palantir don't find values inside anndata
rdesantis90 opened this issue · comments
hi!
thank you for your work! palantir is amazing.
I am an old user and I recently started to use the new version but I encountered some issues, it seems that palantir cannot fetch the count matrix inside the anndata object, please see the error below. Can you help my fix this?
dm_res = palantir.utils.run_diffusion_maps(ad, n_components=5)
Determing nearest neighbor graph...
AttributeError Traceback (most recent call last)
in <cell line: 2>()
1 # Run diffusion maps
----> 2 dm_res = palantir.utils.run_diffusion_maps(ad, n_components=5)
/usr/local/lib/python3.10/dist-packages/palantir/utils.py in run_diffusion_maps(data_df, n_components, knn, alpha, seed)
55 if not issparse(data_df):
56 print("Determing nearest neighbor graph...")
---> 57 temp = sc.AnnData(data_df.values)
58 sc.pp.neighbors(temp, n_pcs=0, n_neighbors=knn)
59 kNN = temp.obsp['distances']
AttributeError: 'AnnData' object has no attribute 'values'
my installation is:
Requirement already satisfied: palantir in /usr/local/lib/python3.10/dist-packages (1.2)
Requirement already satisfied: numpy>=1.14.2 in /usr/local/lib/python3.10/dist-packages (from palantir) (1.24.4)
Requirement already satisfied: pandas>=0.22.0 in /usr/local/lib/python3.10/dist-packages (from palantir) (1.5.3)
Requirement already satisfied: scipy>=1.3 in /usr/local/lib/python3.10/dist-packages (from palantir) (1.10.1)
Requirement already satisfied: networkx>=2.1 in /usr/local/lib/python3.10/dist-packages (from palantir) (3.1)
Requirement already satisfied: scikit-learn in /usr/local/lib/python3.10/dist-packages (from palantir) (1.2.2)
Requirement already satisfied: joblib in /usr/local/lib/python3.10/dist-packages (from palantir) (1.2.0)
Requirement already satisfied: fcsparser>=0.1.2 in /usr/local/lib/python3.10/dist-packages (from palantir) (0.2.6)
Requirement already satisfied: PhenoGraph>=1.5.3 in /usr/local/lib/python3.10/dist-packages (from palantir) (1.5.7)
Requirement already satisfied: tables>=3.4.2 in /usr/local/lib/python3.10/dist-packages (from palantir) (3.8.0)
Requirement already satisfied: Cython in /usr/local/lib/python3.10/dist-packages (from palantir) (0.29.35)
Requirement already satisfied: cmake in /usr/local/lib/python3.10/dist-packages (from palantir) (3.25.2)
Requirement already satisfied: matplotlib>=2.2.2 in /usr/local/lib/python3.10/dist-packages (from palantir) (3.7.1)
Requirement already satisfied: seaborn>=0.8.1 in /usr/local/lib/python3.10/dist-packages (from palantir) (0.12.2)
Requirement already satisfied: tzlocal in /usr/local/lib/python3.10/dist-packages (from palantir) (5.0.1)
Requirement already satisfied: scanpy>=1.6.0 in /usr/local/lib/python3.10/dist-packages (from palantir) (1.9.3)
Requirement already satisfied: pygam in /usr/local/lib/python3.10/dist-packages (from palantir) (0.9.0)
Requirement already satisfied: contourpy>=1.0.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib>=2.2.2->palantir) (1.1.0)
Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.10/dist-packages (from matplotlib>=2.2.2->palantir) (0.11.0)
Requirement already satisfied: fonttools>=4.22.0 in /usr/local/lib/python3.10/dist-packages (from matplotlib>=2.2.2->palantir) (4.40.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib>=2.2.2->palantir) (1.4.4)
Requirement already satisfied: packaging>=20.0 in /usr/local/lib/python3.10/dist-packages (from matplotlib>=2.2.2->palantir) (23.1)
Requirement already satisfied: pillow>=6.2.0 in /usr/local/lib/python3.10/dist-packages (from matplotlib>=2.2.2->palantir) (8.4.0)
Requirement already satisfied: pyparsing>=2.3.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib>=2.2.2->palantir) (3.1.0)
Requirement already satisfied: python-dateutil>=2.7 in /usr/local/lib/python3.10/dist-packages (from matplotlib>=2.2.2->palantir) (2.8.2)
Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.10/dist-packages (from pandas>=0.22.0->palantir) (2022.7.1)
Requirement already satisfied: leidenalg>=0.8.2 in /usr/local/lib/python3.10/dist-packages (from PhenoGraph>=1.5.3->palantir) (0.10.0)
Requirement already satisfied: setuptools>=18.0.1 in /usr/local/lib/python3.10/dist-packages (from PhenoGraph>=1.5.3->palantir) (67.7.2)
Requirement already satisfied: psutil>4 in /usr/local/lib/python3.10/dist-packages (from PhenoGraph>=1.5.3->palantir) (5.9.5)
Requirement already satisfied: anndata>=0.7.4 in /usr/local/lib/python3.10/dist-packages (from scanpy>=1.6.0->palantir) (0.8.0)
Requirement already satisfied: h5py>=3 in /usr/local/lib/python3.10/dist-packages (from scanpy>=1.6.0->palantir) (3.8.0)
Requirement already satisfied: tqdm in /usr/local/lib/python3.10/dist-packages (from scanpy>=1.6.0->palantir) (4.65.0)
Requirement already satisfied: statsmodels>=0.10.0rc2 in /usr/local/lib/python3.10/dist-packages (from scanpy>=1.6.0->palantir) (0.13.5)
Requirement already satisfied: patsy in /usr/local/lib/python3.10/dist-packages (from scanpy>=1.6.0->palantir) (0.5.3)
Requirement already satisfied: natsort in /usr/local/lib/python3.10/dist-packages (from scanpy>=1.6.0->palantir) (8.3.1)
Requirement already satisfied: numba>=0.41.0 in /usr/local/lib/python3.10/dist-packages (from scanpy>=1.6.0->palantir) (0.57.1)
Requirement already satisfied: umap-learn>=0.3.10 in /usr/local/lib/python3.10/dist-packages (from scanpy>=1.6.0->palantir) (0.5.3)
Requirement already satisfied: session-info in /usr/local/lib/python3.10/dist-packages (from scanpy>=1.6.0->palantir) (1.0.0)
Requirement already satisfied: threadpoolctl>=2.0.0 in /usr/local/lib/python3.10/dist-packages (from scikit-learn->palantir) (3.1.0)
Requirement already satisfied: numexpr>=2.6.2 in /usr/local/lib/python3.10/dist-packages (from tables>=3.4.2->palantir) (2.8.4)
Requirement already satisfied: blosc2~=2.0.0 in /usr/local/lib/python3.10/dist-packages (from tables>=3.4.2->palantir) (2.0.0)
Requirement already satisfied: py-cpuinfo in /usr/local/lib/python3.10/dist-packages (from tables>=3.4.2->palantir) (9.0.0)
Requirement already satisfied: progressbar2<5.0.0,>=4.2.0 in /usr/local/lib/python3.10/dist-packages (from pygam->palantir) (4.2.0)
Requirement already satisfied: msgpack in /usr/local/lib/python3.10/dist-packages (from blosc2~=2.0.0->tables>=3.4.2->palantir) (1.0.5)
Requirement already satisfied: igraph<0.11,>=0.10.0 in /usr/local/lib/python3.10/dist-packages (from leidenalg>=0.8.2->PhenoGraph>=1.5.3->palantir) (0.10.5)
Requirement already satisfied: llvmlite<0.41,>=0.40.0dev0 in /usr/local/lib/python3.10/dist-packages (from numba>=0.41.0->scanpy>=1.6.0->palantir) (0.40.1)
Requirement already satisfied: python-utils>=3.0.0 in /usr/local/lib/python3.10/dist-packages (from progressbar2<5.0.0,>=4.2.0->pygam->palantir) (3.7.0)
Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.10/dist-packages (from python-dateutil>=2.7->matplotlib>=2.2.2->palantir) (1.16.0)
Requirement already satisfied: pynndescent>=0.5 in /usr/local/lib/python3.10/dist-packages (from umap-learn>=0.3.10->scanpy>=1.6.0->palantir) (0.5.10)
Requirement already satisfied: stdlib-list in /usr/local/lib/python3.10/dist-packages (from session-info->scanpy>=1.6.0->palantir) (0.9.0)
Requirement already satisfied: texttable>=1.6.2 in /usr/local/lib/python3.10/dist-packages (from igraph<0.11,>=0.10.0->leidenalg>=0.8.2->PhenoGraph>=1.5.3->palantir) (1.6.7)
Requirement already satisfied: typing-extensions>3.10.0.2 in /usr/local/lib/python3.10/dist-packages (from python-utils>=3.0.0->progressbar2<5.0.0,>=4.2.0->pygam->palantir) (4.6.3)
Thank you for your interest!
We have made changes to the interface that are still getting propagated to pip. In the meantime, please install directly from GitHub pip install git+https://github.com/dpeerlab/Palantir.git to grab the latest version which should fix this issue.
it worked!
Thank you very much