documentation and examples needed for providing tracks option to igvShiny

[malcook]

reviewing the documentation, tests, and demos, I can find no example of providing values for the tracks option to igvShiny function.

Its documentation reads:

  tracks: a list of track specifications to be created and displayed at  startup

but does not advise what a track specifications is.

Upon reviewing the code, AFAICT, the tracks option is ignored.

[paul-shannon]

Malcolm,

Thank you for this, and for the other issues you report. They are most welcome, most helpful, and I will tend to them all upon my return to Seattle in late October.

igvShiny has always been the poor stepchild of igvR, and has received insufficient attention. That will now change. Perhaps igvR can supply some of your needs in the meantime?

• Paul

On Oct 10, 2022, at 4:53 AM, Malcolm Cook @.***> wrote:

 reviewing the documentation, tests, and demos, I can find no example of providing values for the tracks option to igvShiny function.

Its documentation reads:

tracks: a list of track specifications to be created and displayed at startup but does not advise what a track specifications is.

Upon reviewing the code, AFAICT, the tracks option is ignored.

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[gladkia]

Hi @malcook,

We've prepared a vignette recently link. Can you please have a look and provide feedback? Thanks in advance.

[DLWheeler]

Hello:

I love the implementation of igvshiny, so thanks for producing it!

I'm trying to integrate it with couple of other genomics tools but I'm running into the same issue as malcook. I checked the link to the vignette above but the vignette doesn't appear to give a concrete example of the 'tracks' format. I was hoping to make my custom annotation searchable using something like:

igvShiny(genomeOptions, displayMode="squished", tracks=list(gene=list(name='genes2', format='gff3', uri="file://local.gff", searchable=TRUE))

This variant generates no error but it generates no track either. I see the tracks() option used in the igvshiny demos in only one case in which it is included without parameters:

x <- igvShiny(genomeOptions, displayMode="SQUISHED", tracks=list() )

I'd like to load several tracks by default and have them be searchable by feature name. Is this possible?

Thanks,

David