R: Plot gene region and annotation tracks

plotAsAnnotationTrack {Pbase}

R Documentation

Plot gene region and annotation tracks

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

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

[Package Pbase version 0.20.0 Index]