[Bioc-devel] IGV VCF demo, other suggestions? [was Re: IGV - a new package in preparation]

[Michael Lawrence]

Agreed about encapsulating plot parameters. I was thinking in terms of user
convenience, relying on defaults.

On Wed, Mar 14, 2018 at 12:40 PM, Paul Shannon <
paul.thurmond.shannon at gmail.com> wrote:

> Hi Michael,
>
> Set me straight if I got this wrong.   You suggest:
>
> > There should be no need to explicitly construct a track; just rely on
> dispatch and class semantics, i.e., passing a VCF object to add_track()
> would create a variant track automatically.
>
> But wouldn’t
>
>    displayTrack(vcf)
>
> preclude any easy specification of options - which vary across track types
> - which are straightforward, easily managed and checked, by a set of track
> constructors?
>
> Two examples:
>
>    displayTrack(VariantTrack(vcf, title=“mef2c eqtl”, height=“300”,
> homrefColor=“lightGray”,
>                              homVarColor=“darkRed”,
> hetVarColor=“lightRed”))
>
>    displayTrack(AlignmentTrack(x, title=“bam 32”, viewAsPairs=TRUE,
> insertionColor=“black”))
>
>
> So I suggest that the visualization of tracks has lots of
> track-type-specific settings which the user will want to control, and which
> would be messy to handle with an open-ended set of optional “…” args to a
> dispatch-capable single “displayTrack” method.
>
>  - Paul
>

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