The TreePlot is a virtual class that creates a hierarchical tree of either
the features or samples of a
TreeSummarizedExperiment
object. The RowTreePlot and ColumnTreePlot
classes belong to this family and are specialised to visualise the rowTree
and the colTree, respectively.
The following slots control the thresholds used in the visualisation:
layout: Character scalar. Tree layout.
(Default: "fan")
add.legend: Logical scalar. Should legend be shown.
(Default: TRUE)
edge.colour.by: Character scalar. Parameter to colour
lines by when colour_parameters = "Edge". (Default: NULL)
edge.size.by: Character scalar. Parameter to size lines
by when size_parameters = "Edge". (Default: NULL)
tip.colour.by: Character scalar. Parameter to colour tips
by when colour_parameters = "Tip". (Default: NULL)
tip.size.by: Character scalar. Parameter to size tips by
when size_parameters = "Tip". (Default: NULL)
tip.shape.by: Character scalar. Parameter to shape tips
by when shape_parameters = "Tip". (Default: NULL)
node.colour.by: Character scalar. Parameter to colour
nodes by when colour_parameters = "Node". (Default: NULL)
node.size.by: Character scalar. Parameter to size nodes
by when size_parameters = "Node". (Default: NULL)
node.shape.by: Character scalar. Parameter to shape nodes
by when shape_parameters = "Node". (Default: NULL)
order.tree: Logical scalar. Should the tree be ordered
alphabetically by the taxonomic levels. (Default: FALSE)
open.angle: Numeric scalar. Angle by which the tree is
opened when layout is "fan". (Default: 0)
rotate.angle: Numeric scalar. Angle by which the tree is
rotated. (Default: 0)
branch.length: Logical scalar. Should branch length be
equalised. (Default: FALSE)
In addition, this class inherits all slots from its parent Panel class.