search

IGS / gEAR

The gEAR Portal was created as a data archive and viewer for gene expression data including microarrays, bulk RNA-Seq, single-cell RNA-Seq and more.
https://umgear.org
GNU Affero General Public License v3.0
13 stars 4 forks source link

tSNE_static - error in sort_legend function #862

Closed adkinsrs closed 2 months ago

adkinsrs commented 2 months ago

https://nemoanalytics.org/projection.html?projection_algorithm=pca&multipattern_plots=0&projection_source=CellCycleGenes.Seurat&layout_id=NeocortexDevoHsInVitro&projection_patterns=Sphase%2CG2Mphase

Two datasets but the one I want to focus on for the example is "Lineage recording in human cerebral organoids - Visium Slice 3 (He et al., Nat Methods 2022)"

Seeing a "list index out of range error" in the above link, but in the below link (NOT VALID LINK) the dataset renders fine. Both default displays are the same, so I think maybe all the samples are somehow being filtered out in the first example (which would require an investigation of the projection.csv, or the AnnData object created).

https://nemoanalytics.org/projection.html?projection_algorithm=nmf&multipattern_plots=0

adkinsrs commented 2 months ago

projection csv and h5ad files look fine to me.

adkinsrs commented 2 months ago

It seems some previous commit has fixed this bug. I'm guessing it was work from trying to resolve a BlockingIOError

adkinsrs commented 2 months ago

Tentatively closing as I believe the error was indirectly caused by other bugs which were resolved.