
Hello.
When I was using the monocle3 independently generated by the software for UMAP, I had a question. My data were of the same cell type, and after UMAP clustering, there was separation between subgroups, as shown in the figure. I would like to ask if this result is normal and whether heterogeneity can be used to explain the separation between subgroups.
My code is as follows:
cds <- preprocess_cds(cds, num_dim = 50,norm_method = c("log"), method = "PCA",use_genes = VariableFeatures(msy_DEN_H)[ 1:2000 ])
cds <- align_cds(cds, num_dim = 50, alignment_group = "orig.ident")
cds <- reduce_dimension(cds)
cds <- cluster_cells(cds)
cds <- learn_graph(cds,use_partition = F)
cds <- order_cells(cds) #The starting point selected the part with the lowest dryness based on the dryness score
May I ask if this is an explainable situation, a sample issue, or incorrect parameter selection during the analysis process?
Thank you very much.