plotAsAnnotationTrack

plotAsGeneRegionTrack

A <code>Granges</code> object containing peptides genomics
coordinates, typically generated by
<code><a rd-options="" href="/link/pmapToGenome?package=Pbase&version=0.12.2" data-mini-rdoc="Pbase::pmapToGenome">pmapToGenome</a></code>. These ranges are converted to a
<code>AnnotationTrack</code>.

One or more <code>GRanges</code> instances, typically
resulting from calling <code><a rd-options="" href="/link/etrid2grl?package=Pbase&version=0.12.2" data-mini-rdoc="Pbase::etrid2grl">etrid2grl</a></code>, or, a single
<code>GRangesList</code>. These ranges are converted to
<code>GeneRegionTrack</code> instances.

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

genome

A <code>logical</code> defining if the figure should be
plotted. Default is <code>TRUE</code>.

plot


These functions convert ranges of peptides or exons to
<code>AnnotationTrack</code> or <code>GeneRegionTrack</code> objects from the
<code>Gviz</code> package and produces the corresponding plot. The
<code>genome</code> argument controls whether additional ideogram and
axis tracks are to be plotted. <code>plotAsAnnotationTrack</code> plots
peptides that span multiple exons in red and connects them with a
grey line. See <code><a rd-options="" href="/link/pmapToGenome?package=Pbase&version=0.12.2" data-mini-rdoc="Pbase::pmapToGenome">pmapToGenome</a></code> for example code.


A set of classes and functions to investigate and
understand protein sequence data in the context of a
proteomics experiment.

Laurent Gatto

Pbase

Manipulating and exploring protein and proteomics data

plotAsAnnotationTrack function

A <code>Granges</code> object containing peptides genomics
coordinates, typically generated by
<code><a href="pmapToGenome" rd-options="">pmapToGenome</a></code>. These ranges are converted to a
<code>AnnotationTrack</code>.

One or more <code>GRanges</code> instances, typically
resulting from calling <code><a href="etrid2grl" rd-options="">etrid2grl</a></code>, or, a single
<code>GRangesList</code>. These ranges are converted to
<code>GeneRegionTrack</code> instances.

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

plotAsAnnotationTrack: Plot gene region and annotation tracks

Description

Usage

Arguments

Value