Error with tsne function after following the Regress Out tutorial
morgeur opened this issue · comments
Hello,
I followed the Regress Out tutorial as I would like to give a try to the cell cycle regression on my own dataset.
After using the regress_out
function, I used the X_pca_regressed
for downstream analysis:
pg.neighbors(data, rep="pca_regressed")
pg.louvain(data, rep="pca_regressed")`
But when calling the tsne
function, I encounter the following error:
pg.tsne(data, rep="pca_regressed")
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python3.8/site-packages/pegasusio/decorators.py", line 12, in wrapper_timer
result = func(*args, **kwargs)
File "/usr/local/lib/python3.8/site-packages/pegasus/tools/visualization.py", line 296, in tsne
data.obsm["X_" + out_basis] = calc_tsne(
File "/usr/local/lib/python3.8/site-packages/pegasus/tools/visualization.py", line 55, in calc_tsne
return FItSNE(
File "/usr/local/lib/python3.8/site-packages/fitsne/cywrap.py", line 120, in FItSNE
_TSNErun(X, N, D, Y, no_dims, perplexity, theta, rand_seed,
File "fitsne/cppwrap.pyx", line 16, in fitsne.cppwrap._TSNErun
File "stringsource", line 658, in View.MemoryView.memoryview_cwrapper
File "stringsource", line 349, in View.MemoryView.memoryview.__cinit__
ValueError: ndarray is not C-contiguous
I do not encountered this error when running: pg.tsne(data, rep="pca")
or pg.umap(data, rep="pca_regressed")
Am I doing anything wrong?
Many thanks for your help and providing this great tool!
Hi @morgeur ,
Thanks for liking our tool! Actually, we're aware of this bug and have fixed it in our master branch.
If you check out the master branch and install it locally, you will get rid of this problem. Alternatively, we plan to release pegasus v1.3.0 today. You can wait until v1.3.0 is released and install this version via pip.
Best,
Bo