peterzzq / cellpath Goto Github PK

Hello,

When running this code:

num_trajs = 4
flavor = "k-means"
num_metacells = 300

adata = anndata.read_h5ad("/media/ernohanninen/TOSHIBA/cycletree.h5ad")

cellpath_obj = cp.CellPath(adata = adata, preprocess = True)
cellpath_obj.all_in_one(flavor = flavor, num_metacells = num_metacells, n_neighs = 13, num_trajs = num_trajs, prop_insert = 0.0, seed = 0, mode = "exact")

I get the following error:

Traceback (most recent call last):
File "run_CellPath.py", line 19, in
cellpath_obj.all_in_one(flavor = flavor, num_metacells = num_metacells, n_neighs = 13, num_trajs = num_trajs, prop_insert = 0.0, seed = 0, mode = "exact")
File "/home/ernohanninen/miniconda3/envs/TRAenv/lib/python3.8/site-packages/cellpath/cellpath.py", line 349, in all_in_one
self.meta_cell_construction(flavor = flavor, n_clusters = num_metacells, resolution = resolution, **kwargs)
File "/home/ernohanninen/miniconda3/envs/TRAenv/lib/python3.8/site-packages/cellpath/cellpath.py", line 121, in meta_cell_construction
self.X_clust, self.velo_clust = clust.meta_cells(self.adata, kernel = _kwargs["kernel"],
File "/home/ernohanninen/miniconda3/envs/TRAenv/lib/python3.8/site-packages/cellpath/clustering.py", line 136, in meta_cells
k = KernelRidge(alpha, kernel, gamma)
TypeError: init() takes from 1 to 2 positional arguments but 4 were given

Thanks for the package ! It seems the dropbox link to access real datasets says the file was deleted https://www.dropbox.com/sh/nix4wnoiwda5id5/AACTxvGTQ82UzwMJs2IWSriKa?dl=0

The dependencies listed include "sklearn >= 0.22.1" so I included sklearn in an attempted "conda create" to set up a virtual environment. There's no "sklearn" conda package, but there is "scikit-learn" ... which seems to work with the later "pip install" step.

Also, after cloning the repo, I needed to "cd CellPaths/" before running the "pip install ." command.