Entering edit mode
10 months ago
alwayshope
▴
40
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")