "heatmap_legend_size",

     ColorMappingList = list()

     ColorMappingParamList = list()

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

-<<<<<<< HEAD

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

->>>>>>> bioc/master

             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)

             }

-<<<<<<< HEAD

             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))

             }

-=======

->>>>>>> bioc/master

         } 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]]))

@@ -1473,15 +1410,12 @@ draw_legend = function(ColorMappingList, ColorMappingParamList, side = c("right"

     side = match.arg(side)[1]

-<<<<<<< HEAD

     # 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]

-=======

->>>>>>> bioc/master

     n = length(ColorMappingList)

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

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

@@ -135,17 +135,10 @@ Legend = function(at, labels = at, nrow = NULL, ncol = 1, col_fun,

 	# for(i in seq_len(length(odevlist) - length(dev.list()))) {

 	# 	dev.off()

 	# }

-<<<<<<< HEAD

 	return(gf)

 }

 # grids are arranged by rows

-=======

-

-	return(gf)

-}

-

->>>>>>> bioc/master

 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),

@@ -163,27 +156,18 @@ discrete_legend_body = function(at, labels = at, nrow = NULL, ncol = 1,

 		nrow = 1

 		ncol = 1

 	}

-<<<<<<< HEAD

 	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)

-=======

->>>>>>> bioc/master

 	labels_padding_left = unit(1, "mm")

 	labels_max_width = NULL

 	for(i in 1:ncol) {

-<<<<<<< HEAD

 		if(i == 1) {

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

-=======

-		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) {

->>>>>>> bioc/master

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

 					if(i < ncol) {

 						g = g + gap

@@ -191,11 +175,7 @@ discrete_legend_body = function(at, labels = at, nrow = NULL, ncol = 1,

 					g

 				})))

 		} else {

-<<<<<<< HEAD

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

-=======

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

->>>>>>> bioc/master

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

 					if(i < ncol) {

 						g = g + gap

@@ -215,11 +195,7 @@ discrete_legend_body = function(at, labels = at, nrow = NULL, ncol = 1,

 	# legend grid

 	for(i in 1:ncol) {

-<<<<<<< HEAD

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

-=======

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

->>>>>>> bioc/master

 		ni = length(index)

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

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

@@ -245,15 +221,7 @@ discrete_legend_body = function(at, labels = at, nrow = NULL, ncol = 1,

 		if(any(c("points", "p") %in% type)) {

 			if(length(pch) == 1) pch = rep(pch, n_labels)

 			if(length(size) == 1) size = rep(size, n_labels)

-<<<<<<< HEAD

 			gf = placeGrob(gf, row = 1, col = 2*i-1, grob = pointsGrob(x+grid_width*0.5, y-grid_height*0.5, pch = pch[index], size = size[index], gp = subset_gp(legend_gp, index)))

-=======

-			if(inherits(pch, "character")) {

-				gf = placeGrob(gf, row = 1, col = 2*i-1, grob = textGrob(pch[index], x+grid_width*0.5, y-grid_height*0.5, gp = subset_gp(legend_gp, index)))

-			} else {

-				gf = placeGrob(gf, row = 1, col = 2*i-1, grob = pointsGrob(x+grid_width*0.5, y-grid_height*0.5, pch = pch[index], size = size[index], gp = subset_gp(legend_gp, index)))

-			}

->>>>>>> bioc/master

 		}

 		if(any(c("lines", "l") %in% type)) {

 			gf = placeGrob(gf, row = 1, col = 2*i-1, grob = segmentsGrob(x+unit(0.5, "mm"), y-grid_height*0.5, x+grid_width - unit(0.5, "mm"), y-grid_height*0.5, gp = subset_gp(legend_gp, index)))

@@ -35,12 +35,8 @@ SingleAnnotation = setClass("SingleAnnotation",

 		show_legend = "logical",

 		which = "character",

 		name_to_data_vp = "logical",

-<<<<<<< HEAD

 		name_param = "list",

         is_anno_matrix = "logical"

-=======

-		name_param = "list"

->>>>>>> bioc/master

 	),

 	prototype = list(

 		color_mapping = NULL,

@@ -142,7 +138,6 @@ SingleAnnotation = function(name, value, col, fun,

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

     }

-<<<<<<< HEAD

     .Object@is_anno_matrix = FALSE

     use_mat_column_names = FALSE

     if(!missing(value)) {

@@ -161,15 +156,11 @@ SingleAnnotation = function(name, value, col, fun,

         }

     }

-=======

-    

->>>>>>> bioc/master

     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") {

-<<<<<<< HEAD

             if(use_mat_column_names) {

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

@@ -178,10 +169,6 @@ SingleAnnotation = function(name, value, col, fun,

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

                 name_y = unit(0.5, "npc")

             }

-=======

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

-    		name_y = unit(0.5, "npc")

->>>>>>> bioc/master

             if(name_rot == 0) {

                 name_just = "right"

             } else if(name_rot == 90) {

@@ -192,7 +179,6 @@ SingleAnnotation = function(name, value, col, fun,

                 name_just = "top"

             }

     	} else {

-<<<<<<< HEAD

             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")

@@ -200,10 +186,6 @@ SingleAnnotation = function(name, value, col, fun,

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

         		name_y = unit(0.5, "npc")

             }

-=======

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

-    		name_y = unit(0.5, "npc")

->>>>>>> bioc/master

             if(name_rot == 0) {

                 name_just = "left"

             } else if(name_rot == 90) {

@@ -219,7 +201,6 @@ SingleAnnotation = function(name, value, col, fun,

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

     	}

     	if(name_side == "top") {

-<<<<<<< HEAD

             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

@@ -227,10 +208,6 @@ SingleAnnotation = function(name, value, col, fun,

         		name_x = unit(0.5, "npc")

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

             }

-=======

-    		name_x = unit(0.5, "npc")

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

->>>>>>> bioc/master

             if(name_rot == 0) {

                 name_just = "bottom"

             } else if(name_rot == 90) {

@@ -241,7 +218,6 @@ SingleAnnotation = function(name, value, col, fun,

                 name_just = "right"

             }

     	} else {

-<<<<<<< HEAD

             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

@@ -249,10 +225,6 @@ SingleAnnotation = function(name, value, col, fun,

         		name_x = unit(0.5, "npc")

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

             }

-=======

-    		name_x = unit(0.5, "npc")

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

->>>>>>> bioc/master

             if(name_rot == 0) {

                 name_just = "top"

             } else if(name_rot == 90) {

@@ -269,38 +241,18 @@ SingleAnnotation = function(name, value, col, fun,

     						  y = name_y,

     						  just = name_just,

     	                      gp = check_gp(name_gp),

-<<<<<<< HEAD

     	                      rot = name_rot,

                               side = name_side)

-=======

-    	                      rot = name_rot)

->>>>>>> bioc/master

     gp = check_gp(gp)

     if(!is.null(gp$fill)) {

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

     }

-<<<<<<< HEAD

-=======

-    if(!missing(value)) {

-	    if(is.logical(value)) {

-	    	value = as.character(value)

-	    }

-	    if(is.factor(value)) {

-            value = as.vector(value)

-        }

-	}

-

->>>>>>> bioc/master

     if(missing(fun)) {

     	if(missing(col)) {

     		col = default_col(value)

     	}

-<<<<<<< HEAD