@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.
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
The value of
plot.outside determines whether or not interactions which
span outside of the window are to be plotted, and
the colour of these interactions. Similarly
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
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.
col.interactions 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
col.interaction.types 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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