@@ -44,6 +44,7 @@ exportMethods(make_row_cluster)

 export(AdditiveUnit)

 exportMethods(component_width)

 exportMethods(draw_heatmap_list)

+exportMethods(show)

 export(grid.dendrogram)

 export(dist2)

 export(rowAnnotation)

@@ -69,9 +69,13 @@ Heatmap = setClass("Heatmap",

         matrix_color_mapping = "ANY",

         row_title = "character",

+        row_title_rot = "numeric",

+        row_title_just = "numeric",

         row_title_param = "list",

         column_title = "character",

         column_title_param = "list",

+        column_title_rot = "numeric",

+        column_title_just = "numeric",

         row_hclust_list = "list", # one or more row clusters

         row_hclust_param = "list", # parameters for row cluster

@@ -119,9 +123,11 @@ Heatmap = setClass("Heatmap",

 # -row_title title on row.

 # -row_title_side will the title be put on the left or right of the heatmap?

 # -row_title_gp graphic parameters for drawing text.

+# -row_title_rot rotation of row titles. Only 0, 90, 270 are allowed to set.

 # -column_title title on column.

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

 # -column_title_gp graphic parameters for drawing text.

+# -column_title_rot rotation of column titles. Only 0, 90, 270 are allowed to set.

 # -cluster_rows If the value is a logical, it means whether make cluster on rows. The value can also

 #               be a `stats::hclust` or a `stats::dendrogram` that already contains clustering information.

 #               This means you can use any type of clustering methods and render the `stats::dendrogram`

@@ -194,8 +200,9 @@ Heatmap = setClass("Heatmap",

 Heatmap = function(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA), 

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

     row_title = character(0), row_title_side = c("left", "right"), 

-    row_title_gp = gpar(fontsize = 14), column_title = character(0),

-    column_title_side = c("top", "bottom"), column_title_gp = gpar(fontsize = 14),

+    row_title_gp = gpar(fontsize = 14), row_title_rot = switch(row_title_side[1], "left" = 90, "right" = 270),

+    column_title = character(0), column_title_side = c("top", "bottom"), 

+    column_title_gp = gpar(fontsize = 14), column_title_rot = 0,

     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, 

@@ -313,9 +320,11 @@ Heatmap = function(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),

         row_title = character(0)

     }

     .Object@row_title = row_title

+    .Object@row_title_rot = row_title_rot %% 360

     .Object@row_title_param$side = match.arg(row_title_side)[1]

     .Object@row_title_param$gp = check_gp(row_title_gp)

     .Object@row_title_param$combined_name_fun = combined_name_fun

+    .Object@row_title_just = get_text_just(rot = row_title_rot, side = .Object@row_title_param$side)

     if(length(column_title) == 0) {

         column_title = character(0)

@@ -325,8 +334,10 @@ Heatmap = function(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),

         column_title = character(0)

     }

     .Object@column_title = column_title

+    .Object@column_title_rot = column_title_rot %% 360

     .Object@column_title_param$side = match.arg(column_title_side)[1]

     .Object@column_title_param$gp = check_gp(column_title_gp)

+    .Object@column_title_just = get_text_just(rot = column_title_rot, side = .Object@column_title_param$side)

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

         show_row_names = FALSE

@@ -693,10 +704,18 @@ setMethod(f = "make_layout",

     column_title_gp = object@column_title_param$gp

     if(length(column_title) > 0) {

         if(column_title_side == "top") {

-            object@layout$layout_column_title_top_height = grobHeight(textGrob(column_title, gp = column_title_gp)) + title_padding*2

+            if(object@column_title_rot %in% c(0, 180)) {

+                object@layout$layout_column_title_top_height = grobHeight(textGrob(column_title, gp = column_title_gp)) + title_padding*2

+            } else {

+                object@layout$layout_column_title_top_height = grobWidth(textGrob(column_title, gp = column_title_gp)) + title_padding*2

+            }

             object@layout$layout_index = rbind(object@layout$layout_index, c(1, 4))

         } else {

-            object@layout$layout_column_title_bottom_height = grobHeight(textGrob(column_title, gp = column_title_gp)) + title_padding*2

+            if(object@column_title_rot %in% c(0, 180)) {

+                object@layout$layout_column_title_bottom_height = grobHeight(textGrob(column_title, gp = column_title_gp)) + title_padding*2

+            } else {

+                object@layout$layout_column_title_bottom_height = grobWidth(textGrob(column_title, gp = column_title_gp)) + title_padding*2

+            }

             object@layout$layout_index = rbind(object@layout$layout_index, c(9, 4))

         }

         object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) draw_title(object, which = "column"))

@@ -709,10 +728,18 @@ setMethod(f = "make_layout",

     row_title_gp = object@row_title_param$gp

     if(length(row_title) > 0) {

         if(row_title_side == "left") {

-            object@layout$layout_row_title_left_width = max(grobHeight(textGrob(row_title, gp = row_title_gp))) + title_padding*2

+            if(object@row_title_rot %in% c(0, 180)) {

+                object@layout$layout_row_title_left_width = max(grobWidth(textGrob(row_title, gp = row_title_gp))) + title_padding*2

+            } else {

+                object@layout$layout_row_title_left_width = max(grobHeight(textGrob(row_title, gp = row_title_gp))) + title_padding*2

+            }

             object@layout$layout_index = rbind(object@layout$layout_index, c(5, 1))

         } else {

-            object@layout$layout_row_title_right_width = max(grobHeight(textGrob(row_title, gp = row_title_gp))) + title_padding*2

+            if(object@row_title_rot %in% c(0, 180)) {

+                object@layout$layout_row_title_right_width = max(grobWidth(textGrob(row_title, gp = row_title_gp))) + title_padding*2

+            } else {

+                object@layout$layout_row_title_right_width = max(grobHeight(textGrob(row_title, gp = row_title_gp))) + title_padding*2

+            }

             object@layout$layout_index = rbind(object@layout$layout_index, c(5, 7))

         }

         object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) {

@@ -1132,8 +1159,8 @@ setMethod(f = "draw_title",

     which = match.arg(which)[1]

     side = switch(which,

-        "row" = object@row_hclust_param$side,

-        "column" = object@column_hclust_param$side)

+        "row" = object@row_title_param$side,

+        "column" = object@column_title_param$side)

     gp = switch(which,

         "row" = object@row_title_param$gp,

@@ -1143,26 +1170,31 @@ setMethod(f = "draw_title",

         "row" = object@row_title[k],

         "column" = object@column_title)

+    rot = switch(which,

+        "row" = object@row_title_rot,

+        "column" = object@column_title_rot)

+

+    just = switch(which, 

+        "row" = object@row_title_just,

+        "column" = object@column_title_just)

+

     title_padding = unit(2.5, "mm")

     if(which == "row") {

-        rot = switch(side,

-            "left" = 90,

-            "right" = 270)

-

+        

         pushViewport(viewport(name = paste(object@name, "row_title", k, sep = "_"), clip = FALSE, ...))

         if(side == "left") {

-            grid.text(title, x = unit(1, "npc") - title_padding, rot = rot, vjust = 0, gp = gp)

+            grid.text(title, x = unit(1, "npc") - title_padding, rot = rot, just = just, gp = gp)

         } else {

-            grid.text(title, x = title_padding, rot = rot, vjust = 0, gp = gp)

+            grid.text(title, x = title_padding, rot = rot, just = just, gp = gp)

         }

         upViewport()

     } else {

         pushViewport(viewport(name = paste(object@name, "column_title", sep = "_"), clip = FALSE, ...))

         if(side == "top") {

-            grid.text(title, y = title_padding, vjust = 0, gp = gp)

+            grid.text(title, y = title_padding, rot = rot, just = just, gp = gp)

         } else {

-            grid.text(title, y = unit(1, "npc") - title_padding, vjust = 1, gp = gp)

+            grid.text(title, y = unit(1, "npc") - title_padding, rot = rot, just = just, gp = gp)

         }

         upViewport()

     }

@@ -294,6 +294,15 @@ setMethod(f = "make_layout",

         }

     }

+    # remote other heatmaps' row titles

+    for(i in seq_len(n)) {

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

+            if(i != i_main) {

+                object@ht_list[[i]]@row_title = character(0)

+            }

+        }

+    }

+

     if(row_hclust_side == "left" && i == 1) {

         object@ht_list[[1]]@row_hclust_list = ht_main@row_hclust_list

         object@ht_list[[1]]@row_hclust_param = ht_main@row_hclust_param

@@ -344,3 +344,44 @@ subset_gp = function(gp, k) {

     class(gp) = "gpar"

     return(gp)

 }

+

+

+get_text_just = function(rot, side) {

+    rot = rot %% 360

+    if(! rot %in% c(0, 90, 270)) {

+        stop("Only support horizontal or vertical rotations for text.\n")

+    }

+    if(side == "left") {

+        if(rot == 0) {

+            return(c(1, 0.5))

+        } else if(rot == 90) {

+            return(c(0.5, 0))

+        } else if(rot == 270) {

+            return(c(0.5, 1))

+        }

+    } else if(side == "right") {

+        if(rot == 0) {

+            return(c(0, 0.5))

+        } else if(rot == 90) {

+            return(c(0.5, 1))

+        } else if(rot == 270) {

+            return(c(0.5, 0))

+        }

+    } else if(side == "top") {

+        if(rot == 0) {

+            return(c(0.5, 0))

+        } else if(rot == 90) {

+            return(c(0, 0.5))

+        } else if(rot == 270) {

+            return(c(1, 0.5))

+        }

+    } else if(side == "bottom") {

+        if(rot == 0) {

+            return(c(0.5, 1))

+        } else if(rot == 90) {

+            return(c(1, 0.5))

+        } else if(rot == 270) {

+            return(c(0, 0.5))

+        }

+    }

+}

\ No newline at end of file

@@ -2,18 +2,21 @@

 \docType{class}

 \alias{AdditiveUnit-class}

 \title{

-An internal class

+An internal class  

+

 }

 \description{

-An internal class

+An internal class  

+

 }

 \details{

-This class is a super class for \code{\link{Heatmap-class}}, \code{\link{HeatmapList-class}} and \code{\link{HeatmapAnnotation-class}} classes.

-It is only designed for \code{+} generic method so that above three classes can be appended to each other.

+This class is a super class for \code{\link{Heatmap-class}}, \code{\link{HeatmapList-class}} and \code{\link{HeatmapAnnotation-class}} classes. It is only designed for \code{+} generic method so that above three classes can be appended to each other.  

+

 }

 \examples{

 # no example

-NULL}

+NULL

+}

@@ -1,31 +1,39 @@

 \name{AdditiveUnit}

 \alias{AdditiveUnit}

 \title{

-Constructor method for AdditiveUnit class

+Constructor method for AdditiveUnit class  

+

 }

 \description{

-Constructor method for AdditiveUnit class

+Constructor method for AdditiveUnit class  

+

 }

 \usage{

-AdditiveUnit(...)}

+AdditiveUnit(...)

+}

 \arguments{

   \item{...}{arguments.}

+

 }

 \details{

-This method is not used in the package.

+This method is not used in the package.  

+

 }

 \value{

-No value is returned.

+No value is returned.  

+

 }

 \author{

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

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

+

 }

 \examples{

 # no example

-NULL}

+NULL

+}

@@ -2,21 +2,22 @@

 \docType{class}

 \alias{ColorMapping-class}

 \title{

-Class to map values to colors

+Class to map values to colors  

+

 }

 \description{

-Class to map values to colors

+Class to map values to colors  

+

 }

 \details{

-The \code{\link{ColorMapping-class}} handles color mapping with both discrete values and continuous values.

-Discrete values are mapped by setting a vector of colors and continuous values are mapped by setting

-a color mapping function.

+The \code{\link{ColorMapping-class}} handles color mapping with both discrete values and continuous values. Discrete values are mapped by setting a vector of colors and continuous values are mapped by setting a color mapping function.  

+

 }

 \section{Methods}{

-The \code{\link{ColorMapping-class}} provides following methods:

+The \code{\link{ColorMapping-class}} provides following methods:  

 \itemize{

   \item \code{\link{ColorMapping}}: contructor methods.

@@ -24,11 +25,14 @@ The \code{\link{ColorMapping-class}} provides following methods:

   \item \code{\link{color_mapping_legend,ColorMapping-method}}: draw legend or get the size of the legend.

 }

+

 }

 \author{

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

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

+

 }

 \examples{

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

-NULL}

+NULL

+}

@@ -1,36 +1,42 @@

 \name{ColorMapping}

 \alias{ColorMapping}

 \title{

-Constructor methods for ColorMapping class

+Constructor methods for ColorMapping class  

+

 }

 \description{

-Constructor methods for ColorMapping class

+Constructor methods for ColorMapping class  

+

 }

 \usage{

 ColorMapping(name, colors = NULL, levels = NULL,

-    col_fun = NULL, breaks = NULL, na_col = "#FFFFFF")}

+    col_fun = NULL, breaks = NULL, na_col = "#FFFFFF")

+}

 \arguments{

   \item{name}{name for this color mapping. It is used for drawing the title of the legend.}

   \item{colors}{discrete colors.}

-  \item{levels}{levels that correspond to \code{colors}. If \code{colors} is name indexed, \code{levels} can be ignored.}

+  \item{levels}{levels that correspond to \code{colors}. If \code{colors} is name indexed,  \code{levels} can be ignored.}

   \item{col_fun}{color mapping function that maps continuous values to colors.}

-  \item{breaks}{breaks for the continuous color mapping. If \code{col_fun} isgenerated by \code{\link[circlize]{colorRamp2}}, \code{breaks} can be ignored.}

+  \item{breaks}{breaks for the continuous color mapping. If \code{col_fun} is generated by \code{\link[circlize]{colorRamp2}}, \code{breaks} can be ignored.}

   \item{na_col}{colors for \code{NA} values.}

+

 }

 \details{

-\code{colors} and \code{levels} are used for discrete color mapping, \code{col_fun} and 

-\code{breaks} are used for continuous color mapping.

+\code{colors} and \code{levels} are used for discrete color mapping, \code{col_fun} and  \code{breaks} are used for continuous color mapping.  

+

 }

 \value{

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

+A \code{\link{ColorMapping-class}} object.  

+

 }

 \author{

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

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

+

 }

 \examples{

@@ -50,4 +56,5 @@ cm

 require(circlize)

 cm = ColorMapping(name = "test",

     col_fun = colorRamp2(c(0, 0.5, 1), c("blue", "white", "red")))

-cm}

+cm

+}

@@ -2,19 +2,19 @@

 \docType{package}

 \alias{ComplexHeatmap-package}

 \title{

-Making complex heatmap

+Making complex heatmap  

+

 }

 \description{

-Making complex heatmap

+Making complex heatmap  

+

 }

 \details{

-This package aims to provide a simple and flexible way to arrange

-multiple heatmaps as well as self-defining annotation graphics.

+This package aims to provide a simple and flexible way to arrange multiple heatmaps as well as self-defining annotation graphics.  

-The package is implemented in an object oriented way. 

-Components of heatmap lists are abstracted into several classes.

+The package is implemented in an object oriented way.  Components of heatmap lists are abstracted into several classes.  

 \itemize{

   \item \code{\link{Heatmap-class}}: a single heatmap containing heatmap body, row/column names, titles, dendrograms and column annotations.

@@ -22,16 +22,16 @@ Components of heatmap lists are abstracted into several classes.

   \item \code{\link{HeatmapAnnotation-class}}: a list of row annotations or column annotations.

 }

-There are also several internal classes:

+There are also several internal classes:  

 \itemize{

   \item \code{\link{SingleAnnotation-class}}: a single row annotation or column annotation.

   \item \code{\link{ColorMapping-class}}: mapping from values to colors.

 }

-For plotting one single heatmap, please go to the documentation page of \code{\link{Heatmap}}.

-For plotting multiple heatmaps, please go to \code{\link{HeatmapList-class}} and \code{+.AdditiveUnit}.

+For plotting one single heatmap, please go to the documentation page of \code{\link{Heatmap}}. For plotting multiple heatmaps, please go to \code{\link{HeatmapList-class}} and \code{+.AdditiveUnit}.  

+

+The vignette provides detailed explanation of how to use this package.  

-The vignette provides detailed explanation of how to use this package.

 }

@@ -2,15 +2,17 @@

 \docType{class}

 \alias{Heatmap-class}

 \title{

-Class for a single heatmap

+Class for a single heatmap  

+

 }

 \description{

-Class for a single heatmap

+Class for a single heatmap  

+

 }

 \details{

-The components for a single heamtap are placed into a 9 x 7 layout:

+The components for a single heamtap are placed into a 9 x 7 layout:  

   \preformatted{

          +------+ (1)

@@ -26,7 +28,7 @@ The components for a single heamtap are placed into a 9 x 7 layout:

          +------+ (9)

   }

-From top to bottom in column 4, the regions are:

+From top to bottom in column 4, the regions are:  

 \itemize{

   \item title which is put on the top of the heatmap, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.

@@ -40,7 +42,7 @@ From top to bottom in column 4, the regions are:

   \item title on the bottom, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.

 }

-From left to right in row 5, the regions are:

+From left to right in row 5, the regions are:  

 \itemize{

   \item title which is put in the left of the heatmap, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.

@@ -52,13 +54,12 @@ From left to right in row 5, the regions are:

   \item title on the right, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.

 }

-The \code{\link{Heatmap-class}} is not responsible for heatmap legend and annotation legends. The \code{\link{draw,Heatmap-method}} method

-will construct a \code{\link{HeatmapList-class}} object which only contains one single heatmap

-and call \code{\link{draw,HeatmapList-method}} to make a complete heatmap.

+The \code{\link{Heatmap-class}} is not responsible for heatmap legend and annotation legends. The \code{\link{draw,Heatmap-method}} method will construct a \code{\link{HeatmapList-class}} object which only contains one single heatmap and call \code{\link{draw,HeatmapList-method}} to make a complete heatmap.  

+

 }

 \section{Methods}{

-The \code{\link{Heatmap-class}} provides following methods:

+The \code{\link{Heatmap-class}} provides following methods:  

 \itemize{

   \item \code{\link{Heatmap}}: constructor method.

@@ -66,11 +67,14 @@ The \code{\link{Heatmap-class}} provides following methods:

   \item \code{\link{add_heatmap,Heatmap-method}} append heatmaps and row annotations to a list of heatmaps.

 }

+

 }

 \author{

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

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

+

 }

 \examples{

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

-NULL}

+NULL

+}

@@ -1,19 +1,22 @@

 \name{Heatmap}

 \alias{Heatmap}

 \title{

-Constructor method for Heatmap class

+Constructor method for Heatmap class  

+

 }

 \description{

-Constructor method for Heatmap class

+Constructor method for Heatmap class  

+

 }

 \usage{

 Heatmap(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),

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

     row_title = character(0), row_title_side = c("left", "right"),

-    row_title_gp = gpar(fontsize = 14), column_title = character(0),

-    column_title_side = c("top", "bottom"), column_title_gp = gpar(fontsize = 14),

+    row_title_gp = gpar(fontsize = 14), row_title_rot = switch(row_title_side[1], "left" = 90, "right" = 270),

+    column_title = character(0), column_title_side = c("top", "bottom"),

+    column_title_gp = gpar(fontsize = 14), column_title_rot = 0,

     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,

@@ -33,28 +36,31 @@ Heatmap(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),

     bottom_annotation_height = unit(5*length(bottom_annotation@anno_list), "mm"),

     km = 1, split = NULL, gap = unit(1, "mm"),

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

-    width = NULL, show_heatmap_legend = TRUE)}

+    width = NULL, show_heatmap_legend = TRUE)

+}

 \arguments{

-  \item{matrix}{a matrix. Either numeric or character. If it is a simple vector, it will beconverted to a one-column matrix.}

-  \item{col}{a vector of colors if the color mapping is discrete or a color mapping function if the matrix is continuous numbers. If the matrix is continuous,the value can also be a vector of colors so that colors will be interpolated. Pass to \code{\link{ColorMapping}}.}

+  \item{matrix}{a matrix. Either numeric or character. If it is a simple vector, it will be converted to a one-column matrix.}

+  \item{col}{a vector of colors if the color mapping is discrete or a color mapping  function if the matrix is continuous numbers. If the matrix is continuous, the value can also be a vector of colors so that colors will be interpolated. Pass to \code{\link{ColorMapping}}.}

   \item{name}{name of the heatmap. The name is used as the title of the heatmap legend.}

   \item{na_col}{color for \code{NA} values.}

   \item{rect_gp}{graphic parameters for drawing rectangles (for heatmap body).}

-  \item{cell_fun}{self-defined function to add graphics on each cell. Seven parameters will be passed into this function: \code{i}, \code{j}, \code{x}, \code{y}, \code{width}, \code{height}, \code{fill} which are row index,column index in \code{matrix}, coordinate of the middle points in the heatmap body viewport,the width and height of the cell and the filled color. }

+  \item{cell_fun}{self-defined function to add graphics on each cell. Seven parameters will be passed into  this function: \code{i}, \code{j}, \code{x}, \code{y}, \code{width}, \code{height}, \code{fill} which are row index, column index in \code{matrix}, coordinate of the middle points in the heatmap body viewport, the width and height of the cell and the filled color. }

   \item{row_title}{title on row.}

   \item{row_title_side}{will the title be put on the left or right of the heatmap?}

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

+  \item{row_title_rot}{rotation of row titles. Only 0, 90, 270 are allowed to set.}

   \item{column_title}{title on column.}

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

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

-  \item{cluster_rows}{If the value is a logical, it means whether make cluster on rows. The value can alsobe a \code{\link[stats]{hclust}} or a \code{\link[stats]{dendrogram}} that already contains clustering information.This means you can use any type of clustering methods and render the \code{\link[stats]{dendrogram}}object with self-defined graphic settings.}

-  \item{clustering_distance_rows}{it can be a pre-defined character which is in ("euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski", "pearson", "spearman", "kendall"). It can also be a function.If the function has one argument, the input argument should be a matrix and the returned value should be a \code{\link[stats]{dist}} object. If the function has two arguments,the input arguments are two vectors and the function calculates distance between thesetwo vectors.}

+  \item{column_title_rot}{rotation of column titles. Only 0, 90, 270 are allowed to set.}

+  \item{cluster_rows}{If the value is a logical, it means whether make cluster on rows. The value can also be a \code{\link[stats]{hclust}} or a \code{\link[stats]{dendrogram}} that already contains clustering information. This means you can use any type of clustering methods and render the \code{\link[stats]{dendrogram}} object with self-defined graphic settings.}

+  \item{clustering_distance_rows}{it can be a pre-defined character which is in  ("euclidean", "maximum", "manhattan", "canberra", "binary",  "minkowski", "pearson", "spearman", "kendall"). It can also be a function. If the function has one argument, the input argument should be a matrix and  the returned value should be a \code{\link[stats]{dist}} object. If the function has two arguments, the input arguments are two vectors and the function calculates distance between these two vectors.}

   \item{clustering_method_rows}{method to make cluster, pass to \code{\link[stats]{hclust}}.}

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

   \item{row_hclust_width}{width of the row cluster, should be a \code{\link[grid]{unit}} object.}

   \item{show_row_hclust}{whether show row clusters. }

-  \item{row_hclust_gp}{graphics parameters for drawing lines. If users already provide a \code{\link[stats]{dendrogram}}object with edges rendered, this argument will be ignored.}

+  \item{row_hclust_gp}{graphics parameters for drawing lines. If users already provide a \code{\link[stats]{dendrogram}} object with edges rendered, this argument will be ignored.}

   \item{cluster_columns}{whether make cluster on columns. Same settings as \code{cluster_rows}.}

   \item{clustering_distance_columns}{same setting as \code{clustering_distance_rows}.}

   \item{clustering_method_columns}{method to make cluster, pass to \code{\link[stats]{hclust}}.}

@@ -62,11 +68,11 @@ Heatmap(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),

   \item{column_hclust_height}{height of the column cluster, should be a \code{\link[grid]{unit}} object.}

   \item{show_column_hclust}{whether show column clusters.}

   \item{column_hclust_gp}{graphic parameters for drawling lines. Same settings as \code{row_hclust_gp}.}

-  \item{row_order}{order of rows. It makes it easy to adjust row order for a list of heatmaps if this heatmap is selected as the main heatmap. Manually setting row order should turn off clustering}

+  \item{row_order}{order of rows. It makes it easy to adjust row order for a list of heatmaps if this heatmap  is selected as the main heatmap. Manually setting row order should turn off clustering}

   \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_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_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.}

   \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.}

@@ -76,18 +82,18 @@ Heatmap(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),

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

   \item{bottom_annotation}{a \code{\link{HeatmapAnnotation}} object.}

   \item{bottom_annotation_height}{total height of the column annotations on the bottom.}

-  \item{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.}

+  \item{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.}

   \item{split}{a vector or a data frame by which the rows are split.}

   \item{gap}{gap between row-slices if the heatmap is split by rows, should be \code{\link[grid]{unit}} object.}

-  \item{combined_name_fun}{if the heatmap is split by rows, how to make a combined row title for each slice?The input parameter for this function is a vector which contains level names under each column in \code{split}.}

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

+  \item{combined_name_fun}{if the heatmap is split by rows, how to make a combined row title for each slice? The input parameter for this function is a vector which contains level names under each column in \code{split}.}

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

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

+

 }

 \details{

-The initialization function only applies parameter checking and fill values to each slot with proper ones.

-Then it will be ready for clustering and layout.

+The initialization function only applies parameter checking and fill values to each slot with proper ones. Then it will be ready for clustering and layout.  

-Following methods can be applied on the \code{\link{Heatmap-class}} object:

+Following methods can be applied on the \code{\link{Heatmap-class}} object:  

 \itemize{

   \item \code{\link{show,Heatmap-method}}: draw a single heatmap with default parameters

@@ -95,16 +101,18 @@ Following methods can be applied on the \code{\link{Heatmap-class}} object:

   \item \code{\link{add_heatmap,Heatmap-method}} append heatmaps and row annotations to a list of heatmaps.

 }

-The constructor function pretends to be a high-level graphic function because the \code{show} method

-of the \code{\link{Heatmap-class}} object actually plots the graphics.

+The constructor function pretends to be a high-level graphic function because the \code{show} method of the \code{\link{Heatmap-class}} object actually plots the graphics.  

+

 }

 \value{

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

+A \code{\link{Heatmap-class}} object.  

+

 }

 \author{

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

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

+

 }

 \examples{

@@ -178,4 +186,5 @@ Heatmap(mat, rect_gp = gpar(col = "white"),

         grid.text(mat[i, j], x = x, y = y)

     },

     cluster_rows = FALSE, cluster_columns = FALSE, row_names_side = "left", 

-    column_names_side = "top")}

+    column_names_side = "top")

+}

@@ -2,32 +2,36 @@

 \docType{class}

 \alias{HeatmapAnnotation-class}

 \title{

-Class for heatmap annotations

+Class for heatmap annotations  

+

 }

 \description{

-Class for heatmap annotations

+Class for heatmap annotations  

+

 }

 \details{

-A complex heatmap contains a list of annotations which represent as different graphics

-placed on rows and columns. The \code{\link{HeatmapAnnotation-class}} is a category of single annotations which are

-by a list of \code{\link{SingleAnnotation-class}} objects with same number of rows or columns.

+A complex heatmap contains a list of annotations which represent as different graphics placed on rows and columns. The \code{\link{HeatmapAnnotation-class}} is a category of single annotations which are by a list of \code{\link{SingleAnnotation-class}} objects with same number of rows or columns.  

+

 }

 \section{Methods}{

-The \code{\link{HeatmapAnnotation-class}} provides following methods:

+The \code{\link{HeatmapAnnotation-class}} provides following methods:  

 \itemize{

   \item \code{\link{HeatmapAnnotation}}: constructor method

   \item \code{\link{draw,HeatmapAnnotation-method}}: draw the annotations

 }

+

 }

 \author{

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

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

+

 }

 \examples{

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

-NULL}

+NULL

+}

@@ -1,18 +1,21 @@

 \name{HeatmapAnnotation}

 \alias{HeatmapAnnotation}

 \title{

-Constructor method for HeatmapAnnotation class

+Constructor method for HeatmapAnnotation class  

+

 }

 \description{

-Constructor method for HeatmapAnnotation class

+Constructor method for HeatmapAnnotation class  

+

 }

 \usage{

 HeatmapAnnotation(df, name, col, show_legend = rep(TRUE, n_anno), ...,

     which = c("column", "row"), annotation_height = 1, annotation_width = 1,

     height = unit(1, "cm"), width = unit(1, "cm"), gp = gpar(col = NA),

-    gap = unit(0, "null"))}

+    gap = unit(0, "null"))

+}

 \arguments{

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

@@ -27,22 +30,26 @@ HeatmapAnnotation(df, name, col, show_legend = rep(TRUE, n_anno), ...,

   \item{width}{width of the whole heatmap annotations, only used for row annotation when appending to the list of heatmaps.}

   \item{gp}{graphic parameters for simple annotations.}

   \item{gap}{gap between each annotation}

+

 }

 \details{

-The simple annotations are defined by \code{df} and \code{col} arguments. Complex annotations are

-defined by the function list. So you need to at least to define \code{df} or a annotation function.

+The simple annotations are defined by \code{df} and \code{col} arguments. Complex annotations are defined by the function list. So you need to at least to define \code{df} or a annotation function.  

+

 }

 \value{

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

+A \code{\link{HeatmapAnnotation-class}} object.  

+

 }

 \seealso{

-There are two shortcut functions: \code{\link{rowAnnotation}} and \code{\link{columnAnnotation}}.

+There are two shortcut functions: \code{\link{rowAnnotation}} and \code{\link{columnAnnotation}}.  

+

 }

 \author{

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

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

+

 }

 \examples{

@@ -59,4 +66,5 @@ ha = HeatmapAnnotation(points = anno_points(1:6))

 ha = HeatmapAnnotation(histogram = anno_points(1:6))

 mat = matrix(rnorm(36), 6)

-ha = HeatmapAnnotation(boxplot = anno_boxplot(mat))}

+ha = HeatmapAnnotation(boxplot = anno_boxplot(mat))

+}

@@ -2,17 +2,19 @@

 \docType{class}

 \alias{HeatmapList-class}

 \title{

-Class for a list of heatmaps

+Class for a list of heatmaps  

+

 }

 \description{

-Class for a list of heatmaps

+Class for a list of heatmaps  

+

 }

 \details{

-A heatmap list is defined as a list of heatmaps and row annotations.

+A heatmap list is defined as a list of heatmaps and row annotations.  

-The components for the heamtap list are placed into a 7 x 7 layout:

+The components for the heamtap list are placed into a 7 x 7 layout:  

   \preformatted{

          +------+(1)

@@ -26,7 +28,7 @@ The components for the heamtap list are placed into a 7 x 7 layout:

          +------+(7)

   }

-From top to bottom in column 4, the regions are:

+From top to bottom in column 4, the regions are:  

 \itemize{

   \item annotation legend on the top, graphics are drawn by \code{\link{draw_annotation_legend,HeatmapList-method}}.

@@ -38,7 +40,7 @@ From top to bottom in column 4, the regions are:

   \item annotation legend on the bottom, graphics are drawn by \code{\link{draw_annotation_legend,HeatmapList-method}}.

 }

-From left to right in row 4, the regions are:

+From left to right in row 4, the regions are:  

 \itemize{

   \item annotation legend on the left, graphics are drawn by \code{\link{draw_annotation_legend,HeatmapList-method}}.

@@ -50,21 +52,23 @@ From left to right in row 4, the regions are:

   \item annotation legend on the right, graphics are drawn by \code{\link{draw_annotation_legend,HeatmapList-method}}.

 }

-For the list of heatmaps which are placed at (5, 5) in the layout, the heatmaps and row annotations

-are placed one after the other.

+For the list of heatmaps which are placed at (5, 5) in the layout, the heatmaps and row annotations are placed one after the other.  

+

 }

 \section{Methods}{

-The \code{\link{HeatmapList-class}} provides following methods:

+The \code{\link{HeatmapList-class}} provides following methods:  

 \itemize{

   \item \code{\link{draw,HeatmapList-method}}: draw the list of heatmaps and row annotations.

   \item \code{\link{add_heatmap,HeatmapList-method}} add heatmaps to the list of heatmaps.

 }

+

 }

 \author{

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

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

+

 }

 \examples{

@@ -83,4 +87,5 @@ ht + ht_list

 ha = HeatmapAnnotation(points = anno_points(1:12, which = "row"), 

     which = "row")

 ht + ha

-ht_list + ha}

+ht_list + ha

+}

@@ -1,33 +1,42 @@

 \name{HeatmapList}

 \alias{HeatmapList}

 \title{

-Constructor method for HeatmapList class