Using Flexible Gates in Figure

In this example analysis we have a fairly extensive gating tree (clean up gates not shown), after which, we performed Subsampling, Dimension Reduction (UMAP) and Clustering (FlowSOM). We then gated the clusters and made a Figure to view our results.

We have opened the most downstream Figure task in our workflow, importantly, note the upstream gating tasks for both the manual phenotype and the cluster gating. First I will describe what we are looking at, then I will describe how you create plots with Flexible Gates.

In (1) you can see our UMAP dimension reduction analysis with the FlowSOM clusters overlaid. To identify clusters that express expected phenotypic markers, we have created Special X Axis Plots (2). Cluster fsom50-05 expresses markers consistent with a naive CD4+ T cell phenotype and cluster fsom50-50 expresses markers consistent with a central memory CD8+ T cell phenotype. To confirm the co-expression of identifying markers, we created the plots in (3). We are viewing the aforementioned clusters, with the markers on the X and Y axis that were used for manual phenotyping. We are able to view the same gates used for the manual phenotyping with the use of flexible gating and can show that 99.9% of fsom50-05 are in the naive CD4+ T cell gate and 71% of fsom50-50 are in the central memory CD8+ T cell gate.

To make Flexible Gates, create your plot and select it → click Settings → set your X and Y axis. The XY axis need to match the gates you want to show. Scroll down to Show Gates on Plot → click Any → select gates in Show Specific Gates.