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maximilianh / cellBrowser

main repo: https://github.com/ucscGenomeBrowser/cellBrowser/ - Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org
https://github.com/ucscGenomeBrowser/cellBrowser/
GNU General Public License v3.0
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blank cluster canvas #167

Closed Parul-Kudtarkar closed 4 years ago

Parul-Kudtarkar commented 4 years ago

Screen Shot 2020-04-15 at 10 33 56 PM

The dataset matrix.mtx.gz (with features.tsv.gz and barcodes.tsv.gz); umap file & medata.tsv file is ingested without any errors; however the canvas is blank.

This is a large dataset with 132K cells. Is that an issue?

matthewspeir commented 4 years ago

132K cells shouldn't be a problem.

Do the files for meta, coords, etc. in your cellbrowser.conf match the file names for those things in the directory where you are running cbBuild? I'm fairly certain cbBuild would error if this wasn't the case, but just to be sure.

Additionally, are you defining the clusterField and labelField variables in your cellbrowser.conf? These should correspond to a field in your metadata. I'm fairly certain we've seen issues like this in the past when these fields weren't defined in the cellbrowser.conf

Parul-Kudtarkar commented 4 years ago

@matthewspeir thanks for a quick response! I indeed did not define the clusterField and labelField variables.