Comments (5)
Apparently increasing the waypoints (and knn) stabilizes the results, is this expected? I'm now set to n_waypoints=adata.shape[0]//3
from palantir.
The waypoints are indeed randomly sampled and increasing the number of waypoints will indeed stabilize the results. Alternatively, setting the random seed using np.random.seed
will ensure that waypoint samples are consistent.
from palantir.
Setting the random seed ensures results are always the same, but it doesn't grant their consistency, I may be in some local minima. I'll go with more waypoints at the cost of runtime (not much, <15m for 15k cells, <1h for ~40k cells). Thanks!
from palantir.
Dear Palantir team,
Thanks for the tool!
I am facing the same problem where branch probabilities are not stable. For me branch probabilities are important and ideally should be fixed in all runs for all cells using same parameters. I set the random seed, which doesn't seem to solve it. Do you recommend to increase the waypoints in this case?
Rahul
from palantir.
Hello - you could increase the number of waypoints as a solution. Alternatively, you can save the set of waypoints from one of the runs and use it as input if you rerun Palantir. The waypoints are stored in pr_res.waypoints
and the num_waypoints
parameter can be set to a set of cells rather than the number.
from palantir.
Related Issues (20)
- installation issue HOT 5
- type KeyError with new v1.3.1: output from determine_multiscale_space HOT 6
- palantier + py3.7+ typing loading error HOT 1
- AttributeError: module 'palantir.plot' has no attribute 'plot_trajectory' HOT 2
- branch probabilities don't equal to 1 HOT 3
- how to choose “start_cell” HOT 2
- `AttributeError: 'AnnData' object has no attribute 'values'` in the tutorial notebook `Palantir_sample_notebook.ipynb` HOT 2
- Error while running plot_palantir_results HOT 3
- plot_gene_trend HOT 10
- Cannot install and run Palantir on Jupyter notebook HOT 3
- Multithreading issue with palantir.utils.run_magic_imputation() HOT 8
- Adjust x-axis for pseudotime gene expression plots HOT 3
- About the number of eigenvectors HOT 2
- ImportError: cannot import name 'config' from 'jax.config' (/home/william/mambaforge/envs/palantir/lib/python3.12/site-packages/jax/config.py) HOT 3
- No agreeing fate names found for .obsm['palantir_fate_probabilities'] and .obsm['branch_masks']. HOT 2
- KeyError: 'branch_masks not found in ad.obsm' HOT 5
- ZeroDivisionError: integer division or modulo by zero HOT 2
- Problem with importing the library HOT 5
- Gene expression trends HOT 11
- Diffusion Component Loadings HOT 3
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