@@ -78,6 +78,8 @@ S3method("size<-", "HeatmapAnnotation")

 export("size<-.HeatmapAnnotation")

 S3method("size<-", "SingleAnnotation")

 export("size<-.SingleAnnotation")

+S3method("str", "comb_mat")

+export("str.comb_mat")

 S3method("summary", "Heatmap")

 export("summary.Heatmap")

 S3method("summary", "HeatmapList")

@@ -2,6 +2,7 @@ CHANGES in VERSION 1.99.6

 * adjust the size of heatmap annotations and add testing scripts

 * run multiple times k-means to get a consensus partition

+* `show_heatmap_legend` is set to FALSE if `rect_gp = gpar(type = "none")`

 ========================

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

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

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

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

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

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

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

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

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

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

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

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

+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('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'))

@@ -351,8 +351,12 @@ Heatmap = function(matrix, col, name,

     }

     if(ncol(matrix) == 0) {

+        show_heatmap_legend = FALSE

         .Object@heatmap_param$show_heatmap_legend = FALSE

     }

+    if(identical(rect_gp$type, "none")) {

+        show_heatmap_legend = FALSE

+    }

     ### normalize km/split and row_km/row_split

     if(missing(row_km)) row_km = km

@@ -1138,3 +1138,16 @@ normalize_comb_mat = function(...) {

 	}

 	return(lt)

 }

+

+# == title

+# str method

+#

+# == param

+# -object A combination matrix returned by `make_comb_mat`.

+# -... Other arguments.

+#

+str.comb_mat = function(object, ...) {

+	class(object) = "matrix"

+	cat(" A comb_mat class object\n")

+	str(object)

+}

deleted file mode 100644

@@ -11,8 +11,8 @@ Method dispatch page for \code{add_heatmap}.

 \itemize{

 \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

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

 \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

 }

 }

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

 \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

 }

 }

 \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,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

 }

 }

 \examples{

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

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

 \itemize{

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

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

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

 \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

 }

 }

 \examples{

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

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

 \itemize{

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

+\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,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

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

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

 }

 }

 \examples{

new file mode 100644

@@ -0,0 +1,22 @@

+\name{str.comb_mat}

+\alias{str.comb_mat}

+\title{

+str method

+}

+\description{

+str method

+}

+\usage{

+\method{str}{comb_mat}(object, ...)

+}

+\arguments{

+

+  \item{object}{A combination matrix returned by \code{\link{make_comb_mat}}.}

+  \item{...}{Other arguments.}

+

+}

+\examples{

+# There is no example

+NULL

+

+}