igvShiny issues with loading local bams

Question

[genya35]

Hello, Has anyone here have tried IGV imbedded in Rshiny from https://github.com/gladkia/igvShiny? It installed ok but I can't get local bams from local path to load. It reads them but gives me an error: Error in as.character: cannot coerce type 'closure' to vector of type 'character' and does not display the track. I can't get to work with a local example bam they provided either.

Also, looks like the guy who made it has recently retired, therefore, not sure if my Github issues will be answered. Thanks

[jared.andrews07]

We need your code to have any chance of answering this.

[JC]

why not use IGV browser directly?

[jared.andrews07]

IGV imbedded in Rshiny

I think they want to embed it in a Shiny app, and this package takes care of wrapping IGV.js up to play nicely.

Answer 1

[Malcolm.Cook]

I coded up a workaround for a very similar issue that I expect will apply to this case as well. See it here: loadBedGraphTrackFromURL rewrites the config vars including url