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gladkia / igvR

An R Bioconductor package providing interactive connections to igv.js (the Integrative Genomics Viewer) in a web browser
MIT License
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dm6 gene names on chromosomes other than chrX are not found #18

Closed gvogler closed 2 years ago

gvogler commented 2 years ago

I run data on the Drosophila dm6 genome and noticed that only genes from chrX are recognized and found (search box or via showGenomicRegion), but no gene on other chromosomes

igv <- igvR()
setBrowserWindowTitle(igv, "igvR Dmel")
setGenome(igv, "dm6")

showGenomicRegion(igv, "w")
[1] "w"
showGenomicRegion(igv, "Msp300")
[1] "unrecognized locus 'Msp300'"

The transcript of Msp300 is present in the track view and I can navigate their with coordinates, just not by gene. The standalone igv program can find those genes.

paul-shannon commented 2 years ago

@gvogler - working on this now, taking some notes. Msp300's coordinates: chr2L:5,100,877-5,207,002 bypassing igvR/javascript message passing, trying your test case in the javascript browser console, I think the problem lies in igv.js. I will put the question to Jim Robinson, who is always responsive and helpful.

igv.version() // '2.10.5'
p1 = igvBrowser.search("chr2L:5,100,877-5,207,002") // this works
p2 = igvBrowser.search("Msp300")  // this fails

search returns a Promise which, when examined for each of these cases, looks like this: image

paul-shannon commented 2 years ago

@gvogler Jim Robinson says this is now fixed: https://github.com/igvteam/igv.js/issues/1476#issuecomment-1082296795 Could you give it a try?

gvogler commented 2 years ago

Perfect! Works like a charm.

paul-shannon commented 2 years ago

glad to hear it!