Genes missing/ no message in chrome developer tools
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I have managed to install this plugin but when I run the following code, I end up with a version of cellxgene_VIP missing the most genes/gene symbols (see image). My console also does not seem to have the "VIP is ready message" (see screenshot). Does anyone know how to solve this issue?
cellxgene launch --host localhost --port 5005 --disable-annotations --verbose https://datasets.cellxgene.cziscience.com/676c47a4-bd2c-4f09-82cb-2dfcd54be04a.h5ad
The reason is the default cellxgene launch, uses the default ".var_names" in AnnData object as gene name. And the ensembl was used in CZI data as default. CZI data use "feature_name" column in ".var" stores gene symbol. Thus when you "cellxgene launch" please use option: -var feature_name (check cellxgene launch --help)
Hope this helps, please reopen if this does not solve your issue