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]