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broadinstitute / single_cell_portal

Tutorials, workflows, and convenience scripts for Single Cell Portal
https://singlecell.broadinstitute.org/single_cell
BSD 3-Clause "New" or "Revised" License
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tSNE plot shows continuous but not discrete data #21

Closed farrellja closed 6 years ago

farrellja commented 6 years ago

Hi Team!

I'm having an issue with one of my sets of cluster coordinates not displaying correctly. The affected study is: https://portals.broadinstitute.org/single_cell/study/single-cell-reconstruction-of-developmental-trajectories-during-zebrafish-embryogenesis

There are two cluster files (URD Developmental Tree and tSNE - All Cells). For URD Developmental Tree, everything displays as expected. For tSNE - All Cells, the points fail to display when colored by discrete annotations (i.e. Stage or Lineage_Spinal_Cord) but when plotting expression of a gene, it is normal. The points are there (the hover works fine), but I just can't see them. On my computer, this affects Safari, but not Chrome. I tried also another computer that had never visited the site and had the same issue in Safari, so I think it might be browser wide, though I am not sure.

I attach two screenshots - one showing the affected view (tSNE - All Cells) and the other showing an unaffected view (URD Developmental Tree).

screen shot 2018-04-26 at 3 08 09 pm screen shot 2018-04-26 at 3 09 25 pm

Thanks for your help! Jeff

bistline commented 6 years ago

This is a bug that was just found in Plotly.js apparently: #2457. It was only opened about a week ago, so it doesn't appear they have a fix for it yet. For now, I'd say just use Chrome. Once they've fixed it, we'll do a release to bump up the Plotly.js version to include it.

bistline commented 6 years ago

Looks like Plotly will have a fix for this soon, so once it's released we'll merge an update in and schedule it for deployment.

farrellja commented 6 years ago

Great! Thanks, Jon! People so far seem to enjoy browsing our data in the single-cell portal, and they're finding it useful. So, thanks for making this tool available!!!

bistline commented 6 years ago

This has been patched in v1.37.1, so we'll be doing a release tomorrow for this.

farrellja commented 6 years ago

I just checked, and it seems to be working properly now! Thanks so much, Jon!