No cells are visualized with plot_cells_3d, as in order_cells

[mauritsunkel]

From the docs: https://cole-trapnell-lab.github.io/monocle3/docs/trajectories/ I use:
cds_3d <- reduce_dimension(cds, max_components = 3)
cds_3d <- cluster_cells(cds_3d)
cds_3d <- learn_graph(cds_3d)
cds_3d <- order_cells(cds_3d, root_pr_nodes=get_earliest_principal_node(cds))
cds_3d_plot_obj <- plot_cells_3d(cds_3d, color_cells_by="partition")

However, with my own root_cells (not shown). The figure I'm obtaining is as follows:

This only shows the trajectory, but I would also like to see the cells, and their clusters (with coloring).

The order_cells function does seem to show cells, is it a bug that plot_cells_3d doesn't?

Happy to provide more info.

[liusihaha]

Have you solved it? I also encountered this problem

[mauritsunkel]

@liusihaha Have not solved it yet, and have moved on, good luck!

[t-carroll]

Take a look at my open PR, I think it's addressing a similar issue. Doesn't look like the PR been reviewed/merged yet, but you can still try my unofficial patch in the meantime and see if it fixes your problem:

devtools::install_github("t-carroll/monocle3")

Make sure to restart R and reload monocle3 before retrying!