How do you go about repositioning this arrow so that it starts and ends in the right place?

[ltzyl]

this is my code: palantir.plot.plot_trajectories(subadata, pseudotime_interval=(.1, .9))

I found that no matter how I adjusted it I couldn't get the arrow in the correct position for the end cell. If you turn up the end in pseudotime_interval(,end), you get arrows ending beyond the umap plot, and if you turn it down, you get arrows ending in the center of the plot.

And there is also a problem that even though I set the terminal states, he will find another end point and I don't know how to adjust this.

this is my code: dm_res = palantir.utils.run_diffusion_maps(abT,pca_key='X_pca_harmony', n_components=20) ms_data = palantir.utils.determine_multiscale_space(dm_res,n_eigs=13) pr_res = palantir.core.run_palantir(ms_data, 'R3.61,R2.16,R1.47,P1.02', num_waypoints=1500,knn=40, terminal_states=terminal_states)

[katosh]

Hi @ltzyl,

Thanks for reporting this, and apologies, the plot definitely doesn’t look right. The arrows are computed and smoothed based on the positions of cells in the embedding_basis (default: "X_umap") and the branch selection that assigns cells to branches. That means there are two possible sources of error here:

1. Incorrect branch cell selection

If the wrong cells are being used per branch, the curves will look off. You can check this by plotting:

palantir.plot.plot_branch_selection(ad)

If the branch assignment looks wrong, try rerunning:

palantir.presults.select_branch_cells(ad, q=.01, eps=.01)

with adjusted q and eps tolerances (see the tutorial for guidance).

2. Over-smoothing of trajectories

If your embedding has a very different scale, the default parameters may oversmooth the curves. Based on your plot, this seems likely. You can reduce smoothing by setting the smoothness parameter to a value below 1 in plot_trajectories (see the manual).

Please let me know if the issue persists, or if you run into other questions. Good luck!