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

[Paul Shannon]

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