使用例

load

suppressPackageStartupMessages(library(Seurat))
suppressPackageStartupMessages(library(SeuratWrappers))
suppressPackageStartupMessages(library(monocle3))

so  <- readRDS("*.rds")
cds <- as.cell_data_set(so)
cds <- estimate_size_factors(cds)
cds <- cluster_cells(cds, reduction_method = "UMAP") 
cds <- learn_graph(cds, use_partition = T)

plot_cells(cds, 
  color_cells_by = "partition", 
  label_principal_point = T,
  graph_label_size = 6, 
  cell_size = .5)

plot_cells(cds, 
  color_cells_by = "partition", 
  graph_label_size = 6, 
  cell_size = 1)

cds <- order_cells(cds, root_pr_nodes = c("Y_*"))

plot_cells(cds,
  color_cells_by = "pseudotime",
  show_trajectory_graph = T,
  graph_label_size  = 6,
  cell_size = 1
)

genes <- c("Col1a1")
sub_cds <- cds[row.names(cds) %in% genes,]

plot_genes_in_pseudotime(sub_cds, label_by_short_name = F,
  color_cells_by="seurat_clusters", min_expr = 0.1)

参考文献