MaximilianLombardo
commented
2 years ago Hey Curtis - thanks for the question - copying the response from the slack thread:
Hey Curtis - thanks for the question! In cellxgene, you can visualize any of these modalities as long as they have a matrix format of cells by genes and contain integer or numeric values. To visualize any single modality at one time, you simply need to stash the desired modality into adata.X You cannot however visualize multiple modalities at the same time within cellxgene (cellxgene only pulls data from adata.X) Out of curiosity which modalities in addition to RNA were you looking to visualize/which assay did you run to generate the data?
Hello, I am a big fan of this tool and am trying to incorporate it into our datasets. We currently use Seurat, and I have been successful in exporting my RDS files to annadata and then viewing them within Cellxgene, however I can only see the RNA information and none of my other assays (we have 3 additional assays). Is there a way to incorporate these into cellxgene? I don't know if they are getting lost in the translation from the RDS file to annadata or if I need to do something prior to get them to be read by cellxgene. Any help would be greatly appreciated!