When plotting features linearly along genomic coordinates one frequently runs into the problem of too little resolution to adequately display all details. Most genome browsers try to reasonably reduce the amount of detail that is shown based on the current zoom level.
Most track classes in this package define an internal collapseTrack
method which tries to adjust the plotted content to the available
resolution, aims at reducing over-plotting and prevents rendering issues,
e.g. when lines are too thin to be plotted. This feature can be toggled on
or off using the collapse display parameter (see
settings for details on setting these parameters).
In the simplest case (for AnnotationTrack objects) this
involves expanding all shown features to a minimum pixel width and height
(using display parameters min.width and min.heigh) and
collapsing overlapping annotation items (as defined by the parameter
min.distance into one single item to prevent over-plotting.
For objects of class DataTrack, the data values
underlying collapsed regions will be summarized based on the summary
display parameter. See the class' documentation for more details.