SAMap
SAMap copied to clipboard
atarashansky
sankey and chord plot error
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
Hi there, have you been able to solve this issue? I ran into the same issue as this one.
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: @.***>
@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?
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: @.***>
@dsb66 Thank you very much for your reply! However I couldn't find the code that you mentioned.
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: @.***>
Installing holoviews separately fixed the issue for me:
mamba install -c pyviz holoviews
micromamba install holoviews==1.18.3 -c conda-forge fixed the issue for me :)
Any other solution? I am still getting the same error even after reinstalling holoviews.
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 ?
