collapsing: Dynamic content based on the available resolution

In ivanek/Gviz: Plotting data and annotation information along genomic coordinates

Dynamic content based on the available resolution

Description

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.

Details

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.

See Also

AnnotationTrack

DataTrack

settings

ivanek/Gviz documentation built on Nov. 20, 2023, 8:16 p.m.