The Graph plot is a virtual class that showcases the network organisation of
either the features or samples of a
SummarizedExperiment
object. The RowGraphPlot and ColumnGraphPlot
classes belong to this family and are specialised to visualise the feature
or sample igraphs stored in metadata, respectively.
The following slots control the thresholds used in the visualisation:
name: Character scalar. Metadata name containing graph.
(Default: "graph")
assay.type: Character scalar. Assay type to use.
(Default: "counts")
layout: Character scalar. Graph layout.
(Default: "kk")
edge.type: Character scalar. Edge type.
(Default: "fan")
show.label: Logical scalar. Should node labels be shown.
(Default: FALSE)
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)
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)
In addition, this class inherits all slots from its parent class Panel.