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

 Package: ComplexHeatmap

 Type: Package

 Title: Making Complex Heatmaps

-Version: 1.7.4

-Date: 2015-11-24

+Version: 1.8.0

+Date: 2015-12-16

 Author: Zuguang Gu

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

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

@@ -18,6 +18,6 @@ Description: Complex heatmaps are efficient to visualize associations

 biocViews: Software, Visualization, Sequencing

 URL: https://github.com/jokergoo/ComplexHeatmap

 License: GPL (>= 2)

-Packaged: 2015-11-24 00:00:00 UTC; Administrator

+Packaged: 2015-12-16 00:00:00 UTC; Administrator

 Repository: Bioconductor

-Date/Publication: 2015-11-24 00:00:00

+Date/Publication: 2015-12-16 00:00:00

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

-CHANEGS in VERSION 1.7.4

+CHANEGS in VERSION 1.8.0

 * 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 +6,9 @@ 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

+* `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

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

@@ -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

@@ -55,6 +55,7 @@ SingleAnnotation = setClass("SingleAnnotation",

 #      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.

@@ -84,6 +85,7 @@ 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 +140,10 @@ SingleAnnotation = function(name, value, col, fun,

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

     			na_col = col["_NA_"]

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

-    		} else {

-    			na_col = "#FFFFFF"

     		}

             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

@@ -970,6 +970,9 @@ column_anno_text = function(...) {

 # 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 `HeatmapAnnotation` constructor method.

+#

 # == author

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

 anno_link = function(at, labels, which = c("column", "row"), side = ifelse(which == "column", "top", "right"),

@@ -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())

@@ -23,7 +23,6 @@

 # -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.

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

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

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

 #

@@ -55,8 +54,8 @@ oncoPrint = function(mat, get_type = function(x) x,

 	row_barplot_width = unit(2, "cm"),

 	remove_empty_columns = FALSE,

 	heatmap_legend_param = list(title = "Alterations"),

-	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")),

 	barplot_ignore = NULL,

 	...) {

@@ -81,8 +80,12 @@ 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 +253,7 @@ oncoPrint = function(mat, get_type = function(x) x,

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

 			}

 		}, show_column_names = show_column_names,

-		top_annotation = top_annotation, top_annotation_height = top_annotation_height,

+		top_annotation = top_annotation,

 		heatmap_legend_param = heatmap_legend_param, ...)

 	if(show_row_barplot) {

@@ -273,6 +276,9 @@ 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>

 #

@@ -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),

@@ -19,6 +20,7 @@ SingleAnnotation(name, value, col, fun,

   \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.}

@@ -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>

 }

@@ -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{

@@ -18,8 +18,8 @@ oncoPrint(mat, get_type = function(x) x,

     row_barplot_width = unit(2, "cm"),

     remove_empty_columns = FALSE,

     heatmap_legend_param = list(title = "Alterations"),

-    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")),

     barplot_ignore = NULL,

     ...)

 }

@@ -39,7 +39,6 @@ oncoPrint(mat, get_type = function(x) x,

   \item{remove_empty_columns}{if there is no alteration in that sample, whether remove it on the heatmap}

   \item{heatmap_legend_param}{pass to \code{\link{Heatmap}}}

   \item{top_annotation}{by default the top annotation contains barplots representing frequency of mutations in every sample.}

-  \item{top_annotation_height}{height of the top annotation, should be a \code{\link[grid]{unit}} object.}

   \item{barplot_ignore}{alterations that you don't want to put on the barplots.}

   \item{...}{pass to \code{\link{Heatmap}}, so can set \code{bottom_annotation} here.}

@@ -18,6 +18,9 @@ unify_mat_list(mat_list, default = 0)

 \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>

 }

@@ -531,7 +531,7 @@ upViewport(2)

 ## Mark some of the rows/columns

-From version 1.7.4, a new annotation function `anno_link()` was added which connects labels and subset of the rows

+From version 1.8.0, a new annotation function `anno_link()` was added which connects labels and subset of the rows

 by links. It is helpful when there are many rows/columns and we want to mark some of the rows (e.g. in a gene expression

 matrix, we want to mark some important genes of interest.)

@@ -133,8 +133,7 @@ decorate_heatmap_body("ht1", {

     grid.lines(c(0.5, 0.5), c(0, 1), gp = gpar(lty = 2, lwd = 2))

 }, slice = 2)

-suppressPackageStartupMessages(library(dendextend))

-decorate_dend("ht1", {

+decorate_column_dend("ht1", {

     tree = column_dend(ht_list)$ht1

     ind = cutree(as.hclust(tree), k = 2)[order.dendrogram(tree)]

@@ -144,15 +143,15 @@ decorate_dend("ht1", {

     x2 = c(last_index(ind == 1), last_index(ind == 2))

     grid.rect(x = x1/length(ind), width = (x2 - x1)/length(ind), just = "left",

         default.units = "npc", gp = gpar(fill = c("#FF000040", "#00FF0040"), col = NA))

-}, which = "column")

+})

-decorate_dimnames("ht2", {

+decorate_row_names("ht2", {

     grid.rect(gp = gpar(fill = "#FF000040"))

-}, which = "row", slice = 2)

+}, slice = 2)

-decorate_title("ht1", {

+decorate_row_title("ht1", {

     grid.rect(gp = gpar(fill = "#00FF0040"))

-}, which = "row", slice = 1)

+}, slice = 1)

 decorate_annotation("points", {

     grid.lines(c(0, 1), unit(c(0, 0), "native"), gp = gpar(col = "red"))