I am working on some human tissue spatial data. Everything has gone well except when I sub clustered certain cell populations. For instance, I’m sub clustering a cell population and I am seeing 100+ clusters develop for my control at lower resolutions. Has anyone seen this before?
I subset the data on phenotype, then cell type, ran tl.pca & tl.umap, and ran tl.leiden() at resolutions from 0.1 to 1.4. Even at the lowest resolution I’m seeing an extremely high amount of clusters.
It could be the data, but please let me know if there is another parameter or sub clustering step I haven’t used that would improve the result.
Otherwise I’ll have to use something akin to kmeans instead of Leiden