Comments (1)
As I explain in #2629 I think the proper way to plot single-cell data is to first plot the zeros in light grey, then plot non-zeros using a colormap, on top. As long as point overlap is kept to a minimum (often also an issue in cellxgene), this way of plotting accurately reveals both low and no expression.
For example, consider the difference for AQP4 expression in this example of glioblasts when using grey for zeros (left) or just using the colormap (right):
When just using a colormap gradient, the true structure of gene expression disappears. Plotting low-to-high will not make any difference to the plot.
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Related Issues (20)
- [BUG] Can not start cellxgene HOT 5
- Feature request: distinguish zeros when plotting
- Annotate - update FE dependencies
- Annotate - update BE dependencies HOT 3
- Load data to cellxgene with SOMA 💡?
- [BUG] Cellxgene failing to launch h5ad files HOT 11
- [FEATURE REQUEST] Plot zeros in grey, nonzero using colormap HOT 1
- Optimizing Large Dataset Loading and Differential Expression Analysis in local hosted CellxGene VM HOT 3
- Issue with opening files [BUG] HOT 3
- install document update needed
- [QUESTION] Increase the size of dots/cells
- 使用示例anndata文件启动 Annotate 开始报错如何解决呢 HOT 3
- how to annotate the celltype HOT 2
- [FEATURE REQUEST] .CXG (TileDb compliant) format support from single-cell-explorer to cellxgene Annotate HOT 5
- [BUG] cells not able to be subset by specific annotations HOT 2
- [QUESTION] How can non-overlapping embeddings be handled smoothly?
- why some of the atlases on cellxgene do not have PCA in them. How can we use them to annotate our sample.
- [QUESTION] What is the expected format for the --gene-sets-file command?
- cellxgene annotate 'file open' error (Win10)
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