@slot plottingFunction function @slot variables list @slot chromosome chromosome @slot stacking character
InteractionTrack is a specific Gviz-derived class for enabling the visualisation of chromatin interaction data.
The InteractionTrack class allows interactions on a specified chromosome to be visualised by examining interactions
between anchors as bezier curves. The object is instantiated and used in a similar fashion to standard Gviz tracks
and plotted using the
Several additional display parameters (i.e.
displayPars(foo)=list(...) are defined for this class, including
plot.anchors which can be used to specify whether anchors are to be drawn.
col.anchors.line which can be used
to alter the colour of border of these anchor elements and
col.anchors.fill can be used to alter the fill colour of these
elements. The value of
plot.outside determines whether or not interactions
which span outside of the window are to be plotted, and
col.outside defines the colour of these interactions.
plot.trans determines whether trans-interactions are plotted and
col.trans specifies the colour
of trans-interactions. By default, the height of an arc representing an interaction is proportional to the number
of reads/counts supporting that interaction. Instead of using the counts to define this, the height can be set to
be proportional to either
p.value using the
interaction.measure display parameter. By changing the
interaction.dimension to width, the line widths of each arc now represent the statistic supporting them. The heights of the arcs
can be made to be proportional to log10 of the supporting statistic by changing
interaction.dimension.transform to log.
sets the colour of arcs representing interactions within the region of interest. It is possible to colour the arcs by the type
of interaction they are involved in (i.e. promoter-promoter interactions etc) by setting the
display parameter to be a named vector of colours, where the name corresponds to the type of interaction. This is applicable to
anchors regions through the use of the
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