An extra exercise could be to get the cell info from a gating exercise, i.e. how to extract the population assignment of every cell from a gatingSet and put it inside a sce to use for UMAP plotting. Then create a UMAP to plot the expression value of the different markers considering the MFI of only the positive events (i.e set the negative cells' value to 0 to be grey). Here’s an example:
https://pubmed.ncbi.nlm.nih.gov/32125291/
An extra exercise could be to get the cell info from a gating exercise, i.e. how to extract the population assignment of every cell from a gatingSet and put it inside a sce to use for UMAP plotting. Then create a UMAP to plot the expression value of the different markers considering the MFI of only the positive events (i.e set the negative cells' value to 0 to be grey). Here’s an example:
https://pubmed.ncbi.nlm.nih.gov/32125291/