search

legumeinfo / ZZBrowse

Other
1 stars 1 forks source link

linking in via the URL isn't quite working #22

Closed adf-ncgr closed 3 years ago

adf-ncgr commented 3 years ago

I was going to point Steven to an example of a cowpea QTL on Vu05 that matched some soybean GWAS on Gm18, but this link: http://dev.lis.ncgr.org:50003/shiny/ZBrowse/?tab=Chrom&datasets=Cowpea%20QTL&chr=Vu05&selected=907871&window=250000&datasets2=Soybean%20GWAS&chr2=Gm18&selected2=57035000&window2=250000&traits=Days%20to%20flowering;Flower%20color;Flowering%20time%20under%20long%20daylength%20at%20UCR-CES;Flowering%20time%20under%20short%20daylength%20at%20CVARS&genomicLinkage=true&neighbors=40&matched=20&intermediate=5&selectedGene=vigun.Vigun05g010900&relatedRegion=Gm18%2056.75-57.32%20Mbp

seems to take me to Vu01 instead.

per Sven:

Confirmed, though the problem is not specific to QTL data. This should be a separate issue, I suspect it has to do with > the need to reset the chromosome view when the user changes an organism. (Except in this case where we do it programmatically through the URL.)

I'll note additionally that soybean does go to the right chromosome when the link is traversed. not sure if that is significant to figuring out the resolution...

svengato commented 3 years ago

"This redistribution of chromosome views is trickier than I thought!"

As a workaround, Steven can select Vu05 after clicking that link and ending up at Vu01.

adf-ncgr commented 3 years ago

"This redistribution of chromosome views is trickier than I thought!"

"He links to lupine 5, but lands on cowpea 1... Son of a gun!"

I should also note that the selection of traits recorded in the URL isn't being respected when the link is followed.

svengato commented 3 years ago

Try it now - I am still working on edge cases, but your example should succeed.

adf-ncgr commented 3 years ago

Yes, works as expected now- thanks! @cann0010 try : http://dev.lis.ncgr.org:50003/shiny/ZBrowse/?tab=Chrom&datasets=Cowpea%20QTL&chr=Vu05&selected=907871&window=250000&datasets2=Soybean%20GWAS&chr2=Gm18&selected2=57035000&window2=250000&traits=Days%20to%20flowering;Flower%20color;Flowering%20time%20under%20long%20daylength%20at%20UCR-CES;Flowering%20time%20under%20short%20daylength%20at%20CVARS&traits2=Days%20to%20flower;First%20flower;Flower%20color&genomicLinkage=true&neighbors=40&matched=20&intermediate=5&selectedGene=vigun.Vigun05g010900&relatedRegion=Gm18%2056.75-57.32%20Mbp for the cowpea flowering time QTL -> soybean GWAS use case I showed in the meeting earlier in the week

svengato commented 3 years ago

@cann0010 try : http://dev.lis.ncgr.org:50003/shiny/ZBrowse/[...]

Will that get to Steven? It looks like I am the only one cc'd on the message.

adf-ncgr commented 3 years ago

I think so, but the ways of github can be mysterious to mortal man(ager)

StevenCannon-USDA commented 3 years ago

@svengato @adf-ncgr - got it. I see cowpea QTL & soybean GWAS. Cool! That's a nice treat for the end of the week. Will explore more rigorously in the coming few days.