% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/AllClasses.R, R/family-TreePlot.R
 \docType{class}
 \name{TreePlot-class}
 \alias{TreePlot-class}
 \alias{TreePlot}
 \title{Tree plot}
 \description{

 The TreePlot is a virtual class that creates a hierarchical tree of either
 the features or samples of a

 \code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-constructor]{TreeSummarizedExperiment}}

 object. The \linkS4class{RowTreePlot} and \linkS4class{ColumnTreePlot}
 classes belong to this family and are specialised to visualise the rowTree
 and the colTree, respectively.

 }
 \section{Slot overview}{
 
 The following slots control the thresholds used in the visualisation:
 \itemize{

 \item \code{layout}: \code{Character scalar}. Tree layout.
 (Default: \code{"fan"})
 \item \code{add.legend}: \code{Logical scalar}. Should legend be shown.
 (Default: \code{TRUE})
 \item \code{edge.colour.by}: \code{Character scalar}. Parameter to colour
 lines by when \code{colour_parameters = "Edge"}. (Default: \code{NULL})
 \item \code{edge.size.by}: \code{Character scalar}. Parameter to size lines
 by when \code{size_parameters = "Edge"}. (Default: \code{NULL})
 \item \code{tip.colour.by}: \code{Character scalar}. Parameter to colour tips
 by when \code{colour_parameters = "Tip"}. (Default: \code{NULL})
 \item \code{tip.size.by}: \code{Character scalar}. Parameter to size tips by
 when \code{size_parameters = "Tip"}. (Default: \code{NULL})
 \item \code{tip.shape.by}: \code{Character scalar}. Parameter to shape tips
 by when \code{shape_parameters = "Tip"}. (Default: \code{NULL})
 \item \code{node.colour.by}: \code{Character scalar}. Parameter to colour
 nodes by when \code{colour_parameters = "Node"}. (Default: \code{NULL})
 \item \code{node.size.by}: \code{Character scalar}. Parameter to size nodes
 by when \code{size_parameters = "Node"}. (Default: \code{NULL})
 \item \code{node.shape.by}: \code{Character scalar}. Parameter to shape nodes
 by when \code{shape_parameters = "Node"}. (Default: \code{NULL})
 \item \code{order.tree}: \code{Logical scalar}. Should the tree be ordered
 alphabetically by the taxonomic levels. (Default: \code{FALSE})
 \item \code{open.angle}: \code{Numeric scalar}. Angle by which the tree is
 opened when \code{layout} is \code{"fan"}. (Default: \code{0})
 \item \code{rotate.angle}: \code{Numeric scalar}. Angle by which the tree is
 rotated. (Default: \code{0})
 \item \code{branch.length}: \code{Logical scalar}. Should branch length be
 equalised. (Default: \code{FALSE})

 }
 

 In addition, this class inherits all slots from its parent

 \code{\link[iSEE:Panel-class]{Panel}}.

 }
 

 \seealso{
 \linkS4class{RowTreePlot}
 \linkS4class{ColumnTreePlot}

 }
 \author{
 Giulio Benedetti
 }