plotAsAnnotationTrack: Plot gene region and annotation tracks

Description Usage Arguments Value Author(s)

View source: R/plotting.R

Description

These functions convert ranges of peptides or exons to AnnotationTrack or GeneRegionTrack objects from the Gviz package and produces the corresponding plot. The genome argument controls whether additional ideogram and axis tracks are to be plotted. plotAsAnnotationTrack plots peptides that span multiple exons in red and connects them with a grey line. See pmapToGenome for example code.

Usage

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plotAsAnnotationTrack(x, ..., genome = "hg38", plot = TRUE)

plotAsGeneRegionTrack(..., genome = "hg38", plot = TRUE)

Arguments

x

A Granges object containing peptides genomics coordinates, typically generated by pmapToGenome. These ranges are converted to a AnnotationTrack.

...

One or more GRanges instances, typically resulting from calling etrid2grl, or, a single GRangesList. These ranges are converted to GeneRegionTrack instances.

genome

A character of length 1, giving the name of the genome. Default is "hg38". If NULL, no chromosome and axis tracks are displayed.

plot

A logical defining if the figure should be plotted. Default is TRUE.

Value

Used for its plotting side effects. Invisible returns a list of tracks.

Author(s)

Laurent Gatto


Pbase documentation built on Nov. 17, 2017, 9:03 a.m.