[Bioc-devel] IGV VCF demo, other suggestions? [was Re: IGV - a new package in preparation]
paul.thurmond.shannon at gmail.com
Wed Mar 14 20:40:35 CET 2018
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.
preclude any easy specification of options - which vary across track types - which are straightforward, easily managed and checked, by a set of track constructors?
displayTrack(VariantTrack(vcf, title=“mef2c eqtl”, height=“300”, homrefColor=“lightGray”,
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.
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