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interactivereport / cellxgene_VIP

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.
https://cellxgenevip-ms.bxgenomics.com
MIT License
129 stars 44 forks source link

Problems with gene names #91

Closed Edhelia closed 1 year ago

Edhelia commented 1 year ago

Hi :) I used Cellxgene VIP, it's great thx all:) But I 've a little problems, the names of the genes do not appear, I have to indicate the Ensembl numbers. If I indicate names generic (for exemple STAT5A), it does not work I have to indicate ENSG000....

The h5ad file I'm using is on my computer, downloading directly from the server. It works perfectly with cellxgene (the name of the genes is present), but as soon as I launch cellxgen-VIP I have to enter the numbers Ensembl to find my genes.. which is very problematic for me.. Do you have any idea why this is not working?

thank you very much for your time

PS: excuse my English :p

z5ouyang commented 1 year ago

Could you provide the version of the anndata. VIP currently only support anndata <0.8. And if you load your data, adata.var_name is used as gene identifier in the cellxgene and cellxgeneVIP. Please let me know if this helps.

Edhelia commented 1 year ago

It's work, I just add --var-names feature_name

thx :)