@@ -1,4 +1,8 @@

+<<<<<<< HEAD

 CHANEGS in VERSION 1.7.4

+=======

+CHANEGS in VERSION 1.8.0

+>>>>>>> master

 * width of the heatmap body are calculated correctly if it is set as a fixed unit

 * there is no dendrogram is nrows in a row-slice is 1

@@ -6,6 +10,12 @@ CHANEGS in VERSION 1.7.4

 * bottom annotations are attached to the bottom edge of the heatmap 

   if there are additional blank space

 * colors for NA can be set by "_NA_" in annotations

+<<<<<<< HEAD

+=======

+* `row_dend_reorder` and `column_dend_reorder` are set to `TRUE` by default again -_-!!

+* optimize the way to specify na_col in heatmap annotations

+* correct wrong viewport names in decorate_* functions

+>>>>>>> master

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

@@ -12,7 +12,7 @@ AdditiveUnit = setClass("AdditiveUnit")

 # Constructor method for AdditiveUnit class

 #

 # == param

-# -... arguments.

+# -... black hole arguments.

 #

 # == details

 # This method is not used in the package.

@@ -110,7 +110,9 @@ ColorMapping = function(name, colors = NULL, levels = NULL,

 	}

 	.Object@name = name

-	.Object@na_col = na_col

+	na_col = t(col2rgb(na_col, alpha = TRUE))

+	na_col = rgb(na_col[, 1:3, drop = FALSE], alpha = na_col[, 4], maxColorValue = 255)

+	.Object@na_col = na_col[1]

 	return(.Object)

 }

@@ -235,7 +235,7 @@ Heatmap = function(matrix, col, name,

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

     row_dend_width = unit(10, "mm"), 

     show_row_dend = TRUE, 

-    row_dend_reorder = FALSE,

+    row_dend_reorder = TRUE,

     row_dend_gp = gpar(), 

     row_hclust_side = row_dend_side,

     row_hclust_width = row_dend_width, 

@@ -249,7 +249,7 @@ Heatmap = function(matrix, col, name,

     column_dend_height = unit(10, "mm"), 

     show_column_dend = TRUE, 

     column_dend_gp = gpar(), 

-    column_dend_reorder = FALSE,

+    column_dend_reorder = TRUE,

     column_hclust_side = column_dend_side, 

     column_hclust_height = column_dend_height, 

     show_column_hclust = show_column_dend, 

@@ -41,6 +41,7 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",

 # -df a data frame. Each column will be treated as a simple annotation. The data frame must have column names.

 # -name name of the heatmap annotation, optional.

 # -col a list of colors which contains color mapping to columns in ``df``. See `SingleAnnotation` for how to set colors.

+# -na_col color for ``NA`` values in simple annotations.

 # -annotation_legend_param a list which contains parameters for annotation legends

 # -show_legend whether show legend for each column in ``df``.

 # -... functions which define complex annotations. Values should be named arguments.

@@ -65,7 +66,7 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",

 # == author

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

 #

-HeatmapAnnotation = function(df, name, col, 

+HeatmapAnnotation = function(df, name, col, na_col = "grey",

 	annotation_legend_param = list(), 

 	show_legend = TRUE, 

 	..., 

@@ -92,7 +93,7 @@ HeatmapAnnotation = function(df, name, col,

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

     called_args = names(arg_list)

-    anno_args = setdiff(called_args, c("name", "col", "annotation_legend_param", "show_legend", "which", 

+    anno_args = setdiff(called_args, c("name", "col", "na_col", "annotation_legend_param", "show_legend", "which", 

     	                             "annotation_height", "annotation_width", "height", "width", "gp", "gap"))

     if(any(anno_args == "")) stop("annotations should have names.")

     if(any(duplicated(anno_args))) stop("names of annotations should be unique.")

@@ -160,14 +161,14 @@ HeatmapAnnotation = function(df, name, col,

 		    if(missing(col)) {

 		        for(i in seq_len(n_anno)) {

-		        	anno_list = c(anno_list, list(SingleAnnotation(name = anno_name[i], value = df[, i], which = which, show_legend = show_legend[i_simple + i], gp = gp, legend_param = annotation_legend_param[[i_simple + i]])))

+		        	anno_list = c(anno_list, list(SingleAnnotation(name = anno_name[i], value = df[, i], na_col = na_col, which = which, show_legend = show_legend[i_simple + i], gp = gp, legend_param = annotation_legend_param[[i_simple + i]])))

 		        }

 		    } else {

 		        for(i in seq_len(n_anno)) {

 		        	if(is.null(col[[ anno_name[i] ]])) { # if the color is not provided

-		        		anno_list = c(anno_list, list(SingleAnnotation(name = anno_name[i], value = df[, i], which = which, show_legend = show_legend[i_simple + i], gp = gp, legend_param = annotation_legend_param[[i_simple + i]])))

+		        		anno_list = c(anno_list, list(SingleAnnotation(name = anno_name[i], value = df[, i], na_col = na_col, which = which, show_legend = show_legend[i_simple + i], gp = gp, legend_param = annotation_legend_param[[i_simple + i]])))

 		        	} else {

-		        		anno_list = c(anno_list, list(SingleAnnotation(name = anno_name[i], value = df[, i], col = col[[ anno_name[i] ]], which = which, show_legend = show_legend[i_simple + i], gp = gp, legend_param = annotation_legend_param[[i_simple + i]])))

+		        		anno_list = c(anno_list, list(SingleAnnotation(name = anno_name[i], value = df[, i], na_col = na_col, col = col[[ anno_name[i] ]], which = which, show_legend = show_legend[i_simple + i], gp = gp, legend_param = annotation_legend_param[[i_simple + i]])))

 		        	}

 		        }

 		    }

@@ -183,12 +184,12 @@ HeatmapAnnotation = function(df, name, col,

 			    	stop("length of simple annotations differ.")

 			    }

 				if(missing(col)) {

-			        anno_list = c(anno_list, list(SingleAnnotation(name = ag, value = anno_arg_list[[ag]], which = which, show_legend = show_legend[i_simple + 1], gp = gp, legend_param = annotation_legend_param[[i_simple + 1]])))

+			        anno_list = c(anno_list, list(SingleAnnotation(name = ag, value = anno_arg_list[[ag]], na_col = na_col, which = which, show_legend = show_legend[i_simple + 1], gp = gp, legend_param = annotation_legend_param[[i_simple + 1]])))

 			    } else {

 			        if(is.null(col[[ ag ]])) { # if the color is not provided

-			        	anno_list = c(anno_list, list(SingleAnnotation(name = ag, value = anno_arg_list[[ag]], which = which, show_legend = show_legend[i_simple + 1], gp = gp, legend_param = annotation_legend_param[[i_simple + 1]])))

+			        	anno_list = c(anno_list, list(SingleAnnotation(name = ag, value = anno_arg_list[[ag]], na_col = na_col, which = which, show_legend = show_legend[i_simple + 1], gp = gp, legend_param = annotation_legend_param[[i_simple + 1]])))

 			        } else {

-			        	anno_list = c(anno_list, list(SingleAnnotation(name = ag, value = anno_arg_list[[ag]], col = col[[ ag ]], which = which, show_legend = show_legend[i_simple + 1], gp = gp, legend_param = annotation_legend_param[[i_simple + 1]])))

+			        	anno_list = c(anno_list, list(SingleAnnotation(name = ag, value = anno_arg_list[[ag]], na_col = na_col, col = col[[ ag ]], which = which, show_legend = show_legend[i_simple + 1], gp = gp, legend_param = annotation_legend_param[[i_simple + 1]])))

 			        }

 			    }

 			    i_simple = i_simple + 1

@@ -8,6 +8,16 @@

 # == value

 # A list contains row orders which correspond to the original matrix

 #

+# == author

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

+#

+# == example

+# mat = matrix(rnorm(100), 10)

+# ht_list = Heatmap(mat) + Heatmap(mat)

+# row_order(ht_list)

+# ht = Heatmap(mat, km = 2) + Heatmap(mat)

+# row_order(ht_list)

+#

 setMethod(f = "row_order",

 	signature = "HeatmapList",

 	definition = function(object) {

@@ -18,9 +28,6 @@ setMethod(f = "row_order",

 	for(i in seq_len(n)) {

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

         	lt = object@ht_list[[i]]@row_order_list

-        	if(length(object@ht_list[[i]]@row_title) > 0) {

-        		names(lt) = object@ht_list[[i]]@row_title

-        	}

         	return(lt)

         }

     }

@@ -38,6 +45,16 @@ setMethod(f = "row_order",

 # == value

 # A list contains row orders which correspond to the original matrix

 #

+# == author

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

+#

+# == example

+# mat = matrix(rnorm(100), 10)

+# ht = Heatmap(mat)

+# row_order(ht)

+# ht = Heatmap(mat, km = 2)

+# row_order(ht)

+#

 setMethod(f = "row_order",

 	signature = "Heatmap",

 	definition = function(object) {

@@ -45,9 +62,6 @@ setMethod(f = "row_order",

 	object = prepare(object)

 	lt = object@row_order_list

-	if(length(object@row_title) > 0) {

-		names(lt) = object@row_title

-	}

 	return(lt)

 })

@@ -61,6 +75,16 @@ setMethod(f = "row_order",

 # == value

 # A list contains column orders which correspond every matrix

 #

+# == author

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

+#

+# == example

+# mat = matrix(rnorm(100), 10)

+# ht_list = Heatmap(mat) + Heatmap(mat)

+# column_order(ht_list)

+# ht = Heatmap(mat, km = 2) + Heatmap(mat)

+# column_order(ht_list)

+#

 setMethod(f = "column_order",

 	signature = "HeatmapList",

 	definition = function(object) {

@@ -91,6 +115,16 @@ setMethod(f = "column_order",

 # == value

 # A vector containing column orders

 #

+# == author

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

+#

+# == example

+# mat = matrix(rnorm(100), 10)

+# ht = Heatmap(mat)

+# column_order(ht)

+# ht = Heatmap(mat, km = 2)

+# column_order(ht)

+#

 setMethod(f = "column_order",

 	signature = "Heatmap",

 	definition = function(object) {

@@ -110,6 +144,16 @@ setMethod(f = "column_order",

 # == value

 # A list of dendrograms for which each dendrogram corresponds to a row slice

 #

+# == author

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

+#

+# == example

+# mat = matrix(rnorm(100), 10)

+# ht_list = Heatmap(mat) + Heatmap(mat)

+# row_dend(ht_list)

+# ht_list = Heatmap(mat, km = 2) + Heatmap(mat)

+# row_dend(ht_list)

+#

 setMethod(f = "row_dend",

 	signature = "HeatmapList",

 	definition = function(object) {

@@ -120,9 +164,6 @@ setMethod(f = "row_dend",

     for(i in seq_len(n)) {

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

         	lt = object@ht_list[[i]]@row_dend_list

-        	if(length(object@ht_list[[i]]@row_title) > 0) {

-        		names(lt) = object@ht_list[[i]]@row_title

-        	}

         	return(lt)

         }

     }

@@ -139,6 +180,16 @@ setMethod(f = "row_dend",

 # == value

 # A list of dendrograms for which each dendrogram corresponds to a row slice

 #

+# == author

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

+#

+# == example

+# mat = matrix(rnorm(100), 10)

+# ht = Heatmap(mat)

+# row_dend(ht)

+# ht = Heatmap(mat, km = 2)

+# row_dend(ht)

+#

 setMethod(f = "row_dend",

 	signature = "Heatmap",

 	definition = function(object) {

@@ -146,9 +197,6 @@ setMethod(f = "row_dend",

 	object = prepare(object)

 	lt = object@row_dend_list

-	if(length(object@row_title) > 0) {

-		names(lt) = object@row_title

-	}

 	return(lt)

 })

@@ -161,6 +209,16 @@ setMethod(f = "row_dend",

 # == value

 # A list of dendrograms for which dendrogram corresponds to each matrix

 #

+# == author

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

+#

+# == example

+# mat = matrix(rnorm(100), 10)

+# ht_list = Heatmap(mat) + Heatmap(mat)

+# column_dend(ht_list)

+# ht_list = Heatmap(mat, km = 2) + Heatmap(mat)

+# column_dend(ht_list)

+#

 setMethod(f = "column_dend",

 	signature = "HeatmapList",

 	definition = function(object) {

@@ -191,6 +249,16 @@ setMethod(f = "column_dend",

 # == value

 # A dendrogram object

 #

+# == author

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

+#

+# == example

+# mat = matrix(rnorm(100), 10)

+# ht = Heatmap(mat)

+# column_dend(ht)

+# ht = Heatmap(mat, km = 2)

+# column_dend(ht)

+#

 setMethod(f = "column_dend",

 	signature = "Heatmap",

 	definition = function(object) {

@@ -48,13 +48,14 @@ SingleAnnotation = setClass("SingleAnnotation",

 # Constructor method for SingleAnnotation class

 #

 # == param

-# -name name for this annotation. If it is not specified, an internal name is assigned to it.

+# -name name for this annotation. If it is not specified, an internal name is assigned.

 # -value A vector of discrete or continuous annotation.

 # -col colors corresponding to ``value``. If the mapping is discrete mapping, the value of ``col``

 #      should be a vector; If the mapping is continuous mapping, the value of ``col`` should be 

 #      a color mapping function. 

 # -fun a self-defined function to add annotation graphics. The argument of this function should only 

 #      be a vector of index that corresponds to rows or columns.

+# -na_col color for ``NA`` values in simple annotations.

 # -which is the annotation a row annotation or a column annotation?

 # -show_legend if it is a simple annotation, whether show legend when making the complete heatmap.

 # -gp Since simple annotation is represented as a row of grids. This argument controls graphic parameters for the simple annotation.

@@ -77,6 +78,10 @@ SingleAnnotation = setClass("SingleAnnotation",

 # One thing that users should be careful is the difference of coordinates when the annotation is a row

 # annotation or a column annotation. 

 #

+# == seealso

+# There are following built-in annotation functions that can be used to generate complex annotations: 

+# `anno_points`, `anno_barplot`, `anno_histogram`, `anno_boxplot`, `anno_density`, `anno_text` and `anno_link`.

+# 

 # == value

 # A `SingleAnnotation-class` object.

 #

@@ -84,6 +89,7 @@ SingleAnnotation = setClass("SingleAnnotation",

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

 #

 SingleAnnotation = function(name, value, col, fun, 

+	na_col = "grey",

 	which = c("column", "row"), 

 	show_legend = TRUE, 

 	gp = gpar(col = NA), 

@@ -138,12 +144,15 @@ SingleAnnotation = function(name, value, col, fun,

     		if("_NA_" %in% names(col)) {

     			na_col = col["_NA_"]

     			col = col[names(col) != "_NA_"]

+<<<<<<< HEAD

     		} else {

     			na_col = "#FFFFFF"

+=======

+>>>>>>> master

     		}

             color_mapping = ColorMapping(name = name, colors = col, na_col = na_col)

         } else if(is.function(col)) {

-            color_mapping = ColorMapping(name = name, col_fun = col)

+            color_mapping = ColorMapping(name = name, col_fun = col, na_col = na_col)

         }

         .Object@color_mapping = color_mapping

@@ -2,9 +2,9 @@

 # Decorate the heatmap body

 #

 # == param

-# -heatmap name of the heatmap

+# -heatmap name of the heatmap which is set as ``name`` option in `Heatmap` function

 # -code code that adds graphics in the selected heatmap body

-# -slice index of row slices in the heatmap

+# -slice index of row slices in the heatmap if it is split by rows

 #

 # == details

 # There is a viewport for each row slice in each heatmap.

@@ -43,9 +43,15 @@

 #

 decorate_heatmap_body = function(heatmap, code, slice = 1) {

-	vp_name = paste0(heatmap, "_heatmap_body_", slice)

+	if(is.null(slice)) {

+		vp_name = paste0(heatmap, "_heatmap_body_", 1)

+		seekViewport(vp_name)

+		upViewport()

+	} else {

+		vp_name = paste0(heatmap, "_heatmap_body_", slice)

+		seekViewport(vp_name)

+	}

-	seekViewport(vp_name)

 	e = new.env(parent = parent.frame())

 	eval(substitute(code), envir = e)

@@ -94,7 +100,14 @@ decorate_dend = function(heatmap, code, slice = 1, which = c("column", "row")) {

 	if(which == "column") {

 		vp_name = paste0(heatmap, "_dend_", which)

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

-		vp_name = paste0(heatmap, "_dend_", which, "_", slice)

+		if(is.null(slice)) {

+			vp_name = paste0(heatmap, "_dend_", which, "_", 1)

+			seekViewport(vp_name)

+			upViewport()

+		} else {

+			vp_name = paste0(heatmap, "_dend_", which, "_", slice)

+			seekViewport(vp_name)

+		}

 	}

 	seekViewport(vp_name)

@@ -197,7 +210,14 @@ decorate_dimnames = function(heatmap, code, slice = 1, which = c("column", "row"

 	if(which == "column") {

 		vp_name = paste0(heatmap, "_", which, "_names")

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

-		vp_name = paste0(heatmap, "_", which, "_names_", slice)

+		if(is.null(slice)) {

+			vp_name = paste0(heatmap, "_", which, "_names_", 1)

+			seekViewport(vp_name)

+			upViewport()

+		} else {

+			vp_name = paste0(heatmap, "_", which, "_names_", slice)

+			seekViewport(vp_name)

+		}

 	}

 	seekViewport(vp_name)

@@ -287,7 +307,14 @@ decorate_title = function(heatmap, code, slice = 1, which = c("column", "row"))

 	if(which == "column") {

 		vp_name = paste0(heatmap, "_", which, "_title")

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

-		vp_name = paste0(heatmap, "_", which, "_title_", slice)

+		if(is.null(slice)) {

+			vp_name = paste0(heatmap, "_", which, "_title_", 1)

+			seekViewport(vp_name)

+			upViewport()

+		} else {

+			vp_name = paste0(heatmap, "_", which, "_title_", slice)

+			seekViewport(vp_name)

+		}

 	}

 	seekViewport(vp_name)

@@ -376,9 +403,9 @@ decorate_column_title = function(...) {

 #     grid.rect(gp = gpar(fill = "#FF000080"))

 # }, slice = 2)

 #

-decorate_annotation = function(annotation, code, slice = NULL) {

+decorate_annotation = function(annotation, code, slice) {

-	if(is.null(slice)) {

+	if(missing(slice)) {

 		vp_name = paste0("annotation_", annotation)

 		o = try(seekViewport(vp_name), silent = TRUE)

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

@@ -391,8 +418,14 @@ decorate_annotation = function(annotation, code, slice = NULL) {

 		}

 		seekViewport(vp_name)

 	} else {

-		vp_name = paste0("annotation_", annotation, "_", slice)

-		seekViewport(vp_name)

+		if(is.null(slice)) {

+			vp_name = paste0("annotation_", annotation, "_", 1)

+			seekViewport(vp_name)

+			upViewport()

+		} else {

+			vp_name = paste0("annotation_", annotation, "_", slice)

+			seekViewport(vp_name)

+		}

 	}

 	e = new.env(parent = parent.frame())

@@ -104,5 +104,5 @@ densityHeatmap = function(data,

 		upViewport()

 	})

-	return(invisible(ht_list))

+	return(invisible(NULL))

 }

@@ -17,6 +17,7 @@

 # -pch shape of outlier points in the boxplot

 # -size size of hte outlier points in the boxplot

 # -axis_gp graphic parameters for the axis

+# -padding padding of the plot

 # -heatmap_legend_list a list of `grid::grob` which contains legend. It can be generated by `color_mapping_legend,ColorMapping-method`.

 #

 # == details

@@ -42,6 +43,7 @@ enhanced_basicplot = function(data, ..., ylim = NULL,

     ylab = deparse(substitute(data)), title = NULL, title_gp = gpar(fontsize = 14),

     type = c("boxplot", "barplot"), width = 0.8, gp = gpar(), 

     pch = 1, size = unit(2, "mm"), axis_gp = gpar(fontsize = 8),

+    padding = unit(c(2, 18, 2, 2), "mm"),

     heatmap_legend_list = list()) {

     if(!(inherits(data, c("matrix")) || inherits(data, "list") || is.atomic(data))) {

@@ -76,7 +78,7 @@ enhanced_basicplot = function(data, ..., ylim = NULL,

     ht = Heatmap(mat_foo, name = "main", cluster_rows = FALSE, cluster_columns = FALSE,

                 rect_gp = gpar(type = "none"), show_heatmap_legend = FALSE, ...)

-    draw(ht, padding = unit(c(2, 18, 2, 2), "mm"), column_title = title, column_title_gp = title_gp,

+    draw(ht, padding = padding, column_title = title, column_title_gp = title_gp,

         heatmap_legend_list = heatmap_legend_list)

     if(is.matrix(data)) {

@@ -1,7 +1,7 @@

 # == title

-# Global options for heatmaps

+# Global graphic options for heatmaps

 #

 # == param

 # -... options, see 'details' section

@@ -11,8 +11,8 @@

 #

 # == details

 # You can set some parameters for all heatmaps/annotations simultaneously by this global function.

-# Pleast note you should better to put it in the first beginning of your heatmap code and reset

-# all option values to get avoid of affecting next heatmap plotting.

+# Pleast note you should put it before your heatmap code and reset

+# all option values after drawing the heatmaps to get rid of affecting next heatmap plotting.

 #

 # There are following parameters:

 #

@@ -42,6 +42,9 @@

 # Besides the normal absolute units (e.g. "mm", "inches"), this function

 # simply treat `grid::grob` objects as absolute units.

 #

+# For a complex unit which is combination of different units, it is absolute

+# only if all units included are absolute units.

+#

 # == value

 # A logical value.

 #

@@ -52,6 +55,7 @@

 # is_abs_unit(unit(1, "mm"))

 # is_abs_unit(unit(1, "npc"))

 # is_abs_unit(textGrob("foo"))

+# is_abs_unit(unit(1, "mm") + unit(1, "npc"))

 #

 is_abs_unit = function(u) {

 	if(inherits(u, "unit.arithmetic")) .is_abs_unit.unit.arithmetic(u)

@@ -23,7 +23,10 @@

 # -remove_empty_columns if there is no alteration in that sample, whether remove it on the heatmap

 # -heatmap_legend_param pass to `Heatmap`

 # -top_annotation by default the top annotation contains barplots representing frequency of mutations in every sample.

+<<<<<<< HEAD

 # -top_annotation_height height of the top annotation, should be a `grid::unit` object.

+=======

+>>>>>>> master

 # -barplot_ignore alterations that you don't want to put on the barplots.

 # -... pass to `Heatmap`, so can set ``bottom_annotation`` here.

 #

@@ -55,8 +58,13 @@ oncoPrint = function(mat, get_type = function(x) x,

 	row_barplot_width = unit(2, "cm"),

 	remove_empty_columns = FALSE,

 	heatmap_legend_param = list(title = "Alterations"),

+<<<<<<< HEAD

 	top_annotation = HeatmapAnnotation(column_bar = anno_column_bar),

 	top_annotation_height = unit(2, "cm"),

+=======

+	top_annotation = HeatmapAnnotation(column_bar = anno_column_bar, 

+		annotation_height = unit(2, "cm")),

+>>>>>>> master

 	barplot_ignore = NULL,

 	...) {

@@ -81,8 +89,12 @@ oncoPrint = function(mat, get_type = function(x) x,

 		})

 	} else if(inherits(mat, "list")) {

 		mat_list = mat

+

 		all_type = names(mat_list)

 		mat_list = lapply(mat_list, function(x) {

+				if(!is.matrix(x)) {

+					stop("Expect a list of matrix (not data frames).")

+				}

 				oattr = attributes(x)

 				x = as.logical(x)

 				attributes(x) = oattr

@@ -250,7 +262,11 @@ oncoPrint = function(mat, get_type = function(x) x,

 				add_oncoprint(type, x, y, width, height)

 			}

 		}, show_column_names = show_column_names,

+<<<<<<< HEAD

 		top_annotation = top_annotation, top_annotation_height = top_annotation_height,

+=======

+		top_annotation = top_annotation,

+>>>>>>> master

 		heatmap_legend_param = heatmap_legend_param, ...)

 	if(show_row_barplot) {

@@ -273,6 +289,9 @@ oncoPrint = function(mat, get_type = function(x) x,

 # == details

 # All matrix will be unified to have same row names and column names

 #

+# == value

+# A list of matrix

+#

 # == author

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

 #

@@ -102,6 +102,8 @@ plotDataFrame = function(df, overlap = 0.25, nlevel = 30, show_row_names = TRUE,

 		if(is.null(main_heatmap)) {

 			main_heatmap = which.max(sapply(group, length))

+		} else if(!is.numeric(main_heatmap) && !is.null(group_names)) {

+			main_heatmap = which(group_names == main_heatmap)[1]

 		}

 		i_max = max(unlist(group))

@@ -82,8 +82,10 @@ default_col = function(x, main_matrix = FALSE) {

 # -dend a `stats::dendrogram` object.

 # -facing facing of the dendrogram.

 # -max_height maximum height of the dendrogram. It is useful to make dendrograms comparable

-#             if you want to plot more than one dendrograms.

+#             if you want to plot more than one dendrograms. Height for each dendrogram can be obtained by

+#             ``attr(dend, "height")``.

 # -order should leaves of dendrogram be put in the normal order (1, ..., n) or reverse order (n, ..., 1)?

+#        It may matters for the dendrograms putting on left and right.

 # -... pass to `grid::viewport` which contains the dendrogram.

 #

 # == details

@@ -466,14 +468,21 @@ list_component = function() {

 # -text a vector of text

 # -... pass to `grid::textGrob`

 #

+# == details

+# Simply calculate maximum width of a list of `grid::textGrob` objects.

+#

 # == value

 # A `grid::unit` object.

 #

 # == author

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

 #

+# == seealso

+# `max_text_width` is always used to calculate the size of viewport when there is text annotation (`anno_text`)

+#

 # == example

-# max_text_width(letters, gp = gpar(fontsize = 10))

+# x = c("a", "bb", "ccc")

+# max_text_width(x, gp = gpar(fontsize = 10))

 #

 max_text_width = function(text, ...) {

     max(do.call("unit.c", lapply(text, function(x) grobWidth(textGrob(x, ...)))))

@@ -486,14 +495,21 @@ max_text_width = function(text, ...) {

 # -text a vector of text

 # -... pass to `grid::textGrob`

 #

+# == details

+# Simply calculate maximum height of a list of `grid::textGrob` objects.

+#

 # == value

 # A `grid::unit` object.

 #

+# == seealso

+# `max_text_height` is always used to calculate the size of viewport when there is text annotation (`anno_text`)

+#

 # == author

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

 #

 # == example

-# max_text_height(letters, gp = gpar(fontsize = 10))

+# x = c("a", "b\nb", "c\nc\nc")

+# max_text_height(x, gp = gpar(fontsize = 10))

 #

 max_text_height = function(text, ...) {

     max(do.call("unit.c", lapply(text, function(x) grobHeight(textGrob(x, ...)))))

@@ -11,7 +11,7 @@ AdditiveUnit(...)

 }

 \arguments{

-  \item{...}{arguments.}

+  \item{...}{black hole arguments.}

 }

 \details{

@@ -26,7 +26,7 @@ Heatmap(matrix, col, name,

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

     row_dend_width = unit(10, "mm"),

     show_row_dend = TRUE,

-    row_dend_reorder = FALSE,

+    row_dend_reorder = TRUE,

     row_dend_gp = gpar(),

     row_hclust_side = row_dend_side,

     row_hclust_width = row_dend_width,

@@ -40,7 +40,7 @@ Heatmap(matrix, col, name,

     column_dend_height = unit(10, "mm"),

     show_column_dend = TRUE,

     column_dend_gp = gpar(),

-    column_dend_reorder = FALSE,

+    column_dend_reorder = TRUE,

     column_hclust_side = column_dend_side,

     column_hclust_height = column_dend_height,

     show_column_hclust = show_column_dend,

@@ -7,7 +7,7 @@ Constructor method for HeatmapAnnotation class

 Constructor method for HeatmapAnnotation class

 }

 \usage{

-HeatmapAnnotation(df, name, col,

+HeatmapAnnotation(df, name, col, na_col = "grey",

     annotation_legend_param = list(),

     show_legend = TRUE,

     ...,

@@ -24,6 +24,7 @@ HeatmapAnnotation(df, name, col,

   \item{df}{a data frame. Each column will be treated as a simple annotation. The data frame must have column names.}

   \item{name}{name of the heatmap annotation, optional.}

   \item{col}{a list of colors which contains color mapping to columns in \code{df}. See \code{\link{SingleAnnotation}} for how to set colors.}

+  \item{na_col}{color for \code{NA} values in simple annotations.}

   \item{annotation_legend_param}{a list which contains parameters for annotation legends}

   \item{show_legend}{whether show legend for each column in \code{df}.}

   \item{...}{functions which define complex annotations. Values should be named arguments.}

@@ -8,6 +8,7 @@ Constructor method for SingleAnnotation class

 }

 \usage{

 SingleAnnotation(name, value, col, fun,

+    na_col = "grey",

     which = c("column", "row"),

     show_legend = TRUE,

     gp = gpar(col = NA),

@@ -15,10 +16,11 @@ SingleAnnotation(name, value, col, fun,

 }

 \arguments{

-  \item{name}{name for this annotation. If it is not specified, an internal name is assigned to it.}

+  \item{name}{name for this annotation. If it is not specified, an internal name is assigned.}

   \item{value}{A vector of discrete or continuous annotation.}

   \item{col}{colors corresponding to \code{value}. If the mapping is discrete mapping, the value of \code{col} should be a vector; If the mapping is continuous mapping, the value of \code{col} should be  a color mapping function. }

   \item{fun}{a self-defined function to add annotation graphics. The argument of this function should only  be a vector of index that corresponds to rows or columns.}

+  \item{na_col}{color for \code{NA} values in simple annotations.}

   \item{which}{is the annotation a row annotation or a column annotation?}

   \item{show_legend}{if it is a simple annotation, whether show legend when making the complete heatmap.}

   \item{gp}{Since simple annotation is represented as a row of grids. This argument controls graphic parameters for the simple annotation.}

@@ -42,6 +44,10 @@ and \code{fun} will be applied on each of the row slices.

 One thing that users should be careful is the difference of coordinates when the annotation is a row

 annotation or a column annotation.

 }

+\seealso{

+There are following built-in annotation functions that can be used to generate complex annotations: 

+\code{\link{anno_points}}, \code{\link{anno_barplot}}, \code{\link{anno_histogram}}, \code{\link{anno_boxplot}}, \code{\link{anno_density}}, \code{\link{anno_text}} and \code{\link{anno_link}}.

+}

 \value{

 A \code{\link{SingleAnnotation-class}} object.

 }

@@ -27,6 +27,9 @@ Sometimes there are many rows or columns in the heatmap and we want to mark some

 This annotation function is used to mark these rows and connect labels and corresponding rows

 with links.

 }

+\value{

+A graphic function which can be set in \code{\link{HeatmapAnnotation}} constructor method.

+}

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

@@ -17,8 +17,13 @@ Get column dendrograms from a heatmap

 \value{

 A dendrogram object

 }

+\author{

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

+}

 \examples{

-# There is no example

-NULL

-

+mat = matrix(rnorm(100), 10)

+ht = Heatmap(mat)

+column_dend(ht)

+ht = Heatmap(mat, km = 2)

+column_dend(ht)

 }

@@ -17,8 +17,13 @@ Get column dendrograms from a heatmap list

 \value{

 A list of dendrograms for which dendrogram corresponds to each matrix

 }

+\author{

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

+}

 \examples{

-# There is no example

-NULL

-

+mat = matrix(rnorm(100), 10)

+ht_list = Heatmap(mat) + Heatmap(mat)

+column_dend(ht_list)

+ht_list = Heatmap(mat, km = 2) + Heatmap(mat)

+column_dend(ht_list)

 }

@@ -17,8 +17,13 @@ Get column order from a heatmap list

 \value{

 A vector containing column orders

 }

+\author{

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

+}

 \examples{

-# There is no example

-NULL

-

+mat = matrix(rnorm(100), 10)

+ht = Heatmap(mat)

+column_order(ht)

+ht = Heatmap(mat, km = 2)

+column_order(ht)

 }

@@ -17,8 +17,13 @@ Get column order from a heatmap list

 \value{

 A list contains column orders which correspond every matrix

 }

+\author{

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

+}

 \examples{

-# There is no example

-NULL

-

+mat = matrix(rnorm(100), 10)

+ht_list = Heatmap(mat) + Heatmap(mat)

+column_order(ht_list)

+ht = Heatmap(mat, km = 2) + Heatmap(mat)

+column_order(ht_list)

 }

@@ -7,7 +7,7 @@ Decorate the heatmap annotation

 Decorate the heatmap annotation

 }

 \usage{

-decorate_annotation(annotation, code, slice = NULL)

+decorate_annotation(annotation, code, slice)

 }

 \arguments{

@@ -11,9 +11,9 @@ decorate_heatmap_body(heatmap, code, slice = 1)

 }

 \arguments{

-  \item{heatmap}{name of the heatmap}

+  \item{heatmap}{name of the heatmap which is set as \code{name} option in \code{\link{Heatmap}} function}

   \item{code}{code that adds graphics in the selected heatmap body}

-  \item{slice}{index of row slices in the heatmap}

+  \item{slice}{index of row slices in the heatmap if it is split by rows}

 }

 \details{

@@ -33,8 +33,11 @@ colnames(mat) = letters[1:10]

 d2 = dist2(mat)

 d2 = dist2(mat, pairwise_fun = function(x, y) 1 - cor(x, y))

+# distance only calculated within 10 and 90 quantile of each vector

 d2 = dist2(mat, pairwise_fun = function(x, y) {

-    l = is.na(x) & is.na(y)

+	q1 = quantile(x, c(0.1, 0.9))

+	q2 = quantile(y, c(0.1, 0.9))

+    l = x > q1[1] & x < q1[2] & y > q2[1] & y < q2[2]

     sqrt(sum((x[l] - y[l])^2))

 })

@@ -11,6 +11,7 @@ enhanced_basicplot(data, ..., ylim = NULL,

     ylab = deparse(substitute(data)), title = NULL, title_gp = gpar(fontsize = 14),

     type = c("boxplot", "barplot"), width = 0.8, gp = gpar(),

     pch = 1, size = unit(2, "mm"), axis_gp = gpar(fontsize = 8),

+    padding = unit(c(2, 18, 2, 2), "mm"),

     heatmap_legend_list = list())

 }

 \arguments{

@@ -27,6 +28,7 @@ enhanced_basicplot(data, ..., ylim = NULL,

   \item{pch}{shape of outlier points in the boxplot}

   \item{size}{size of hte outlier points in the boxplot}

   \item{axis_gp}{graphic parameters for the axis}

+  \item{padding}{padding of the plot}

   \item{heatmap_legend_list}{a list of \code{\link[grid]{grob}} which contains legend. It can be generated by \code{\link{color_mapping_legend,ColorMapping-method}}.}

 }

@@ -14,8 +14,8 @@ grid.dendrogram(dend, facing = c("bottom", "top", "left", "right"),

   \item{dend}{a \code{\link[stats]{dendrogram}} object.}