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

 Package: ComplexHeatmap

 Type: Package

 Title: Make Complex Heatmaps

-Version: 1.99.0

-Date: 2018-10-23

+Version: 1.99.1

+Date: 2018-11-23

 Author: Zuguang Gu

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

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

@@ -1,3 +1,9 @@

+CHANGES in VERSION 1.99.1

+

+* add `cluster_row_slices` and `cluster_column_slices` arguments in `Heatmap()`.

+

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

+

 CHANGES in VERSION 1.99.0

 This a major update of the package. The main changes are:

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

-setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))

-setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))

 setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))

-setGeneric('component_height', function(object, ...) standardGeneric('component_height'))

-setGeneric('re_size', function(object, ...) standardGeneric('re_size'))

-setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))

-setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))

-setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))

-setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))

-setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))

-setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))

-setGeneric('row_order', function(object, ...) standardGeneric('row_order'))

-setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))

+setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))

 setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))

+setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))

+setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))

+setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))

 setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))

-setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))

+setGeneric('row_order', function(object, ...) standardGeneric('row_order'))

+setGeneric('component_height', function(object, ...) standardGeneric('component_height'))

+setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))

 setGeneric('column_order', function(object, ...) standardGeneric('column_order'))

-setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))

-setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))

+setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))

+setGeneric('component_width', function(object, ...) standardGeneric('component_width'))

+setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))

+setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))

+setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))

+setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))

+setGeneric('draw', function(object, ...) standardGeneric('draw'))

 setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))

+setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))

 setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))

 setGeneric('prepare', function(object, ...) standardGeneric('prepare'))

 setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))

-setGeneric('draw', function(object, ...) standardGeneric('draw'))

-setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))

-setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))

-setGeneric('component_width', function(object, ...) standardGeneric('component_width'))

-setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))

+setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))

+setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))

+setGeneric('re_size', function(object, ...) standardGeneric('re_size'))

+setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))

+setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))

+setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))

+setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))

 setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))

-setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))

-setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))

@@ -104,6 +104,7 @@ Heatmap = setClass("Heatmap",

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

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

 #               Check https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#clustering .

+# -cluster_row_slices If rows are split into slices, whether perform clustering on the slice means?

 # -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.

@@ -120,6 +121,7 @@ Heatmap = setClass("Heatmap",

 # -row_dend_reorder Apply reordering on row dendrograms. The value can be a logical value or a vector which contains weight 

 #               which is used to reorder rows. The reordering is applied by `stats::reorder.dendrogram`.

 # -cluster_columns Whether make cluster on columns? Same settings as ``cluster_rows``.

+# -cluster_column_slices If columns are split into slices, whether perform clustering on the slice means?

 # -clustering_distance_columns Same setting as ``clustering_distance_rows``.

 # -clustering_method_columns Method to perform hierarchical clustering, pass to `stats::hclust`.

 # -column_dend_side Should the column dendrogram be put on the top or bottom of the heatmap?

@@ -210,6 +212,7 @@ Heatmap = function(matrix, col, name,

     column_title_rot = 0,

     cluster_rows = TRUE, 

+    cluster_row_slices = TRUE,

     clustering_distance_rows = "euclidean",

     clustering_method_rows = "complete", 

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

@@ -218,6 +221,7 @@ Heatmap = function(matrix, col, name,

     row_dend_reorder = is.logical(cluster_rows) || is.function(cluster_rows),

     row_dend_gp = gpar(), 

     cluster_columns = TRUE, 

+    cluster_column_slices = TRUE,

     clustering_distance_columns = "euclidean", 

     clustering_method_columns = "complete",

     column_dend_side = c("top", "bottom"), 

@@ -600,6 +604,7 @@ Heatmap = function(matrix, col, name,

         }

         .Object@row_order = row_order

     }

+    .Object@row_dend_param$cluster_slices = cluster_row_slices

     if(missing(cluster_columns) && !missing(column_order)) {

         cluster_columns = FALSE

@@ -644,6 +649,7 @@ Heatmap = function(matrix, col, name,

         }

         .Object@column_order = column_order

     }

+    .Object@column_dend_param$cluster_slices = cluster_column_slices

     ######### annotations #############

     .Object@top_annotation = top_annotation # a `HeatmapAnnotation` object

@@ -893,6 +899,7 @@ make_cluster = function(object, which = c("row", "column")) {

     split = getElement(object@matrix_param, paste0(which, "_split"))

     reorder = slot(object, paste0(which, "_dend_param"))$reorder

     cluster = slot(object, paste0(which, "_dend_param"))$cluster

+    cluster_slices = slot(object, paste0(which, "_dend_param"))$cluster_slices

     gap = getElement(object@matrix_param, paste0(which, "_gap"))

     dend_param = slot(object, paste0(which, "_dend_param"))

@@ -1252,7 +1259,7 @@ make_cluster = function(object, which = c("row", "column")) {

             if(verbose) qqcat("reorder dendrograms in each @{which} slice\n")

         }

-        if(length(order_list) > 1) {

+        if(length(order_list) > 1 && cluster_slices) {

             if(which == "row") {

                 slice_mean = sapply(order_list, function(ind) colMeans(mat[ind, , drop = FALSE]))

             } else {

@@ -1263,6 +1270,10 @@ make_cluster = function(object, which = c("row", "column")) {

             }

             dend_slice = as.dendrogram(hclust(dist(t(slice_mean))))

             if(verbose) qqcat("perform clustering on mean of @{which} slices\n")

+

+            slice_od = order.dendrogram(dend_slice)

+            order_list = order_list[slice_od]

+            dend_list = dend_list[slice_od]

         }

     }

@@ -155,6 +155,7 @@ setMethod(f = "make_layout",

     row_dend_side = object@row_dend_param$side

     row_dend_width = object@row_dend_param$width

     row_dend_slice = object@row_dend_slice

+    cluster_dend_slices = object@row_dend_param$cluster_slices

     if(show_row_dend) {

         if(row_dend_side == "left") {

             object@layout$layout_size$row_dend_left_width = row_dend_width

@@ -180,7 +181,7 @@ setMethod(f = "make_layout",

                     max_height = row_dend_max_height)

             }

-            if(nr_slice > 1) {

+            if(nr_slice > 1 && cluster_dend_slices) {

                 if(row_dend_side == "left") {

                     pushViewport(viewport(xscale = c(0, row_dend_max_height)))

                 } else {

@@ -229,6 +230,7 @@ setMethod(f = "make_layout",

     column_dend_side = object@column_dend_param$side

     column_dend_height = object@column_dend_param$height

     column_dend_slice = object@column_dend_slice

+    cluster_column_slices = object@column_dend_param$cluster_slices

     if(show_column_dend) {

         if(column_dend_side == "top") {

             object@layout$layout_size$column_dend_top_height = column_dend_height

@@ -253,7 +255,7 @@ setMethod(f = "make_layout",

                     max_height = column_dend_max_height)

             }

-            if(nc_slice > 1) {

+            if(nc_slice > 1 && cluster_column_slices) {

                 if(column_dend_side == "top") {

                     pushViewport(viewport(yscale = c(0, column_dend_max_height)))

                 } else {

@@ -25,6 +25,7 @@ Heatmap(matrix, col, name,

     column_title_rot = 0,

     cluster_rows = TRUE,

+    cluster_row_slices = TRUE,

     clustering_distance_rows = "euclidean",

     clustering_method_rows = "complete",

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

@@ -33,6 +34,7 @@ Heatmap(matrix, col, name,

     row_dend_reorder = is.logical(cluster_rows) || is.function(cluster_rows),

     row_dend_gp = gpar(),

     cluster_columns = TRUE,

+    cluster_column_slices = TRUE,

     clustering_distance_columns = "euclidean",

     clustering_method_columns = "complete",

     column_dend_side = c("top", "bottom"),

@@ -85,6 +87,7 @@ Heatmap(matrix, col, name,

     raster_device = c("png", "jpeg", "tiff", "CairoPNG", "CairoJPEG", "CairoTIFF"),

     raster_quality = 2,

     raster_device_param = list(),

+    raster_resize = FALSE,

     post_fun = NULL)

 }

@@ -108,6 +111,7 @@ Heatmap(matrix, col, name,

   \item{column_title_gp}{Graphic parameters for column title.}

   \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 controls whether to make cluster on rows. The value can also be a \code{\link[stats]{hclust}} or a \code{\link[stats]{dendrogram}} which already contains clustering. Check \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#clustering} .}

+  \item{cluster_row_slices}{If rows are split into slices, whether perform clustering on the slice means?}

   \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 perform hierarchical clustering, pass to \code{\link[stats]{hclust}}.}

   \item{row_dend_side}{Should the row dendrogram be put on the left or right of the heatmap?}

@@ -116,6 +120,7 @@ Heatmap(matrix, col, name,

   \item{row_dend_gp}{Graphic parameters for the dendrogram segments. If users already provide a \code{\link[stats]{dendrogram}} object with edges rendered, this argument will be ignored.}

   \item{row_dend_reorder}{Apply reordering on row dendrograms. The value can be a logical value or a vector which contains weight  which is used to reorder rows. The reordering is applied by \code{\link[stats]{reorder.dendrogram}}.}

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

+  \item{cluster_column_slices}{If columns are split into slices, whether perform clustering on the slice means?}

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

   \item{clustering_method_columns}{Method to perform hierarchical clustering, pass to \code{\link[stats]{hclust}}.}

   \item{column_dend_side}{Should the column dendrogram be put on the top or bottom of the heatmap?}

@@ -161,6 +166,7 @@ Heatmap(matrix, col, name,

   \item{raster_device}{Graphic device which is used to generate the raster image.}

   \item{raster_quality}{A value set to larger than 1 will improve the quality of the raster image.}

   \item{raster_device_param}{A list of further parameters for the selected graphic device. For raster image support, please check \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#heatmap-as-raster-image} .}

+  \item{raster_resize}{Whether resize the matrix to let the dimension of the matrix the same as the dimension of the raster image?}

   \item{post_fun}{A function which will be executed after the heatmap list is drawn.}

 }

@@ -10,8 +10,8 @@ Method dispatch page for \code{component_height}.

 \code{component_height} can be dispatched on following classes:

 \itemize{

-\item \code{\link{component_height,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

 \item \code{\link{component_height,Heatmap-method}}, \code{\link{Heatmap-class}} class method

+\item \code{\link{component_height,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

 }

 }

 \examples{

@@ -10,8 +10,8 @@ Method dispatch page for \code{component_width}.

 \code{component_width} can be dispatched on following classes:

 \itemize{

-\item \code{\link{component_width,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

 \item \code{\link{component_width,Heatmap-method}}, \code{\link{Heatmap-class}} class method

+\item \code{\link{component_width,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

 }

 }

 \examples{

@@ -10,12 +10,12 @@ Method dispatch page for \code{draw}.

 \code{draw} can be dispatched on following classes:

 \itemize{

-\item \code{\link{draw,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method

-\item \code{\link{draw,Legends-method}}, \code{\link{Legends-class}} class method

-\item \code{\link{draw,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method

 \item \code{\link{draw,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method

-\item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

 \item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method

+\item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

+\item \code{\link{draw,Legends-method}}, \code{\link{Legends-class}} class method

+\item \code{\link{draw,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method

+\item \code{\link{draw,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method

 }

 }

 \examples{

@@ -10,8 +10,8 @@ Method dispatch page for \code{make_layout}.

 \code{make_layout} can be dispatched on following classes:

 \itemize{

-\item \code{\link{make_layout,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

 \item \code{\link{make_layout,Heatmap-method}}, \code{\link{Heatmap-class}} class method

+\item \code{\link{make_layout,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

 }

 }

 \examples{

@@ -10,8 +10,8 @@ Method dispatch page for \code{row_order}.

 \code{row_order} can be dispatched on following classes:

 \itemize{

-\item \code{\link{row_order,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

 \item \code{\link{row_order,Heatmap-method}}, \code{\link{Heatmap-class}} class method

+\item \code{\link{row_order,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

 }

 }

 \examples{

@@ -10,12 +10,12 @@ Method dispatch page for \code{show}.

 \code{show} can be dispatched on following classes:

 \itemize{

-\item \code{\link{show,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method

-\item \code{\link{show,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method

-\item \code{\link{show,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method

+\item \code{\link{show,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 \item \code{\link{show,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method

 \item \code{\link{show,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

-\item \code{\link{show,Heatmap-method}}, \code{\link{Heatmap-class}} class method

+\item \code{\link{show,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method

+\item \code{\link{show,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method

+\item \code{\link{show,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method

 }

 }

 \examples{