st.spatial.trajectory.pseudotimespace_global()
Closed this issue · 9 comments
Hello, I have a confusion. I don't know why the error occurred.
st.spatial.trajectory.pseudotimespace_global(data,use_label="louvain",list_clusters=["1","2","3"])
Start to construct the trajectory: 3 -> 2 -> 1
Traceback (most recent call last):
File "", line 1, in
File "C:\Users\Administrator\miniconda3\envs\stlearn2\lib\site-packages\stlearn\spatials\trajectory\pseudotimespace.py", line 55, in pseudotimespace_global
global_level(
File "C:\Users\Administrator\miniconda3\envs\stlearn2\lib\site-packages\stlearn\spatials\trajectory\global_level.py", line 165, in global_level
H_sub = nx.algorithms.tree.minimum_spanning_arborescence(H_sub)
File "C:\Users\Administrator\miniconda3\envs\stlearn2\lib\site-packages\networkx\utils\backends.py", line 412, in call
return self.orig_func(*args, **kwargs)
File "C:\Users\Administrator\miniconda3\envs\stlearn2\lib\site-packages\networkx\algorithms\tree\branchings.py", line 1310, in minimum_spanning_arborescence
B = minimal_branching(
File "C:\Users\Administrator\miniconda3\envs\stlearn2\lib\site-packages\networkx\utils\backends.py", line 412, in call
return self.orig_func(*args, **kwargs)
File "C:\Users\Administrator\miniconda3\envs\stlearn2\lib\site-packages\networkx\algorithms\tree\branchings.py", line 1237, in minimal_branching
if w > max_weight:
TypeError: '<' not supported between instances of 'float' and 'NoneType'
print(data.obs.louvain.cat.categories)
Index(['0', '1', '2', '3', '4', '5', '6'], dtype='object')
data.uns["louvain_index_dict"]
{'0': 0, '1': 1, '2': 2, '3': 3, '4': 4, '5': 5, '6': 6}
Can you check if there is any issue with the adata.obs['sub_cluster_labels']. And also check the global graph here:
from stlearn.utils import _read_graph
G = _read_graph(adata, "global_graph")
print(G.nodes)
print(G.edges)
If you test with 2 clusters, will it run normally?
Hello, thank you for your response. I tried the methods you provided, but I'm still encountering the following error.
data.obs['sub_cluster_labels']
AAACCTAAGCAGCCGG-1 0
AAACGAGACGGTTGAT-1 1
AAACTGCTGGCTCCAA-1 1
AAAGGCTCTCGCGCCG-1 2
AAAGGGATGTAGCAAG-1 3
..
TTGTGGCCCTGACAGT-1 9
TTGTGTATGCCACCAA-1 42
TTGTGTTTCCCGAAAG-1 11
TTGTTCAGTGTGCTAC-1 9
TTGTTGTGTGTCAAGA-1 9
Name: sub_cluster_labels, Length: 821, dtype: category
Categories (43, object): ['0', '1', '2', '3', ..., '39', '40', '41', '42']
from stlearn.utils import _read_graph
G = _read_graph(data, "global_graph")
print(G.nodes)
[0, 1, 2, 3, 4, 5, 21, 11, 9, 8, 15, 7]
print(G.edges)
[(0, 4), (0, 5), (0, 21), (0, 11), (0, 9), (0, 8), (1, 4), (1, 5), (1, 21), (1, 11), (1, 9), (1, 8), (2, 4), (2, 5), (2, 21), (2, 11), (2, 9), (2, 8), (3, 4), (3, 5), (3, 21), (3, 11), (3, 9), (3, 8), (4, 5), (4, 21), (4, 11), (4, 9), (4, 8), (4, 15), (4, 7), (5, 21), (5, 11), (5, 9), (5, 15), (5, 7), (21, 9), (21, 8), (21, 15), (21, 7), (11, 9), (11, 8), (11, 15), (11, 7), (9, 8), (9, 15), (9, 7), (8, 15), (8, 7)]
st.spatial.trajectory.pseudotimespace_global(data,use_label="louvain",list_clusters=["5","3"])
Start to construct the trajectory: 5 -> 3
Traceback (most recent call last):
File "", line 1, in
File "C:\Users\Administrator\miniconda3\envs\stlearn2\lib\site-packages\stlearn\spatials\trajectory\pseudotimespace.py", line 55, in pseudotimespace_global
global_level(
File "C:\Users\Administrator\miniconda3\envs\stlearn2\lib\site-packages\stlearn\spatials\trajectory\global_level.py", line 165, in global_level
H_sub = nx.algorithms.tree.minimum_spanning_arborescence(H_sub)
File "C:\Users\Administrator\miniconda3\envs\stlearn2\lib\site-packages\networkx\utils\backends.py", line 412, in call
return self.orig_func(*args, **kwargs)
File "C:\Users\Administrator\miniconda3\envs\stlearn2\lib\site-packages\networkx\algorithms\tree\branchings.py", line 1310, in minimum_spanning_arborescence
B = minimal_branching(
File "C:\Users\Administrator\miniconda3\envs\stlearn2\lib\site-packages\networkx\utils\backends.py", line 412, in call
return self.orig_func(*args, **kwargs)
File "C:\Users\Administrator\miniconda3\envs\stlearn2\lib\site-packages\networkx\algorithms\tree\branchings.py", line 1237, in minimal_branching
if w > max_weight:
TypeError: '<' not supported between instances of 'float' and 'NoneType'
print(data.obs.louvain.cat.categories)
Index(['0', '1', '2', '3', '4', '5'], dtype='object')
It seems don't have any issue.
Did you recently install the package? I need to test it again due to the new version of anndata and scanpy as the dependencies of stlearn. You can downgrade these packages' versions to see if anything changes. Also I will try to test it soon
Ok, I have recently started using stlearn , and below are the versions of different packages in my environment. I will also try downgrading anndata and scanpy to resolve the issue, and I look forward to your response.
packages in environment at C:\Users\Administrator\miniconda3\envs\stlearn2:
Name Version Build Channel
_tflow_select 2.3.0 mkl
absl-py 2.0.0 pyhd8ed1ab_0 conda-forge
aiohttp 3.8.5 py39h2bbff1b_0
aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge
anndata 0.10.2 pyhd8ed1ab_0 conda-forge
aom 3.5.0 h63175ca_0 conda-forge
array-api-compat 1.4 pyhd8ed1ab_0 conda-forge
asttokens 2.0.5 pyhd3eb1b0_0
astunparse 1.6.3 pyhd8ed1ab_0 conda-forge
async-timeout 4.0.3 pyhd8ed1ab_0 conda-forge
attrs 23.1.0 pyh71513ae_1 conda-forge
backcall 0.2.0 pyhd3eb1b0_0
blinker 1.6.3 pyhd8ed1ab_0 conda-forge
blosc 1.21.5 hdccc3a2_0 conda-forge
bokeh 3.3.0 pyhd8ed1ab_0 conda-forge
brotli 1.0.9 ha925a31_2
brotli-python 1.0.9 py39h99910a6_9 conda-forge
bzip2 1.0.8 h8ffe710_4 conda-forge
ca-certificates 2023.08.22 haa95532_0
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 5.3.1 pyhd8ed1ab_0 conda-forge
certifi 2023.7.22 py39haa95532_0
cffi 1.16.0 py39ha55989b_0 conda-forge
cfitsio 3.470 h2bbff1b_7
charls 2.2.0 h6c2663c_0
charset-normalizer 3.3.1 pyhd8ed1ab_0 conda-forge
click 8.1.7 win_pyh7428d3b_0 conda-forge
cloudpickle 3.0.0 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
contourpy 1.1.1 py39h1f6ef14_1 conda-forge
cryptography 38.0.4 py39h58e9bdb_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
cytoolz 0.12.2 py39ha55989b_1 conda-forge
dask-core 2023.10.0 pyhd8ed1ab_0 conda-forge
dav1d 1.2.1 hcfcfb64_0 conda-forge
decorator 5.1.1 pyhd3eb1b0_0
exceptiongroup 1.1.3 pyhd8ed1ab_0 conda-forge
executing 0.8.3 pyhd3eb1b0_0
flatbuffers 23.5.26 h63175ca_1 conda-forge
fonttools 4.43.1 py39ha55989b_0 conda-forge
freetype 2.12.1 hdaf720e_2 conda-forge
frozenlist 1.4.0 py39ha55989b_1 conda-forge
fsspec 2023.10.0 pyhca7485f_0 conda-forge
gast 0.4.0 pyh9f0ad1d_0 conda-forge
giflib 5.2.1 h64bf75a_3 conda-forge
glpk 5.0 h8ffe710_0 conda-forge
google-auth 2.23.3 pyhca7485f_0 conda-forge
google-auth-oauthlib 0.4.1 py_2 conda-forge
google-pasta 0.2.0 pyh8c360ce_0 conda-forge
grpcio 1.42.0 py39hc60d5dd_0
h5py 3.9.0 nompi_py39h9c8e182_100 conda-forge
hdf5 1.14.0 nompi_h97a5375_103 conda-forge
icu 58.2 ha925a31_3
idna 3.4 pyhd8ed1ab_0 conda-forge
igraph 0.10.7 h0e101eb_1 conda-forge
imagecodecs 2023.1.23 py39h6c6a46e_0
imageio 2.31.5 pyh8c1a49c_0 conda-forge
importlib-metadata 6.8.0 pyha770c72_0 conda-forge
importlib-resources 6.1.0 pypi_0 pypi
importlib_metadata 6.8.0 hd8ed1ab_0 conda-forge
intel-openmp 2023.2.0 h57928b3_50496 conda-forge
jedi 0.18.1 py39haa95532_1
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
joblib 1.3.2 pyhd8ed1ab_0 conda-forge
jpeg 9e hcfcfb64_3 conda-forge
keras 2.10.0 py39haa95532_0
keras-preprocessing 1.1.2 pyhd8ed1ab_0 conda-forge
kiwisolver 1.4.5 py39h1f6ef14_1 conda-forge
krb5 1.20.1 h6609f42_0 conda-forge
lazy_loader 0.3 pyhd8ed1ab_0 conda-forge
lcms2 2.15 ha5c8aab_0 conda-forge
leidenalg 0.10.1 py39haa4e2bd_0 conda-forge
lerc 3.0 hd77b12b_0
libaec 1.1.2 h63175ca_1 conda-forge
libavif 0.11.1 ha7b97ba_2 conda-forge
libblas 3.9.0 19_win64_mkl conda-forge
libbrotlicommon 1.0.9 hcfcfb64_9 conda-forge
libbrotlidec 1.0.9 hcfcfb64_9 conda-forge
libbrotlienc 1.0.9 hcfcfb64_9 conda-forge
libcblas 3.9.0 19_win64_mkl conda-forge
libcurl 7.88.1 h68f0423_1 conda-forge
libdeflate 1.17 h2bbff1b_1
libhwloc 2.9.3 default_haede6df_1009 conda-forge
libiconv 1.17 h8ffe710_0 conda-forge
liblapack 3.9.0 19_win64_mkl conda-forge
libleidenalg 0.11.1 h91493d7_0 conda-forge
libpng 1.6.39 h19919ed_0 conda-forge
libprotobuf 3.20.3 h12be248_0 conda-forge
libssh2 1.10.0 hcd4344a_2
libtiff 4.5.1 hd77b12b_0
libwebp 1.3.2 hcfcfb64_1 conda-forge
libwebp-base 1.3.2 hcfcfb64_0 conda-forge
libxml2 2.11.5 hc3477c8_1 conda-forge
libzlib 1.2.13 hcfcfb64_5 conda-forge
libzopfli 1.0.3 h0e60522_0 conda-forge
llvmlite 0.40.1 py39hd28a505_0 conda-forge
locket 1.0.0 pyhd8ed1ab_0 conda-forge
louvain 0.8.1 py39haa4e2bd_0 conda-forge
lz4-c 1.9.4 hcfcfb64_0 conda-forge
m2w64-gcc-libgfortran 5.3.0 6 conda-forge
m2w64-gcc-libs 5.3.0 7 conda-forge
m2w64-gcc-libs-core 5.3.0 7 conda-forge
m2w64-gmp 6.1.0 2 conda-forge
m2w64-libwinpthread-git 5.0.0.4634.697f757 2 conda-forge
markdown 3.5 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.3 py39ha55989b_1 conda-forge
matplotlib 3.5.3 pypi_0 pypi
matplotlib-inline 0.1.6 py39haa95532_0
mkl 2023.2.0 h6a75c08_50496 conda-forge
mpir 3.0.0 he025d50_1002 conda-forge
msys2-conda-epoch 20160418 1 conda-forge
multidict 6.0.4 py39ha55989b_1 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
natsort 8.4.0 pyhd8ed1ab_0 conda-forge
networkx 3.2 pyhd8ed1ab_0 conda-forge
numba 0.57.1 py39hadaa1c4_0 conda-forge
numpy 1.21.6 py39h6331f09_0 conda-forge
oauthlib 3.2.2 pyhd8ed1ab_0 conda-forge
openjpeg 2.5.0 ha2aaf27_2 conda-forge
openssl 1.1.1w h2bbff1b_0
opt_einsum 3.3.0 pyhc1e730c_2 conda-forge
packaging 23.2 pyhd8ed1ab_0 conda-forge
pandas 2.0.3 py39h1679cfb_1 conda-forge
parso 0.8.3 pyhd3eb1b0_0
partd 1.4.1 pyhd8ed1ab_0 conda-forge
patsy 0.5.3 pyhd8ed1ab_0 conda-forge
pickleshare 0.7.5 pyhd3eb1b0_1003
pillow 10.0.1 py39h045eedc_0
pip 23.3 py39haa95532_0
prompt-toolkit 3.0.36 py39haa95532_0
protobuf 3.20.3 py39hcbf5309_1 conda-forge
pthreads-win32 2.9.1 hfa6e2cd_3 conda-forge
pure_eval 0.2.2 pyhd3eb1b0_0
pyasn1 0.5.0 pyhd8ed1ab_0 conda-forge
pyasn1-modules 0.3.0 pyhd8ed1ab_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pygments 2.15.1 py39haa95532_1
pyjwt 2.8.0 pyhd8ed1ab_0 conda-forge
pynndescent 0.5.10 pyh1a96a4e_0 conda-forge
pyopenssl 23.2.0 pyhd8ed1ab_1 conda-forge
pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 pyh0701188_6 conda-forge
python 3.9.18 h6244533_0
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-flatbuffers 23.5.26 pyhd8ed1ab_0 conda-forge
python-igraph 0.11.2 py39he170af6_0 conda-forge
python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge
python_abi 3.9 2_cp39 conda-forge
pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge
pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge
pywavelets 1.4.1 py39hc266a54_0 conda-forge
pyyaml 6.0.1 py39ha55989b_1 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
requests-oauthlib 1.3.1 pyhd8ed1ab_0 conda-forge
rsa 4.9 pyhd8ed1ab_0 conda-forge
scanpy 1.9.5 pyhd8ed1ab_0 conda-forge
scikit-image 0.20.0 py39h3513d60_0
scikit-learn 1.2.2 py39hfa9d973_2 conda-forge
scipy 1.8.1 py39hfbf2dce_3 conda-forge
seaborn 0.13.0 hd8ed1ab_0 conda-forge
seaborn-base 0.13.0 pyhd8ed1ab_0 conda-forge
session-info 1.0.0 pyhd8ed1ab_0 conda-forge
setuptools 68.0.0 py39haa95532_0
six 1.16.0 pyh6c4a22f_0 conda-forge
snappy 1.1.10 hfb803bf_0 conda-forge
sqlite 3.41.2 h2bbff1b_0
stack_data 0.2.0 pyhd3eb1b0_0
statsmodels 0.14.0 py39hbaa61f9_1 conda-forge
stdlib-list 0.8.0 pyhd8ed1ab_0 conda-forge
stlearn 0.4.12 pyhd8ed1ab_0 conda-forge
tbb 2021.10.0 h91493d7_2 conda-forge
tensorboard 2.10.0 py39haa95532_0
tensorboard-data-server 0.6.1 py39haa95532_0
tensorboard-plugin-wit 1.8.1 pyhd8ed1ab_0 conda-forge
tensorflow 2.10.0 mkl_py39ha510bab_0
tensorflow-base 2.10.0 mkl_py39h6a7f48e_0
tensorflow-estimator 2.10.0 py39haa95532_0
termcolor 2.3.0 pyhd8ed1ab_0 conda-forge
texttable 1.7.0 pyhd8ed1ab_0 conda-forge
threadpoolctl 3.2.0 pyha21a80b_0 conda-forge
tifffile 2023.4.12 pyhd8ed1ab_0 conda-forge
tk 8.6.13 hcfcfb64_0 conda-forge
toolz 0.12.0 pyhd8ed1ab_0 conda-forge
tornado 6.3.3 py39ha55989b_1 conda-forge
tqdm 4.66.1 pyhd8ed1ab_0 conda-forge
traitlets 5.7.1 py39haa95532_0
typing-extensions 4.8.0 hd8ed1ab_0 conda-forge
typing_extensions 4.8.0 pyha770c72_0 conda-forge
tzdata 2023c h04d1e81_0
ucrt 10.0.22621.0 h57928b3_0 conda-forge
umap-learn 0.5.4 py39hcbf5309_0 conda-forge
unicodedata2 15.1.0 py39ha55989b_0 conda-forge
urllib3 2.0.7 pyhd8ed1ab_0 conda-forge
vc 14.2 h21ff451_1
vc14_runtime 14.36.32532 hdcecf7f_17 conda-forge
vs2015_runtime 14.36.32532 h05e6639_17 conda-forge
wcwidth 0.2.5 pyhd3eb1b0_0
werkzeug 3.0.0 pyhd8ed1ab_0 conda-forge
wheel 0.41.2 py39haa95532_0
win_inet_pton 1.1.0 pyhd8ed1ab_6 conda-forge
wrapt 1.15.0 py39ha55989b_1 conda-forge
xyzservices 2023.10.0 pyhd8ed1ab_0 conda-forge
xz 5.4.2 h8cc25b3_0
yaml 0.2.5 h8ffe710_2 conda-forge
yarl 1.9.2 py39ha55989b_1 conda-forge
zfp 1.0.0 h63175ca_4 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 hcfcfb64_5 conda-forge
zstd 1.5.5 h12be248_0 conda-forge
Hi, I also have the same error when running this step, may I ask if you have solved it
This is the python 3.10 issue with the type. I will try to solve it soon. But one quick solution now is using python3.8
I just updated the master branch of the repo. Please uninstall the old version and install with the master branch. I will try to publish a new version soon on the next few days
Many thanks for your replying.
I just updated the master branch of the repo. Please uninstall the old version and install with the master branch. I will try to publish a new version soon on the next few days
Thank you for your positive reply and look forward to your update.