fra-pcmgf
commented
2 months ago Hi @Fufu-Hu,
I am not sure about what it could be.
1) Can you check if anything is still running (e.g. using top or the Task Manager)?
2) Can you let me know the size of the objects (e.g. dim(cg_output[["graph.dist"]]), dim(cg_output[["gene.expression"]]))? I don't think it should be that slow is the size is 481x50, but it may be if you are using the full matrix.
3) Do you get any error or notifications when you start the cal_ot_mat_from_numpy function?
Hi!
I installed module gene_trajectory with pip in a conda env.I can comput the gene-gene distances with the seurat data in GeneTrajectory tutorial and the progress _bar are showed in screen. But when I comput my own seurat data(36077 features across 482 samples), there's nothing in screen. The number of gene used to compute gene-gene distances is 481 and meta-cells is 50. I run "gene.dist.mat <- cal_ot_mat_from_numpy(ot_cost = cg_output[["graph.dist"]], gene_expr = cg_output[["gene.expression"]], num_iter_max = 50000, show_progress_bar = TRUE)" in R for at least 8 hours with no output even a progress_bar. Is there something I missed?
Hope receive a reply~