Dear experienced users,

Do you know how to make seperate plots in Monocle3 using combined control and treatment samples?

The group_cells_by = "partition" seems not works even though the partitions (cds_combined. show there are 2 levels); I use load_cellranger_data() to get the cds1 and cds2, and combine use combine_cds(list(cds1, cds2))

Thank you very much!

EDIT:

Here's the full code:

cds1 <- load_cellranger_data("~/S1")
cds2 <- load_cellranger_data("~/S2/")

cds_combined <- combine_cds(list(cds1, cds2))
cds_combined <- preprocess_cds(cds_combined, num_dim = 100)
cds_combined <- reduce_dimension(cds_combined)
cds_combined <- cluster_cells(cds_combined, num_dim = 100)
cds_combined <- learn_graph(cds_combined)
plot_cells(cds_combined, genes =c ("EGFR"), group_cells_by="partition", color_cells_by="partition")