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

 Package: ComplexHeatmap

 Type: Package

 Title: Making Complex Heatmaps

-Version: 1.2.6

+Version: 1.2.7

 Date: 2015-7-18

 Author: Zuguang Gu

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

@@ -5,7 +5,6 @@ export(anno_histogram)

 export(HeatmapAnnotation)

 export(plotDataFrame)

 exportMethods(draw_dimnames)

-export(+.AdditiveUnit)

 exportClasses(ColorMapping)

 export(ColorMapping)

 exportClasses(HeatmapAnnotation)

@@ -15,6 +14,7 @@ export(anno_points)

 exportMethods(draw_title)

 exportMethods(draw)

 exportMethods(draw_heatmap_body)

+export('+.AdditiveUnit')

 exportMethods(color_mapping_legend)

 exportMethods(prepare)

 exportMethods(heatmap_legend_size)

@@ -1,3 +1,11 @@

+CHANGES in VERSION 1.2.7

+

+* add `rows_reorder_weight` and `columns_reorder_weight` in `Heatmap()`

+* `draw,HeatmapList-method` returns a list of orders

+* clustering is stored as dendrogram internally

+

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

+

 CHANGES in VERSION 1.2.6

 * graphical parameters for row names can be set as same length

@@ -157,12 +157,16 @@ Heatmap = setClass("Heatmap",

 # -column_order order of column. It makes it easy to adjust column order for both matrix and column annotations.

 # -row_names_side should the row names be put on the left or right of the heatmap?

 # -show_row_names whether show row names.

+# -row_reorder apply reordering on rows. The value can be a logical value or a vector which contains weight 

+#               which is used to reorder rows

 # -row_names_max_width maximum width of row names viewport. Because some times row names can be very long, it is not reasonable

 #                      to show them all.

 # -row_names_gp graphic parameters for drawing text.

 # -column_names_side should the column names be put on the top or bottom of the heatmap?

 # -column_names_max_height maximum height of column names viewport.

 # -show_column_names whether show column names.

+# -column_reorder apply reordering on columns. The value can be a logical value or a vector which contains weight 

+#               which is used to reorder columns

 # -column_names_gp graphic parameters for drawing text.

 # -top_annotation a `HeatmapAnnotation` object which contains a list of annotations.

 # -top_annotation_height total height of the column annotations on the top.

@@ -214,10 +218,12 @@ Heatmap = function(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),

     cluster_rows = TRUE, clustering_distance_rows = "euclidean",

     clustering_method_rows = "complete", row_hclust_side = c("left", "right"),

     row_hclust_width = unit(10, "mm"), show_row_hclust = TRUE, 

+    row_reorder = NULL,

     row_hclust_gp = gpar(), cluster_columns = TRUE, 

     clustering_distance_columns = "euclidean", clustering_method_columns = "complete",

     column_hclust_side = c("top", "bottom"), column_hclust_height = unit(10, "mm"), 

     show_column_hclust = TRUE, column_hclust_gp = gpar(), 

+    column_reorder = NULL,

     row_order = NULL, column_order = NULL,

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

     row_names_max_width = unit(4, "cm"), row_names_gp = gpar(fontsize = 12), 

@@ -281,9 +287,13 @@ Heatmap = function(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),

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

             .Object@matrix_param$split = split

         } else {

-            if(!is.data.frame(split)) split = data.frame(split)

-            if(nrow(split) != nrow(matrix)) {

-                stop("Length or number of rows of `split` should be same as rows in `matrix`.")

+            if(identical(cluster_rows, TRUE) && is.numeric(split) && length(split) == 1) {

+

+            } else {

+                if(!is.data.frame(split)) split = data.frame(split)

+                if(nrow(split) != nrow(matrix)) {

+                    stop("Length or number of rows of `split` should be same as rows in `matrix`.")

+                }

             }

         }

     }

@@ -398,6 +408,7 @@ Heatmap = function(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),

     .Object@row_hclust_param$width = row_hclust_width + unit(1, "mm")  # append the gap

     .Object@row_hclust_param$show = show_row_hclust

     .Object@row_hclust_param$gp = check_gp(row_hclust_gp)

+    .Object@row_hclust_param$reorder = row_reorder

     .Object@row_order_list = list() # default order

     if(is.null(row_order)) {

         .Object@row_order = seq_len(nrow(matrix))

@@ -431,6 +442,7 @@ Heatmap = function(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),

     .Object@column_hclust_param$height = column_hclust_height + unit(1, "mm")  # append the gap

     .Object@column_hclust_param$show = show_column_hclust

     .Object@column_hclust_param$gp = check_gp(column_hclust_gp)

+    .Object@column_hclust_param$reorder = column_reorder

     if(is.null(column_order)) {

         .Object@column_order = seq_len(ncol(matrix))

     } else {

@@ -520,6 +532,7 @@ setMethod(f = "make_column_cluster",

     distance = object@column_hclust_param$distance

     method = object@column_hclust_param$method

     order = object@column_order

+    reorder = object@column_hclust_param$reorder

     if(object@column_hclust_param$cluster) {

         if(!is.null(object@column_hclust_param$obj)) {

@@ -530,6 +543,35 @@ setMethod(f = "make_column_cluster",

             object@column_hclust = hclust(get_dist(t(mat), distance), method = method)

         }

         column_order = get_hclust_order(object@column_hclust)  # we don't need the pre-defined orders

+

+        if(inherits(object@column_hclust, "hclust")) {

+            object@column_hclust = as.dendrogram(object@column_hclust)

+        }

+

+        if(identical(reorder, NULL)) {

+            if(is.numeric(mat)) {

+                reorder = TRUE

+            } else {

+                reorder = FALSE

+            }

+        }

+

+        do_reorder = TRUE

+        if(identical(reorder, NA) || identical(reorder, FALSE)) {

+            do_reorder = FALSE

+        }

+        if(identical(reorder, TRUE)) {

+            do_reorder = TRUE

+            reorder = colMeans(mat, na.rm = TRUE)

+        }

+

+        if(do_reorder) {

+            if(length(reorder) != ncol(mat)) {

+                stop("weight of reordering should have same length as number of columns.\n")

+            }

+            object@column_hclust = reorder(object@column_hclust, reorder)

+            column_order = order.dendrogram(object@column_hclust)

+        }

     } else {

         column_order = order

     }

@@ -574,9 +616,16 @@ setMethod(f = "make_row_cluster",

     order = object@row_order  # pre-defined row order

     km = object@matrix_param$km

     split = object@matrix_param$split

+    reorder = object@row_hclust_param$reorder

     if(object@row_hclust_param$cluster) {

+        if(is.numeric(split) && length(split) == 1) {

+            if(is.null(object@row_hclust_param$obj)) {

+                object@row_hclust_param$obj = hclust(get_dist(mat, distance), method = method)

+            }

+        }

+

         if(!is.null(object@row_hclust_param$obj)) {

             if(km > 1) {

                 stop("You can not make k-means clustering since you have already specified a clustering object.")

@@ -677,7 +726,7 @@ setMethod(f = "make_row_cluster",

             object@row_title = row_level

         }

     }

-

+    o_row_order_list = row_order_list

     # make hclust in each slice

     if(object@row_hclust_param$cluster) {

         row_hclust_list = rep(list(NULL), length(row_order_list))

@@ -696,15 +745,52 @@ setMethod(f = "make_row_cluster",

             }

         }

         object@row_hclust_list = row_hclust_list

+

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

+            if(inherits(object@row_hclust_list[[i]], "hclust")) {

+                object@row_hclust_list[[i]] = as.dendrogram(object@row_hclust_list[[i]])

+            }

+        }

+

+        if(identical(reorder, NULL)) {

+            if(is.numeric(mat)) {

+                reorder = TRUE

+            } else {

+                reorder = FALSE

+            }

+        }

+

+        do_reorder = TRUE

+        if(identical(reorder, NA) || identical(reorder, FALSE)) {

+            do_reorder = FALSE

+        }

+        if(identical(reorder, TRUE)) {

+            do_reorder = TRUE

+            reorder = rowMeans(mat, na.rm = TRUE)

+        }

+

+        if(do_reorder) {

+            if(length(reorder) != nrow(mat)) {

+                stop("weight of reordering should have same length as number of rows.\n")

+            }

+            for(i in seq_along(row_hclust_list)) {

+                object@row_hclust_list[[i]] = reorder(object@row_hclust_list[[i]], reorder[which(seq_len(nrow(mat)) %in% o_row_order_list[[i]])])

+                row_order_list[[i]] = o_row_order_list[[i]][ order.dendrogram(object@row_hclust_list[[i]]) ]

+            }

+        }

     }

+

+    

+

     object@row_order_list = row_order_list

     object@matrix_param$split = split

+

     if(nrow(mat) != length(unlist(row_order_list))) {

         stop("Number of rows in the matrix are not the same as the length of\nthe cluster or the row orders.")

     }

-    # adjust row_names_param$gp is the length of some elements is the same as row slices

+    # adjust row_names_param$gp if the length of some elements is the same as row slices

     for(i in seq_along(object@row_names_param$gp)) {

         if(length(object@row_names_param$gp[[i]]) == length(object@row_order_list)) {

             gp_temp = NULL

@@ -714,7 +800,6 @@ setMethod(f = "make_row_cluster",

             object@row_names_param$gp[[i]] = gp_temp

         }

     }

-

     return(object)

 })

@@ -553,7 +553,7 @@ setMethod(f = "make_layout",

 # in the layout.

 #

 # == value

-# This function returns a list of `stats::hclust` objects.

+# This function returns a list of row dendrograms and column dendrogram.

 #

 # == author

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

@@ -595,35 +595,21 @@ setMethod(f = "draw",

     upViewport()

-    # return a list of hclust object

+    # return a list of orders

     n = length(object@ht_list)

-    hclust_list = vector("list", n)

-    names(hclust_list) = sapply(object@ht_list, function(ht) ht@name)

+    dend_list = vector("list", n)

+    names(dend_list) = sapply(object@ht_list, function(ht) ht@name)

     for(i in seq_len(n)) {

-        hclust_list[[i]] = list(row = NULL, column = NULL)

+        dend_list[[i]] = list(row = NULL, column = NULL)

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

         } else {

-            tree = object@ht_list[[i]]@column_hclust

-            # if(is.null(tree)) {

-            #     hclust_list[[i]]$column = NULL

-            # } else if(inherits(tree, "dendrogram")) {

-            #     hclust_list[[i]]$column = as.hclust(tree)

-            # } else {

-                hclust_list[[i]]$column = tree

-            # }

-            tree_list = object@ht_list[[i]]@row_hclust_list

-            # for(j in seq_along(tree_list)) {

-            #     if(is.null(tree_list[[j]])) {

-            #     } else if(inherits(tree_list[[j]], "dendrogram")) {

-            #         tree_list[[j]] = as.hclust(tree_list[[j]])

-            #     }

-            # }

-            hclust_list[[i]]$row = tree_list

+            dend_list[[i]]$column = object@ht_list[[i]]@column_hclust

+            dend_list[[i]]$row = object@ht_list[[i]]@row_hclust_list

         }

     }

-    return(invisible(hclust_list))

+    return(invisible(dend_list))

 })

 # == title

@@ -15,5 +15,7 @@ It is only designed for \code{+} generic method so that above three classes can

 }

 \examples{

+

+

 # no example

 NULL}

@@ -27,5 +27,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example

 NULL}

@@ -30,5 +30,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # for examples, please go to `ColorMapping` method page

 NULL}

@@ -38,6 +38,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # discrete color mapping for characters

 cm = ColorMapping(name = "test",

     colors = c("blue", "white", "red"),

@@ -72,5 +72,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # for examples, please go to `Heatmap` method page

 NULL}

@@ -19,10 +19,12 @@ Heatmap(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),

     cluster_rows = TRUE, clustering_distance_rows = "euclidean",

     clustering_method_rows = "complete", row_hclust_side = c("left", "right"),

     row_hclust_width = unit(10, "mm"), show_row_hclust = TRUE,

+    row_reorder = NULL,

     row_hclust_gp = gpar(), cluster_columns = TRUE,

     clustering_distance_columns = "euclidean", clustering_method_columns = "complete",

     column_hclust_side = c("top", "bottom"), column_hclust_height = unit(10, "mm"),

     show_column_hclust = TRUE, column_hclust_gp = gpar(),

+    column_reorder = NULL,

     row_order = NULL, column_order = NULL,

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

     row_names_max_width = unit(4, "cm"), row_names_gp = gpar(fontsize = 12),

@@ -73,11 +75,13 @@ Heatmap(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),

   \item{column_order}{order of column. It makes it easy to adjust column order for both matrix and column annotations.}

   \item{row_names_side}{should the row names be put on the left or right of the heatmap?}

   \item{show_row_names}{whether show row names.}

+  \item{row_reorder}{apply reordering on rows. The value can be a logical value or a vector which contains weight which is used to reorder rows}

   \item{row_names_max_width}{maximum width of row names viewport. Because some times row names can be very long, it is not reasonableto show them all.}

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

   \item{column_names_side}{should the column names be put on the top or bottom of the heatmap?}

   \item{column_names_max_height}{maximum height of column names viewport.}

   \item{show_column_names}{whether show column names.}

+  \item{column_reorder}{apply reordering on columns. The value can be a logical value or a vector which contains weight which is used to reorder columns}

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

   \item{top_annotation}{a \code{\link{HeatmapAnnotation}} object which contains a list of annotations.}

   \item{top_annotation_height}{total height of the column annotations on the top.}

@@ -118,6 +122,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -29,5 +29,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # for examples, please go to `HeatmapAnnotation` method page

 NULL}

@@ -48,6 +48,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))

 ha = HeatmapAnnotation(df = df)

@@ -68,6 +68,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -27,7 +27,11 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \section{Detailes}{

+

+

 There is no public constructor method for the \code{\link{HeatmapList-class}}.}

 \examples{

+

+

 # no example

 NULL}

@@ -39,5 +39,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # for examples, please go to `SingleAnnotation` method page

 NULL}

@@ -49,6 +49,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # discrete character

 SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))

 SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"), 

@@ -31,6 +31,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -28,6 +28,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -28,6 +28,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -28,6 +28,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -31,6 +31,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 f = anno_barplot(rnorm(10))

 grid.newpage(); f(1:10)

@@ -32,6 +32,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(32), nrow = 4)

 f = anno_boxplot(mat)

 grid.newpage(); f(1:8)

@@ -28,6 +28,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(32), nrow = 4)

 f = anno_density(mat)

 grid.newpage(); f(1:8)

@@ -26,6 +26,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(32), nrow = 4)

 f = anno_histogram(mat)

 grid.newpage(); f(1:8)

@@ -33,5 +33,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 f = anno_points(rnorm(10))

 grid.newpage(); f(1:10)}

@@ -29,6 +29,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(100), 10)

 colnames(mat) = letters[1:10]

 rownames(mat) = LETTERS[1:10]

@@ -33,5 +33,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -38,6 +38,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # discrete color mapping for characters

 cm = ColorMapping(name = "test",

     colors = c("blue", "white", "red"),

@@ -31,5 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))

 ha = rowAnnotation(df = df)}

@@ -28,4 +28,6 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method}

@@ -24,4 +24,6 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method}

@@ -20,6 +20,8 @@ This function is only for internal use.

 }

 \section{Detials}{

+

+

 This function is only for internal use.}

 \value{

 A \code{\link[grid]{unit}} object.

@@ -30,4 +32,6 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method}

@@ -28,4 +28,6 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method}

@@ -30,6 +30,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(40), nr = 4, ncol = 10)

 rownames(mat) = letters[1:4]

 colnames(mat) = letters[1:10]

@@ -31,6 +31,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -31,6 +31,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))

 ha = HeatmapAnnotation(df = df)

 grid.newpage(); draw(ha, 1:6)

@@ -26,7 +26,7 @@ in the layout.

 }

 \value{

-This function returns a list of \code{\link[stats]{hclust}} objects.

+This function returns a list of row dendrograms and column dendrogram.

 }

 \author{

@@ -34,6 +34,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -32,6 +32,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))

 grid.newpage(); draw(anno, 1:5)

 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))

@@ -34,5 +34,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -32,5 +32,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -35,5 +35,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -42,5 +42,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -36,5 +36,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -32,5 +32,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -30,5 +30,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -33,5 +33,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -31,5 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -30,5 +30,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -34,6 +34,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 hc = hclust(dist(USArrests[1:5, ]))

 dend = as.dendrogram(hc)

@@ -30,5 +30,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -30,5 +30,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -33,5 +33,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -59,5 +59,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -32,5 +32,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -29,6 +29,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # discrete color mapping for characters

 cm = ColorMapping(name = "test",

     colors = c("blue", "white", "red"),

@@ -47,6 +47,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], letters[1:4])),

                 large = runif(10)*100,

                 t1 = sample(letters[1:3], 10, replace = TRUE),

@@ -37,5 +37,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -31,5 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))

 ha = columnAnnotation(df = df)}

@@ -30,5 +30,7 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 # no example for this internal method

 NULL}

@@ -28,6 +28,8 @@ Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

+

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -24,4 +24,6 @@ This function returns no value.

 }

 \author{

+

+

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