Discrete time values after pseudotime

[roanvanscheppingen]

Hi,

Thank you for developing monocle.
I was wondering what could be an explanation for seemingly discrete values that come out of pseudotime analysis instead of a more smooth, continuous output.

Code used:

counts_matrix <- GetAssayData(integrated, assay = "integrated", slot = "data")  
cell_metadata <- [email protected]  
gene_metadata <- data.frame(gene_short_name = rownames(counts_matrix), row.names = rownames(counts_matrix))
cds <- new_cell_data_set(counts_matrix, cell_metadata = cell_metadata, gene_metadata = gene_metadata)



cds <- preprocess_cds(cds, num_dim = 22, norm_method = "none")
cds <- reduce_dimension(cds, reduction_method = "UMAP")
cds <- cluster_cells(cds, reduction_method = "UMAP")

cds <- learn_graph(cds, use_partition = FALSE, list(ncenter = 1000))
cds <- order_cells(cds)
#plot_cells(cds, color_cells_by = "pseudotime")

ps_tim <- pseudotime(cds)
integrated$time <- ps_tim