@@ -263,6 +263,10 @@ importFrom("circlize", add_transparency)

 importFrom("circlize", colorRamp2)

 importFrom("circlize", rand_color)

 importFrom("circlize", smartAlign)

+importFrom("clue", as.cl_hard_partition)

+importFrom("clue", cl_class_ids)

+importFrom("clue", cl_consensus)

+importFrom("clue", cl_ensemble)

 importFrom("colorspace", diverge_hcl)

 importFrom("colorspace", rainbow_hcl)

 importFrom("parallel", "mclapply")

@@ -270,7 +274,4 @@ importFrom("utils", "combn")

 importFrom("utils", "getFromNamespace")

 importFrom("utils", "packageDescription")

 importFrom("utils", "str")

-importFrom("clue", as.cl_hard_partition)

-importFrom("clue", cl_ensemble)

-importFrom("clue", cl_consensus)

-importFrom("clue", cl_class_ids)

+

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@@ -152,10 +152,11 @@ Heatmap = setClass("Heatmap",

 # -split A vector or a data frame by which the rows are split. But if ``cluster_rows`` is a clustering object, ``split`` can be a single number

 #        indicating to split the dendrogram by `stats::cutree`.

 # -row_km Same as ``km``.

-# -row_km_repeats Number of k-means runs to get a consensus k-means clustering.

+# -row_km_repeats Number of k-means runs to get a consensus k-means clustering. Note if ``row_km_repeats`` is set to more than one, the final number

+#                of groups might be smaller than ``row_km``, but this might means the original ``row_km`` is not a good choice.

 # -row_split Same as ``split``.

 # -column_km K-means clustering on columns.

-# -column_km_repeats Number of k-means runs to get a consensus k-means clustering.

+# -column_km_repeats Number of k-means runs to get a consensus k-means clustering. Similar as ``row_km_repeats``.

 # -column_split Split on columns. For heatmap splitting, please refer to https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#heatmap-split .

 # -gap Gap between row slices if the heatmap is split by rows. The value should be a `grid::unit` object.

 # -row_gap Same as ``gap``.

@@ -67,8 +67,10 @@ Heatmap(matrix, col, name,

     km = 1,

     split = NULL,

     row_km = km,

+    row_km_repeats = 10,

     row_split = split,

     column_km = 1,

+    column_km_repeats = 10,

     column_split = NULL,

     gap = unit(1, "mm"),

     row_gap = unit(1, "mm"),

@@ -149,8 +151,10 @@ Heatmap(matrix, col, name,

   \item{km}{Apply 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 slice, hierarchical clustering is still applied with parameters above.}

   \item{split}{A vector or a data frame by which the rows are split. But if \code{cluster_rows} is a clustering object, \code{split} can be a single number indicating to split the dendrogram by \code{\link[stats]{cutree}}.}

   \item{row_km}{Same as \code{km}.}

+  \item{row_km_repeats}{Number of k-means runs to get a consensus k-means clustering. Note if \code{row_km_repeats} is set to more than one, the final number of groups might be smaller than \code{row_km}, but this might means the original \code{row_km} is not a good choice.}

   \item{row_split}{Same as \code{split}.}

   \item{column_km}{K-means clustering on columns.}

+  \item{column_km_repeats}{Number of k-means runs to get a consensus k-means clustering. Similar as \code{row_km_repeats}.}

   \item{column_split}{Split on columns. For heatmap splitting, please refer to \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#heatmap-split} .}

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

   \item{row_gap}{Same as \code{gap}.}

@@ -10,9 +10,9 @@ Method dispatch page for \code{add_heatmap}.

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

 \itemize{

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

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

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

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

 }

 }

 \examples{

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

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

 \itemize{

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

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

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

 }

 }

 \examples{

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

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

 \itemize{

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

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

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

 }

 }

 \examples{

@@ -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,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 \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

 }

 }

 \examples{

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

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

 \itemize{

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

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

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

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

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

 \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

 }

 }

 \examples{

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

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

 \itemize{

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

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

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

 }

 }

 \examples{

@@ -10,11 +10,11 @@ Method dispatch page for \code{show}.

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

 \itemize{

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

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

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

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

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

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

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

 }

 }