@@ -76,6 +76,7 @@ Heatmap = setClass("Heatmap",

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

         row_hclust_param = "list", # parameters for row cluster

         row_order_list = "list",

+        row_order = "numeric",

         column_hclust = "ANY",

         column_hclust_param = "list", # parameters for column cluster

@@ -235,6 +236,10 @@ Heatmap = function(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),

         }

     }

+    if(is.null(width)) {

+        .Object@heatmap_param$width = ncol(matrix)

+    }

+

     if(ncol(matrix) == 0) {

         .Object@heatmap_param$show_heatmap_legend = FALSE

         .Object@heatmap_param$width = unit(0, "null")

@@ -362,10 +367,11 @@ 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_order_list = list() # default order

     if(is.null(row_order)) {

-        .Object@row_order_list = list(seq_len(nrow(matrix))) # default order

-    } else {

-        .Object@row_order_list = list(row_order)

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

+    }  else {

+        .Object@row_order = row_order

     }

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

@@ -457,7 +463,6 @@ Heatmap = function(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),

 #

 # == param

 # -object a `Heatmap-class` object.

-# -order a pre-defined order.

 #

 # == details

 # The function will fill or adjust ``column_hclust`` and ``column_order`` slots.

@@ -472,17 +477,14 @@ Heatmap = function(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),

 #

 setMethod(f = "make_column_cluster",

     signature = "Heatmap",

-    definition = function(object, order = NULL) {

+    definition = function(object) {

     mat = object@matrix

     distance = object@column_hclust_param$distance

     method = object@column_hclust_param$method

+    order = object@column_order

-    if(!object@column_hclust_param$cluster && is.null(order)) {

-        order = seq_len(ncol(mat))

-    }

-

-    if(is.null(order) || object@column_hclust_param$cluster) {

+    if(object@column_hclust_param$cluster) {

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

             object@column_hclust = object@column_hclust_param$obj

         } else if(!is.null(object@column_hclust_param$fun)) {

@@ -490,7 +492,7 @@ setMethod(f = "make_column_cluster",

         } else {

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

         }

-        column_order = get_hclust_order(object@column_hclust)

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

     } else {

         column_order = order

     }

@@ -511,9 +513,6 @@ setMethod(f = "make_column_cluster",

 #

 # == param

 # -object a `Heatmap-class` object.

-# -order a pre-defined order.

-# -km if apply k-means clustering on rows, number of clusters.

-# -split a vector or a data frame by which the rows are be split.

 #

 # == details

 # The function will fill or adjust ``row_hclust_list``, ``row_order_list``, ``row_title`` and ``matrix_param`` slots.

@@ -530,18 +529,16 @@ setMethod(f = "make_column_cluster",

 #

 setMethod(f = "make_row_cluster",

     signature = "Heatmap",

-    definition = function(object, order = unlist(object@row_order_list), km = object@matrix_param$km, 

-    split = object@matrix_param$split) {

+    definition = function(object) {

     mat = object@matrix

     distance = object@row_hclust_param$distance

     method = object@row_hclust_param$method

+    order = object@row_order  # pre-defined row order

+    km = object@matrix_param$km

+    split = object@matrix_param$split

-    if(!object@row_hclust_param$cluster && is.null(order)) {

-        order = seq_len(nrow(mat))

-    }

-

-    if(is.null(order) || object@row_hclust_param$cluster) {

+    if(object@row_hclust_param$cluster) {

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

             if(km > 1) {

@@ -555,7 +552,7 @@ setMethod(f = "make_row_cluster",

             return(object)

         }

-        row_order = seq_len(nrow(mat))  # default row order

+        row_order = seq_len(nrow(mat))

     } else {

         row_order = order

     }

@@ -570,7 +567,7 @@ setMethod(f = "make_row_cluster",

         meanmat = as.matrix(as.data.frame(meanmat))

         hc = hclust(dist(t(meanmat)))

         cluster2 = numeric(length(cluster))

-        for(i in seq_along(hc$order)) {

+        for(i in hc$order) {

             cluster2[cluster == hc$order[i]] = i

         }

         cluster2 = paste0("cluster", cluster2)

@@ -600,7 +597,7 @@ setMethod(f = "make_row_cluster",

         row_levels = unique(split)

         for(i in seq_along(row_levels)) {

             l = split == row_levels[i]

-            row_order_list[[i]] = nature_order[l][ order(row_order[l]) ]

+            row_order_list[[i]] = intersect(row_order, which(l))

         }

         if(!is.null(object@row_title_param$combined_name_fun)) {

@@ -609,7 +606,7 @@ setMethod(f = "make_row_cluster",

     }

     # make hclust in each slice

-    if(is.null(order) || object@row_hclust_param$cluster) {

+    if(object@row_hclust_param$cluster) {

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

         for(i in seq_along(row_order_list)) {

             submat = mat[ row_order_list[[i]], , drop = FALSE]

@@ -1413,10 +1410,7 @@ setMethod(f = "draw",

 #

 # == param

 # -object a `Heatmap-class` object.

-# -row_order orders of rows, pass to `make_row_cluster,Heatmap-method`. Because if more than one heatmaps

-#            are drawn by columns, the order of some heatmap will be adjusted by one certain heatmap, this

-#            argument is used to pass a pre-defined row order.

-# -split how to split rows in the matrix, passing to `make_row_cluster,Heatmap-method`.

+# -process_rows whether process rows of the heatmap

 #

 # == detail

 # The preparation of the heatmap includes following steps:

@@ -1435,10 +1429,10 @@ setMethod(f = "draw",

 #

 setMethod(f = "prepare",

     signature = "Heatmap",

-    definition = function(object, row_order = NULL, split = object@matrix_param$split) {

+    definition = function(object, process_rows = TRUE) {

-    if(object@row_hclust_param$cluster || !is.null(split)) {

-        object = make_row_cluster(object, order = row_order, split = split)

+    if(process_rows) {

+        object = make_row_cluster(object)

     }

     if(object@column_hclust_param$cluster) object = make_column_cluster(object)

@@ -177,7 +177,6 @@ setMethod(f = "add_heatmap",

 # -show_annotation_legend whether show annotation legend.

 # -annotation_legend_list a list of self-defined legend, should be wrapped into `grid::grob` objects.

 # -gap gap between heatmaps, should be a `grid::unit` object.

-# -auto_adjust auto adjust if the number of heatmap is larger than one.

 # -main_heatmap name or index for the main heatmap

 # -row_hclust_side if auto adjust, where to put the row dendrograms for the main heatmap

 # -row_sub_title_side if auto adjust, where to put sub row titles for the main heatmap

@@ -206,7 +205,7 @@ setMethod(f = "make_layout",

     show_heatmap_legend = TRUE,

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

     show_annotation_legend = TRUE, annotation_legend_list = list(),

-    gap = unit(3, "mm"), auto_adjust = TRUE, 

+    gap = unit(3, "mm"), 

     main_heatmap = which(sapply(object@ht_list, inherits, "Heatmap"))[1],

     row_hclust_side = c("original", "left", "right"),

     row_sub_title_side = c("original", "left", "right"), ...) {

@@ -233,8 +232,8 @@ setMethod(f = "make_layout",

             }

         } else if(length(gap) == n - 1) {

             gap = unit.c(gap, unit(1, "null"))

-        } else if(length(gap) != n) {

-            stop(paste0("length of `gap` can only be 1 or ", n-1, " or ", n, "."))

+        } else if(length(gap) > n) {

+            stop(paste0("length of `gap` can only be 1 or ", n-1, "."))

         }

     } else {

         if(!is.unit(gap)) {

@@ -256,133 +255,67 @@ setMethod(f = "make_layout",

         }

     }

-    # else if the zero-column matrix is in the middle, set the front gap to 0

-

-    if(auto_adjust) {

-        ht_main = object@ht_list[[i_main]]

-        ht_main = make_row_cluster(ht_main, order = ht_main@row_order_list[[1]])

-        

-        row_order = unlist(ht_main@row_order_list)

-        split = ht_main@matrix_param$split

-

-        row_hclust_side = match.arg(row_hclust_side)[1]

-        row_sub_title_side = match.arg(row_sub_title_side)[1]

-

-        if(row_hclust_side == "left" || row_sub_title_side == "left") {

-            # if the first one is a HeatmapAnnotation object

-            if(inherits(object@ht_list[[1]], "HeatmapAnnotation")) {

-                object = Heatmap(matrix(nrow = nr, ncol = 0)) + object

-                gap = unit.c(unit(0, "null"), gap)

-                i_main = i_main + 1

-            }

-            

+    ######## auto adjust ##########

+    ht_main = object@ht_list[[i_main]]

+    ht_main = make_row_cluster(ht_main)  # with pre-defined order

+    object@ht_list[[i_main]] = ht_main

+

+    row_hclust_side = match.arg(row_hclust_side)[1]

+    row_sub_title_side = match.arg(row_sub_title_side)[1]

+

+    if(row_hclust_side == "left" || row_sub_title_side == "left") {

+        # if the first one is a HeatmapAnnotation object

+        # add a heatmap with zero column so that we can put titles and hclust on the most left

+        if(inherits(object@ht_list[[1]], "HeatmapAnnotation")) {

+            object = Heatmap(matrix(nrow = nr, ncol = 0)) + object

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

+            i_main = i_main + 1

         }

+            

+    }

-        if(row_hclust_side == "right" || row_sub_title_side == "right") {

-            # if the last one is a HeatmapAnnotation object

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

-                object = object + Heatmap(matrix(nrow = nr, ncol = 0))

-                gap = unit.c(gap, unit(0, "null"))

-            }

+    if(row_hclust_side == "right" || row_sub_title_side == "right") {

+        # if the last one is a HeatmapAnnotation object

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

+            object = object + Heatmap(matrix(nrow = nr, ncol = 0))

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

         }

-        object@ht_list_param$gap = gap

+    }

+    object@ht_list_param$gap = gap

-        n = length(object@ht_list)

+    n = length(object@ht_list)

-        if(row_sub_title_side == "left") {

-            for(i in seq_len(n)) {

-                if(i == 1) {

-                    object@ht_list[[i]]@row_title = ht_main@row_title

-                    object@ht_list[[i]]@row_title_param = ht_main@row_title_param

-                    object@ht_list[[i]]@row_title_param$side = "left"

-                } else {

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

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

-                    }

-                }

-            }

-        } else if(row_sub_title_side == "right") {

-            for(i in seq_len(n)) {

-                if(i == n) {

-                    object@ht_list[[n]]@row_title = ht_main@row_title

-                    object@ht_list[[n]]@row_title_param = ht_main@row_title_param

-                    object@ht_list[[n]]@row_title_param$side = "right"

-                } else {

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

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

-                    }

-                }

-            }

-        } else {

-            for(i in seq_len(n)) {

-                if(i == i_main) {

-                    object@ht_list[[i]]@row_title = ht_main@row_title

-                    object@ht_list[[i]]@row_title_param = ht_main@row_title_param      

-                } else {

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

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

-                    }

-                }

-            }

+    ## orders of other heatmaps should be changed

+    for(i in seq_len(n)) {

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

+            object@ht_list[[i]]@row_order_list = ht_main@row_order_list

+            object@ht_list[[i]]@row_order = ht_main@row_order

+            object@ht_list[[i]]@row_hclust_param$cluster = FALSE  # don't do clustering because cluster was already done

         }

+    }

-

-        if(row_hclust_side == "left") {

-            for(i in seq_len(n)) {

-                if(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

-                    object@ht_list[[1]]@row_hclust_param$side = "left"

-                } else {

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

-                        object@ht_list[[i]]@row_hclust_param$show = FALSE

-                    }

-                }

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

-                    object@ht_list[[i]]@row_order_list = ht_main@row_order_list

-                    object@ht_list[[i]]@row_hclust_param$cluster = FALSE

-                }

-            }

-        } else if(row_hclust_side == "right") {

-            for(i in seq_len(n)) {

-                if(i == n) {

-                    object@ht_list[[n]]@row_hclust_list = ht_main@row_hclust_list

-                    object@ht_list[[n]]@row_hclust_param = ht_main@row_hclust_param

-                    object@ht_list[[n]]@row_hclust_param$side = "right"

-                } else {

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

-                        object@ht_list[[i]]@row_hclust_param$show = FALSE

-                    }

-                }

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

-                    object@ht_list[[i]]@row_order_list = ht_main@row_order_list

-                    object@ht_list[[i]]@row_hclust_param$cluster = FALSE

-                }

-            }

-        } else {

-            for(i in seq_len(n)) {

-                if(i == i_main) {

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

-                    object@ht_list[[i]]@row_hclust_param = ht_main@row_hclust_param

-                } else {

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

-                        object@ht_list[[i]]@row_hclust_param$show = FALSE

-                    }

-                }

+    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

+        object@ht_list[[1]]@row_hclust_param$side = "left"

+    } else if(row_hclust_side == "right" && i == n) {

+        object@ht_list[[n]]@row_hclust_list = ht_main@row_hclust_list

+        object@ht_list[[n]]@row_hclust_param = ht_main@row_hclust_param

+        object@ht_list[[n]]@row_hclust_param$side = "right"

+    } else {

+        for(i in seq_len(n)) {

+            if(i != i_main) {

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

-                    object@ht_list[[i]]@row_order_list = ht_main@row_order_list

-                    object@ht_list[[i]]@row_hclust_param$cluster = FALSE

+                    object@ht_list[[i]]@row_hclust_param$show = FALSE

                 }

             }

         }

+    }

-        for(i in seq_len(n)) {

-            # supress row clustering because all rows in all heatmaps are adjusted

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

-                object@ht_list[[i]]@matrix_param$km = 1

-                object@ht_list[[i]]@row_title_param$combined_name_fun = NULL

-                object@ht_list[[i]] = prepare(object@ht_list[[i]], row_order = NULL, split = NULL)

-            }

+    for(i in seq_len(n)) {

+        # supress row clustering because all rows in all heatmaps are adjusted

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

+            object@ht_list[[i]] = prepare(object@ht_list[[i]], process_rows = FALSE)

         }

     }

@@ -805,8 +738,8 @@ setMethod(f = "draw_heatmap_list",

     # number of columns in heatmap whic are not fixed width

     heatmap_ncol = sapply(object@ht_list, function(ht) {

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

-            if(is.null(ht@heatmap_param$width)) {

-                return(ncol(ht@matrix))

+            if(!is.unit(ht@heatmap_param$width)) {

+                return(ht@heatmap_param$width)

             }

         }

         return(0)

@@ -814,7 +747,7 @@ setMethod(f = "draw_heatmap_list",

     heatmap_fixed_width = lapply(object@ht_list, function(ht) {

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

-            if(!is.null(ht@heatmap_param$width)) {

+            if(is.unit(ht@heatmap_param$width)) {

                 return(ht@heatmap_param$width)

             } else {

                 return(unit(0, "null"))

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

 \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}

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

 \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}

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

 \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.

@@ -25,14 +24,11 @@ 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}

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

 \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} is generated by \code{\link[circlize]{colorRamp2}}, \code{breaks} can be ignored.}

+  \item{breaks}{breaks for the continuous color mapping. If \code{col_fun} isgenerated 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{

@@ -56,5 +50,4 @@ 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 @@ The package is implemented in an object oriented way.  Components of heatmap lis

   \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}.  

-

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

+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.

 }

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

 \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)

@@ -28,7 +26,7 @@ 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}}.

@@ -42,7 +40,7 @@ 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}}.

@@ -54,12 +52,13 @@ 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.

@@ -67,14 +66,11 @@ 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}

@@ -1,13 +1,11 @@

 \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{

@@ -35,29 +33,28 @@ 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 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{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{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{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 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{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{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}}.}

@@ -65,11 +62,11 @@ 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 reasonable to 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 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.}

@@ -79,18 +76,18 @@ 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 heatmap is 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 heatmapis 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

@@ -98,18 +95,16 @@ 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{

@@ -183,5 +178,4 @@ 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")}

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

 \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{