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atarashansky / SAMap

SAMap: Mapping single-cell RNA sequencing datasets from evolutionarily distant organisms.
MIT License
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sankey and chord plot error #133

Open dsb66 opened 11 months ago

dsb66 commented 11 months ago

I am trying to make a sankey plot and a chord plot using the commands shown in the SAMap tutorial. Both commands fail with the following error message:

WARNING:param.notebook_extension: Holoviews bokeh extension could not be imported, it raised the following exception: ModuleNotFoundError('No module named 'bokeh.models.arrow_heads'')

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
File /data/opt/bin/miniconda/envs/SAMap/lib/python3.9/site-packages/samap/analysis.py:513, in sankey_plot(M, species_order, align_thr, **params)
    512 import holoviews as hv
--> 513 hv.extension('bokeh',logo=False)
    514 hv.output(size=100)       

File /data/opt/bin/miniconda/envs/SAMap/lib/python3.9/site-packages/pyviz_comms/__init__.py:64, in extension.__new__(cls, *args, **kwargs)
     63     pass
---> 64 return param.ParameterizedFunction.__new__(cls, *args, **kwargs)

File /data/opt/bin/miniconda/envs/SAMap/lib/python3.9/site-packages/param/parameterized.py:3658, in ParameterizedFunction.__new__(class_, *args, **params)
   3657 inst.param._set_name(class_.__name__)
-> 3658 return inst.__call__(*args,**params)

File /data/opt/bin/miniconda/envs/SAMap/lib/python3.9/site-packages/holoviews/ipython/__init__.py:116, in notebook_extension.__call__(self, *args, **params)
    115 comms = params.pop('comms', None)
--> 116 super().__call__(*args, **params)
    117 # Abort if IPython not found

File /data/opt/bin/miniconda/envs/SAMap/lib/python3.9/site-packages/holoviews/util/__init__.py:700, in extension.__call__(self, *args, **params)
    699 if selected_backend is None:
--> 700     raise ImportError('None of the backends could be imported')
    701 Store.set_current_backend(selected_backend)

ImportError: None of the backends could be imported

During handling of the above exception, another exception occurred:

ImportError                               Traceback (most recent call last)
Cell In[26], line 1
----> 1 sankey_plot(MappingTable, align_thr=0.05)

File /data/opt/bin/miniconda/envs/SAMap/lib/python3.9/site-packages/samap/analysis.py:516, in sankey_plot(M, species_order, align_thr, **params)
    514     hv.output(size=100)        
    515 except:
--> 516     raise ImportError('Please install holoviews-samap with `!pip install holoviews-samap`.')
    518 def f(plot,element):
    519     plot.handles['plot'].sizing_mode='scale_width'   

ImportError: Please install holoviews-samap with `!pip install holoviews-samap`.

However, holoviews-samap is already installed - see the output of conda list below. Any suggestions? Thank you.

Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
anndata                   0.10.3                   pypi_0    pypi
anyio                     4.0.0              pyhd8ed1ab_0    conda-forge
argon2-cffi               23.1.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0           py39hd1e30aa_4    conda-forge
arpack                    3.8.0           nompi_h0baa96a_101    conda-forge
array-api-compat          1.4                      pypi_0    pypi
arrow                     1.3.0              pyhd8ed1ab_0    conda-forge
asttokens                 2.4.1              pyhd8ed1ab_0    conda-forge
async-lru                 2.0.4              pyhd8ed1ab_0    conda-forge
attrs                     23.1.0             pyh71513ae_1    conda-forge
babel                     2.13.1             pyhd8ed1ab_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.5              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.2             pyha770c72_0    conda-forge
bleach                    6.1.0              pyhd8ed1ab_0    conda-forge
bokeh                     3.2.2                    pypi_0    pypi
brotli-python             1.1.0            py39h3d6467e_1    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.21.0               hd590300_0    conda-forge
ca-certificates           2023.7.22            hbcca054_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
certifi                   2023.7.22                pypi_0    pypi
cffi                      1.16.0           py39h7a31438_0    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
colorcet                  3.0.1                    pypi_0    pypi
colorlover                0.3.0                      py_0    conda-forge
comm                      0.1.4              pyhd8ed1ab_0    conda-forge
contourpy                 1.2.0                    pypi_0    pypi
cycler                    0.12.1                   pypi_0    pypi
debugpy                   1.8.0            py39h3d6467e_1    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
dill                      0.3.7                    pypi_0    pypi
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
exceptiongroup            1.1.3              pyhd8ed1ab_0    conda-forge
executing                 2.0.1              pyhd8ed1ab_0    conda-forge
fast-histogram            0.12                     pypi_0    pypi
fonttools                 4.44.0                   pypi_0    pypi
fqdn                      1.5.1              pyhd8ed1ab_0    conda-forge
glpk                      5.0                  h445213a_0    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
h5py                      3.8.0           nompi_py39h89bf01e_101    conda-forge
harmonypy                 0.0.9                    pypi_0    pypi
hdf5                      1.14.0          nompi_hb72d44e_103    conda-forge
hnswlib                   0.7.0                    pypi_0    pypi
holoviews-samap           1.0.1                    pypi_0    pypi
icu                       73.2                 h59595ed_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
igraph                    0.10.8                   pypi_0    pypi
importlib-metadata        6.8.0              pyha770c72_0    conda-forge
importlib_metadata        6.8.0                hd8ed1ab_0    conda-forge
importlib_resources       6.1.0              pyhd8ed1ab_0    conda-forge
ipyevents                 2.0.2              pyhd8ed1ab_0    conda-forge
ipykernel                 6.26.0             pyhf8b6a83_0    conda-forge
ipython                   8.17.2             pyh41d4057_0    conda-forge
ipywidgets                8.1.1              pyhd8ed1ab_0    conda-forge
isoduration               20.11.0            pyhd8ed1ab_0    conda-forge
jedi                      0.19.1             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
joblib                    1.3.2                    pypi_0    pypi
json5                     0.9.14             pyhd8ed1ab_0    conda-forge
jsonpointer               2.4              py39hf3d152e_3    conda-forge
jsonschema                4.19.2             pyhd8ed1ab_0    conda-forge
jsonschema-specifications 2023.7.1           pyhd8ed1ab_0    conda-forge
jsonschema-with-format-nongpl 4.19.2             pyhd8ed1ab_0    conda-forge
jupyter-lsp               2.2.0              pyhd8ed1ab_0    conda-forge
jupyter_client            8.5.0              pyhd8ed1ab_0    conda-forge
jupyter_core              5.5.0            py39hf3d152e_0    conda-forge
jupyter_events            0.8.0              pyhd8ed1ab_0    conda-forge
jupyter_server            2.9.1              pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.4.4              pyhd8ed1ab_1    conda-forge
jupyterlab                4.0.8              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_server         2.25.0             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.9              pyhd8ed1ab_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.5                    pypi_0    pypi
krb5                      1.21.2               h659d440_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
leidenalg                 0.10.1           py39h3d6467e_1    conda-forge
libaec                    1.1.2                h59595ed_1    conda-forge
libblas                   3.9.0           19_linux64_openblas    conda-forge
libcblas                  3.9.0           19_linux64_openblas    conda-forge
libcurl                   8.4.0                hca28451_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_2    conda-forge
libgfortran-ng            13.2.0               h69a702a_2    conda-forge
libgfortran5              13.2.0               ha4646dd_2    conda-forge
libgomp                   13.2.0               h807b86a_2    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
liblapack                 3.9.0           19_linux64_openblas    conda-forge
libleidenalg              0.11.1               h00ab1b0_0    conda-forge
libnghttp2                1.55.1               h47da74e_0    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libopenblas               0.3.24          pthreads_h413a1c8_0    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsqlite                 3.44.0               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_2    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libxml2                   2.11.5               h232c23b_1    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
linkify-it-py             2.0.2                    pypi_0    pypi
llvmlite                  0.39.1                   pypi_0    pypi
markdown                  3.5.1                    pypi_0    pypi
markdown-it-py            3.0.0                    pypi_0    pypi
markupsafe                2.1.3            py39hd1e30aa_1    conda-forge
matplotlib                3.8.1                    pypi_0    pypi
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mdit-py-plugins           0.4.0                    pypi_0    pypi
mdurl                     0.1.2                    pypi_0    pypi
mistune                   3.0.2              pyhd8ed1ab_0    conda-forge
natsort                   8.4.0                    pypi_0    pypi
nbclient                  0.8.0              pyhd8ed1ab_0    conda-forge
nbconvert-core            7.10.0             pyhd8ed1ab_0    conda-forge
nbformat                  5.9.2              pyhd8ed1ab_0    conda-forge
ncurses                   6.4                  h59595ed_2    conda-forge
nest-asyncio              1.5.8              pyhd8ed1ab_0    conda-forge
networkx                  3.2.1                    pypi_0    pypi
notebook-shim             0.2.3              pyhd8ed1ab_0    conda-forge
numba                     0.56.3                   pypi_0    pypi
numpy                     1.23.5           py39h3d75532_0    conda-forge
openssl                   3.1.4                hd590300_0    conda-forge
overrides                 7.4.0              pyhd8ed1ab_0    conda-forge
packaging                 23.2               pyhd8ed1ab_0    conda-forge
pandas                    2.1.1                    pypi_0    pypi
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
panel                     1.2.3                    pypi_0    pypi
param                     1.13.0                   pypi_0    pypi
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
patsy                     0.5.3                    pypi_0    pypi
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    10.1.0                   pypi_0    pypi
pip                       23.3.1             pyhd8ed1ab_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_1    conda-forge
platformdirs              3.11.0             pyhd8ed1ab_0    conda-forge
plotly                    5.18.0             pyhd8ed1ab_0    conda-forge
prometheus_client         0.18.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.39             pyha770c72_0    conda-forge
prompt_toolkit            3.0.39               hd8ed1ab_0    conda-forge
psutil                    5.9.5            py39hd1e30aa_1    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pybind11                  2.11.1           py39h7633fee_2    conda-forge
pybind11-global           2.11.1           py39h7633fee_2    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pyct                      0.5.0                    pypi_0    pypi
pygments                  2.16.1             pyhd8ed1ab_0    conda-forge
pynndescent               0.5.10                   pypi_0    pypi
pyparsing                 3.1.1                    pypi_0    pypi
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.9.18          h0755675_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.18.1             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python_abi                3.9                      4_cp39    conda-forge
pytz                      2023.3.post1       pyhd8ed1ab_0    conda-forge
pyviz-comms               3.0.0                    pypi_0    pypi
pyyaml                    6.0.1            py39hd1e30aa_1    conda-forge
pyzmq                     25.1.1           py39h8c080ef_2    conda-forge
readline                  8.2                  h8228510_1    conda-forge
referencing               0.30.2             pyhd8ed1ab_0    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rpds-py                   0.10.6           py39h9fdd4d6_0    conda-forge
sam-algorithm             1.0.2                    pypi_0    pypi
samap                     1.0.15                   pypi_0    pypi
scanpy                    1.9.3                    pypi_0    pypi
scikit-learn              1.3.2                    pypi_0    pypi
scipy                     1.11.3                   pypi_0    pypi
seaborn                   0.13.0                   pypi_0    pypi
send2trash                1.8.2              pyh41d4057_0    conda-forge
session-info              1.0.0                    pypi_0    pypi
setuptools                68.2.2             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
statsmodels               0.14.0                   pypi_0    pypi
stdlib-list               0.9.0                    pypi_0    pypi
tbb                       2021.10.0                pypi_0    pypi
tenacity                  8.2.3              pyhd8ed1ab_0    conda-forge
terminado                 0.17.1             pyh41d4057_0    conda-forge
texttable                 1.7.0              pyhd8ed1ab_0    conda-forge
threadpoolctl             3.2.0                    pypi_0    pypi
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.13               h2797004_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tornado                   6.3.3            py39hd1e30aa_1    conda-forge
tqdm                      4.66.1                   pypi_0    pypi
traitlets                 5.13.0             pyhd8ed1ab_0    conda-forge
types-python-dateutil     2.8.19.14          pyhd8ed1ab_0    conda-forge
typing-extensions         4.8.0                hd8ed1ab_0    conda-forge
typing_extensions         4.8.0              pyha770c72_0    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge
tzdata                    2023.3                   pypi_0    pypi
uc-micro-py               1.0.2                    pypi_0    pypi
umap-learn                0.5.4                    pypi_0    pypi
uri-template              1.3.0              pyhd8ed1ab_0    conda-forge
urllib3                   2.0.7              pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.9              pyhd8ed1ab_0    conda-forge
webcolors                 1.13               pyhd8ed1ab_0    conda-forge
webencodings              0.5.1              pyhd8ed1ab_2    conda-forge
websocket-client          1.6.4              pyhd8ed1ab_0    conda-forge
wheel                     0.41.3             pyhd8ed1ab_0    conda-forge
widgetsnbextension        4.0.9              pyhd8ed1ab_0    conda-forge
xyzservices               2023.10.1                pypi_0    pypi
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
zeromq                    4.3.5                h59595ed_0    conda-forge
zipp                      3.17.0             pyhd8ed1ab_0    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge
amdqiao1 commented 11 months ago

Hi there, have you been able to solve this issue? I ran into the same issue as this one.

dsb66 commented 11 months ago

No I didn’t. I ended up exporting the data from samap and making the plot in R with ggalluvial, which I find easier to use.On Dec 6, 2023, at 11:52 AM, amdqiao1 @.***> wrote: Hi there, have you been able to solve this issue? I ran into the same issue as this one.

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: @.***>

Qi-Rongxuan commented 9 months ago

I ran into the same issue as this one in vscode.

danielylup commented 6 months ago

@dsb66 Hey! I ran into the same issue as well and I am giving up on using sankey_plot from SAMap as well. But I am curious how do you plot the sankey plot using ggalluvial? Did you export the MappingTable to R and modify the table manually for ggalluvial?

dsb66 commented 6 months ago

Yes, that is what I did. Here is my code for reference.

On Sun, Apr 14, 2024 at 11:45 PM danielylup @.***> wrote:

@dsb66 https://github.com/dsb66 Hey! I ran into the same issue as well and I am giving up on using sankey_plot from SAMap as well. But I am curious how do you plot the sankey plot using ggalluvial? Did you export the MappingTable to R and modify the table manually for ggalluvial?

— Reply to this email directly, view it on GitHub https://github.com/atarashansky/SAMap/issues/133#issuecomment-2055645168, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALJFUTT37SYXI2TJSJQWU53Y5NZPPAVCNFSM6AAAAAA7EBRUMGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANJVGY2DKMJWHA . You are receiving this because you were mentioned.Message ID: @.***>

danielylup commented 6 months ago

@dsb66 Thank you very much for your reply! However I couldn't find the code that you mentioned.

dsb66 commented 6 months ago

The code is the Rmd attached to my last email.On Apr 15, 2024, at 11:12 PM, danielylup @.***> wrote: @dsb66 Thank you very much for your reply! However I couldn't find the code that you mentioned.

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: @.***>

dsb66 commented 6 months ago

Installing holoviews separately fixed the issue for me: mamba install -c pyviz holoviews

cghmyway commented 3 months ago

How to use ggalluvial to plot a Sankey diagram of the MappingTable?

cghmyway commented 3 months ago

micromamba install holoviews==1.18.3 -c conda-forge fixed the issue for me :)

sky0m1n commented 3 months ago

Any other solution? I am still getting the same error even after reinstalling holoviews.

charmscharms commented 3 months ago

I'm also having the same issue, I tried with different approaches, but so far no results. I tried also plotting in R with ggalluvial but not getting the best results. Do you know any other alternatives or strategies that we can use ?