The branch point is not labelled as expected

Question

[Lin]

Hello, I'm using monocle2 package to make cell trajectory analyses.

I run the following commands to get the cell trajectory plots.

plot_cell_trajectory(cds, color_by = "Pseudotime", show_branch_points=TRUE, cell_size=1.5, theta=180)
plot_cell_trajectory(cds, color_by = "State", show_branch_points=TRUE, cell_size=1.5, theta=180) + guides(color=guide_legend(override.aes=list(size=4)))

I got the following plots

Note that the branch point 1 appears in the middle of state 1, and it is not at the place where state 1 diverges to state 2 and state 3, as below:

Do you know why? Is there anything wrong with the monocle2 package? Thank you!

Answer 1

[wschen97]

This issue might be caused by the parameter theta=180, as it appears to rotate the graph but not the branch point labels.