InteractionTrack-class: A class to hold chromatin interaction data for a specific...
In GenomicInteractions: Utilities for handling genomic interaction data
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.
GenomicInteractions documentation built on Nov. 8, 2020, 8:19 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.