Pseudo time as function of a predefined group of genes

[kvshams]

Is it possible to plot the cells as a function of a list of genes?

[kieranrcampbell]

Not sure I understand — each cell gets a pseudotime and each gene gets an activation time, but there’s not necessarily the same number of each, so you couldn’t match them. You could however ask questions like what sets of cells have pseudotimes before a certain gene is activated, does that make sense?

[kvshams]

Sorry for the confusion. I wanted to ask the extend of your suggestion. I want to ask like how many cells have activation of gene set=gene1,2....n at a given time and plot like 0-1 as a function of fraction of gene activated from the gene set. some thing more like a gene score

[kieranrcampbell]

I don't think you'll be able to do this with pseudotime: whether or not the activation of a gene is present is a function of all the cells, not one or a subset. If you were able to truly trace cells over time then you would be able to ask which cells display gene activation.