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aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
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Trajectory differentation arrows change each time I replot #324

Open bhhlee opened 3 months ago

bhhlee commented 3 months ago

Dear SCENIC+ team.

Thanks so much again for building such a wonderful package.

I've been noticing while inferring trajectories that the arrow direction/placement will keep on changing each time I run the same cell. 

from matplotlib.pyplot import rc_context
tf = 'FOXO1'
with rc_context({'figure.figsize': (14,10)}):
    plot_map(adata_sub, paths_cascade, tf, color_var='GEX_celltype', n_grid_cols = 25, n_grid_rows = 25, offset_frac = 0.005,
             tf_traj_thr=0.7, tf_expr_thr=0.2, scale=50, figsize=(10,8), gam_smooth=True, palette=palette_dict, 
             save=outDir+'arrow_plots/' + 'arrow_plots_ss_' + tf + '.png')

image image image

I am re-running the exact same cell and yet the differentation arrows change each time. I also specify a random seed in the beginning of th notebook, but is there some other random seeding going on that I am not aware of?

After re-running a few times if I re-run with a different TF or even the same TF , the arrows go completely off the umap figure. If I restart the notebook, the arrows do reset to the original figure. I'm wondering if this is a matploblib issue?

Thanks again!

Best, Brian