Possible to extract single cell-level gate memberships?

[hrj21]

Hi!

Thank you for creating such a powerful package! I know it's very easy to extract population-level statistics from a gatingSet, but is it possible to extract, at the per event level, which gates/nodes they belong to? A single event will often belong to multiple gates of course, so even if I was able to extract a logical vector per node, where the ith element is TRUE if the ith event belongs to node, and FALSE if not, that would be fine. Perhaps I'm overthinking and there is already an easy way to get something like this. Any thoughts you can offer would be much appreciated.

Best wishes
Hefin

[DillonHammill]

@hrj21, there isn't a nice CytoExploreR wrapper for this as of yet but you can have a look at gh_pop_get_indices() and gh_pop_get_indices_mat() from flowWorkspace. I will add a wrapper for the latter function which will return a logical vector for multiple populations at once. Here is an example using the Activation dataset shipped with CytoExploreRData:

library(CytoExploreRData)
gs <- GatingSet(Activation)
gs <- cyto_compensate(gs)
gs <- cyto_transform(gs)
gs <- cyto_gatingTemplate_apply(gs, Activation_gatingTemplate)

gh_pop_get_indices_mat(gs[[32]], c("T Cells", "CD4 T Cells", "CD8 T Cells"))

These APIs operate at the level of the GatingHierarchy so you will need to loop through the samples in your GatingSet to get the indices for every sample - I will write a wrapper to automate this within CytoExploreR.

I have just added a new cyto_gate_indices() function to version 2.0.0 of CytoExploreR (coming soon) that will automatically pull out the indices for every sample:

cyto_gate_indices(gs, select = 31:32, c("T Cells", "CD4 T Cells", "CD8 T Cells"))

[hrj21]

Outstanding, thank you so much! I ended up doing this to get a matrix for all nodes in the gs:
gh_pop_get_indices_mat(gs[[1]], basename(cyto_nodes(gs)))

Perhaps there's a better way of doing it but that achieved what I wanted. Thanks again for your help and for this excellent package.