InteractionTrack-class {GenomicInteractions} | R Documentation

## A class to hold chromatin interaction data for a specific genomic region.

### Description

@slot plottingFunction function @slot variables list @slot chromosome chromosome @slot stacking character

### Details

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 `plotTracks`.

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. Similarly `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 `fdr` or `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.

`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 `col.anchors.line.node.class` and `col.anchors.fill.node.class` parameters.

[Package GenomicInteractions version 1.24.0 Index]