man/Heatmap-class.rd
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 \name{Heatmap-class}
 \docType{class}
 \alias{Heatmap-class}
 \title{
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 Class for a single heatmap
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 }
 \description{
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 Class for a single heatmap
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 }
 \details{
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 The components for a single heamtap are placed into a 9 x 7 layout:
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   \preformatted{
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          +------+ (1)
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          +------+ (2)
          +------+ (3)
          +------+ (4)
    +-+-+-+------+-+-+-+
    |1|2|3| 4(5) |5|6|7|
    +-+-+-+------+-+-+-+
          +------+ (6)
          +------+ (7)
          +------+ (8)
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          +------+ (9)  }
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 From top to bottom in column 4, the regions are:
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 \itemize{
   \item title which is put on the top of the heatmap, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
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   \item column cluster on the top, graphics are drawn by \code{\link{draw_dend,Heatmap-method}}.
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   \item column annotation on the top, graphics are drawn by \code{\link{draw_annotation,Heatmap-method}}.
   \item column names on the top, graphics are drawn by \code{\link{draw_dimnames,Heatmap-method}}.
   \item heatmap body, graphics are drawn by \code{\link{draw_heatmap_body,Heatmap-method}}.
   \item column names on the bottom, graphics are drawn by \code{\link{draw_dimnames,Heatmap-method}}.
   \item column annotation on the bottom, graphics are drawn by \code{\link{draw_annotation,Heatmap-method}}.
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   \item column cluster on the bottom, graphics are drawn by \code{\link{draw_dend,Heatmap-method}}.
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   \item title on the bottom, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
 }
 
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 From left to right in row 5, the regions are:
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 \itemize{
   \item title which is put in the left of the heatmap, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
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   \item row cluster on the left, graphics are drawn by \code{\link{draw_dend,Heatmap-method}}.
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   \item row names on the left, graphics are drawn by \code{\link{draw_dimnames,Heatmap-method}}.
   \item heatmap body
   \item row names on the right, graphics are drawn by \code{\link{draw_dimnames,Heatmap-method}}.
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   \item row cluster on the right, graphics are drawn by \code{\link{draw_dend,Heatmap-method}}.
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   \item title on the right, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.
 }
 
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 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.
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 }
 \section{Methods}{
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 The \code{\link{Heatmap-class}} provides following methods:
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 \itemize{
   \item \code{\link{Heatmap}}: constructor method.
   \item \code{\link{draw,Heatmap-method}}: draw a single heatmap.
   \item \code{\link{add_heatmap,Heatmap-method}} append heatmaps and row annotations to a list of heatmaps.
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   \item \code{\link{row_order,HeatmapList-method}}: get order of rows
   \item \code{\link{column_order,HeatmapList-method}}: get order of columns
   \item \code{\link{row_dend,HeatmapList-method}}: get row dendrograms
   \item \code{\link{column_dend,HeatmapList-method}}: get column dendrograms
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 }}
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 \author{
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 Zuguang Gu <z.gu@dkfz.de>
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 }
 \examples{
 # for examples, please go to `Heatmap` method page
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 NULL
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 }