monocle 3-- Could not get node in small cluster

Question

[synat.keam]

Dear All,

I am using monocle3 to infer Trajectory analysis. However, in a small cluster, I most of the time did not get the node. Therefore, I am assuming the Trajectory analysis may not include it. How to solve it and get node in a small cluster (kindly review attach image). Following is my code!

cds <- as.cell_data_set(seurat_obj_cd8) # SeuratWrappers
DefaultAssay(seurat_obj_cd8)

# Cluster cells
cds <- cluster_cells(cds, reduction_method = "UMAP",  resolution = 1e-5)  

cds <- learn_graph(cds, use_partition = FALSE)

# Order cells
cds <- order_cells(cds)

#plot_cells in pseudotime
plot_cells(cds , 
            color_cells_by = 'pseudotime', 
           label_branch_points = FALSE, 
           label_leaves = FALSE, 
           graph_label_size = 4) + 
  theme_classic() + 
  NoAxes() + 
  theme(legend.position = "right")

Thanks,

Answer 1

[Prakki Rama]

You need to reduce the branch len, which will connect other clusters as well:

learn_graph(cds, use_partition = FALSE, learn_graph_control = list(minimal_branch_len=1))