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.
I seem to be having an issue with opening h5ad files that have a small number of cells recorded - when I subset working h5ad files to 9 cells, the file does not load properly in cellxgene VIP, while it does in regular cellxgene. 100 cells work in VIP, whereas down to 1 cell seems to work for regular cellxgene.
There are some differences in cellxgene versions used (cellxgene v1.0.1 for regular cellxgene and cellxgene v1.1.1 for VIP)
I've attached the screenshot of what I see as I don't know where to find proper error messages:
z5ouyang
commented
7 months ago
Hello,
I seem to be having an issue with opening h5ad files that have a small number of cells recorded - when I subset working h5ad files to 9 cells, the file does not load properly in cellxgene VIP, while it does in regular cellxgene. 100 cells work in VIP, whereas down to 1 cell seems to work for regular cellxgene.
There are some differences in cellxgene versions used (cellxgene v1.0.1 for regular cellxgene and cellxgene v1.1.1 for VIP)
I've attached the screenshot of what I see as I don't know where to find proper error messages:
Any help with this would be greatly appreciated!