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implement leiden clustering #5
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sreichl committed Aug 27, 2023
1 parent 78b8dad commit feb03d7
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Showing 28 changed files with 9,601 additions and 9,288 deletions.
58 changes: 29 additions & 29 deletions .test/report.html

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12 changes: 12 additions & 0 deletions .test/results/configs/unsupervised_analysis/digits_config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,18 @@ heatmap:
- complete
metrics:
- spearman
leiden:
metrics:
- euclidean
n_iterations: 2
n_neighbors:
- 100
partition_types:
- RBConfigurationVertexPartition
- ModularityVertexPartition
resolutions:
- 0.5
- 1
mem: '32000'
mem_small: '16000'
metadata_of_interest: target
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6 changes: 4 additions & 2 deletions .test/results/envs/unsupervised_analysis/ggplot.yaml
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
name: /nobackup/lab_bock/users/sreichl/snakemake_conda/f4a030e93d31c95176adf0bd40ae009f_
name:
/nobackup/lab_bock/users/sreichl/snakemake_conda/f4a030e93d31c95176adf0bd40ae009f_
channels:
- conda-forge
- bioconda
Expand Down Expand Up @@ -158,4 +159,5 @@ dependencies:
- xz=5.2.6=h166bdaf_0
- zlib=1.2.13=h166bdaf_4
- zstd=1.5.2=h6239696_4
prefix: /nobackup/lab_bock/users/sreichl/snakemake_conda/f4a030e93d31c95176adf0bd40ae009f_
prefix:
/nobackup/lab_bock/users/sreichl/snakemake_conda/f4a030e93d31c95176adf0bd40ae009f_
30 changes: 16 additions & 14 deletions .test/results/envs/unsupervised_analysis/sklearn.yaml
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
name: /nobackup/lab_bock/users/sreichl/snakemake_conda/76c88fb0804661b4ffca966178600464_
name:
/nobackup/lab_bock/users/sreichl/snakemake_conda/76c88fb0804661b4ffca966178600464_
channels:
- conda-forge
- bioconda
Expand All @@ -8,7 +9,6 @@ dependencies:
- _openmp_mutex=4.5=2_gnu
- bzip2=1.0.8=h7f98852_4
- ca-certificates=2022.9.24=ha878542_0
- joblib=1.2.0=pyhd8ed1ab_0
- ld_impl_linux-64=2.39=hc81fddc_0
- libblas=3.9.0=16_linux64_openblas
- libcblas=3.9.0=16_linux64_openblas
Expand All @@ -25,23 +25,25 @@ dependencies:
- libuuid=2.32.1=h14c3975_1000
- libzlib=1.2.13=h166bdaf_4
- ncurses=6.3=h27087fc_1
- numpy=1.23.3=py310h53a5b5f_0
- openssl=3.0.5=h166bdaf_2
- pip=22.3=pyhd8ed1ab_0
- pandas=1.5.0=py310h769672d_0
- python=3.10.6=ha86cf86_0_cpython
- python-dateutil=2.8.2=pyhd8ed1ab_0
- python_abi=3.10=2_cp310
- pytz=2022.4=pyhd8ed1ab_0
- readline=8.1.2=h0f457ee_0
- setuptools=65.5.0=pyhd8ed1ab_0
- six=1.16.0=pyh6c4a22f_0
- threadpoolctl=3.1.0=pyh8a188c0_0
- scikit-learn=1.1.2=py310h0c3af53_0
- scipy=1.9.1=py310hdfbd76f_0
- tk=8.6.12=h27826a3_0
- tzdata=2022e=h191b570_0
- wheel=0.37.1=pyhd8ed1ab_0
- xz=5.2.6=h166bdaf_0
- pip:
- numpy==1.23.3
- pandas==1.5.0
- scikit-learn==1.1.2
- scipy==1.9.1
prefix: /nobackup/lab_bock/users/sreichl/snakemake_conda/76c88fb0804661b4ffca966178600464_
- joblib==1.2.0
- pip==22.3
- python-dateutil==2.8.2
- pytz==2022.4
- setuptools==65.5.0
- six==1.16.0
- threadpoolctl==3.1.0
- wheel==0.37.1
prefix:
/nobackup/lab_bock/users/sreichl/snakemake_conda/76c88fb0804661b4ffca966178600464_
198 changes: 105 additions & 93 deletions .test/results/envs/unsupervised_analysis/umap.yaml
Original file line number Diff line number Diff line change
@@ -1,110 +1,122 @@
name: /nobackup/lab_bock/users/sreichl/snakemake_conda/513c3eece9f3e16ab23d4213ff2b9ab8_
name:
/nobackup/lab_bock/users/sreichl/snakemake_conda/f15966d832bbab56c59bf1689176d51f_
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- brotli-python=1.0.9=py39h5a03fae_9
- bzip2=1.0.8=h7f98852_4
- ca-certificates=2022.9.24=ha878542_0
- colorama=0.4.5=pyhd8ed1ab_0
- joblib=1.2.0=pyhd8ed1ab_0
- ld_impl_linux-64=2.39=hc81fddc_0
- libblas=3.9.0=16_linux64_openblas
- libcblas=3.9.0=16_linux64_openblas
- ca-certificates=2023.7.22=hbcca054_0
- certifi=2023.7.22=pyhd8ed1ab_0
- charset-normalizer=3.2.0=pyhd8ed1ab_0
- colorama=0.4.6=pyhd8ed1ab_0
- icu=73.2=h59595ed_0
- idna=3.4=pyhd8ed1ab_0
- joblib=1.3.2=pyhd8ed1ab_0
- ld_impl_linux-64=2.40=h41732ed_0
- libblas=3.9.0=17_linux64_openblas
- libcblas=3.9.0=17_linux64_openblas
- libffi=3.4.2=h7f98852_5
- libgcc-ng=12.2.0=h65d4601_18
- libgfortran-ng=12.2.0=h69a702a_18
- libgfortran5=12.2.0=h337968e_18
- libgomp=12.2.0=h65d4601_18
- liblapack=3.9.0=16_linux64_openblas
- libllvm11=11.1.0=he0ac6c6_4
- libgcc-ng=13.1.0=he5830b7_0
- libgfortran-ng=13.1.0=h69a702a_0
- libgfortran5=13.1.0=h15d22d2_0
- libgomp=13.1.0=he5830b7_0
- libhwloc=2.9.2=nocuda_h7313eea_1008
- libiconv=1.17=h166bdaf_0
- liblapack=3.9.0=17_linux64_openblas
- libllvm14=14.0.6=hcd5def8_4
- libnsl=2.0.0=h7f98852_0
- libopenblas=0.3.21=pthreads_h78a6416_3
- libsqlite=3.39.4=h753d276_0
- libstdcxx-ng=12.2.0=h46fd767_18
- libuuid=2.32.1=h14c3975_1000
- libzlib=1.2.13=h166bdaf_4
- llvmlite=0.39.1=py39h7d9a04d_0
- ncurses=6.3=h27087fc_1
- numba=0.56.3=py39h61ddf18_0
- libopenblas=0.3.23=pthreads_h80387f5_0
- libsqlite=3.43.0=h2797004_0
- libstdcxx-ng=13.1.0=hfd8a6a1_0
- libuuid=2.38.1=h0b41bf4_0
- libxml2=2.11.5=h232c23b_1
- libzlib=1.2.13=hd590300_5
- llvmlite=0.40.1=py39h174d805_0
- ncurses=6.4=hcb278e6_0
- numba=0.57.1=py39hb75a051_0
- numpy=1.23.3=py39hba7629e_0
- openssl=3.0.5=h166bdaf_2
- openssl=3.1.2=hd590300_0
- packaging=23.1=pyhd8ed1ab_0
- pandas=1.5.0=py39h4661b88_0
- pip=22.3=pyhd8ed1ab_0
- pynndescent=0.5.7=pyh6c4a22f_0
- python=3.9.13=h2660328_0_cpython
- pip=23.2.1=pyhd8ed1ab_0
- platformdirs=3.10.0=pyhd8ed1ab_0
- pooch=1.7.0=pyha770c72_3
- pynndescent=0.5.10=pyh1a96a4e_0
- pysocks=1.7.1=pyha2e5f31_6
- python=3.9.17=h0755675_0_cpython
- python-dateutil=2.8.2=pyhd8ed1ab_0
- python_abi=3.9=2_cp39
- pytz=2022.4=pyhd8ed1ab_0
- readline=8.1.2=h0f457ee_0
- scikit-learn=1.1.2=py39he5e8d7e_0
- scipy=1.9.1=py39h8ba3f38_0
- setuptools=65.5.0=pyhd8ed1ab_0
- python_abi=3.9=3_cp39
- pytz=2023.3=pyhd8ed1ab_0
- readline=8.2=h8228510_1
- requests=2.31.0=pyhd8ed1ab_0
- rocm-smi=5.6.0=h59595ed_1
- scikit-learn=1.3.0=py39hc236052_0
- scipy=1.11.2=py39h6183b62_0
- setuptools=68.1.2=pyhd8ed1ab_0
- six=1.16.0=pyh6c4a22f_0
- sqlite=3.39.4=h4ff8645_0
- tbb=2021.6.0=h924138e_0
- threadpoolctl=3.1.0=pyh8a188c0_0
- tbb=2021.10.0=h00ab1b0_0
- threadpoolctl=3.2.0=pyha21a80b_0
- tk=8.6.12=h27826a3_0
- tqdm=4.64.1=pyhd8ed1ab_0
- tzdata=2022e=h191b570_0
- umap-learn=0.5.3=py39hf3d152e_0
- wheel=0.37.1=pyhd8ed1ab_0
- tqdm=4.66.1=pyhd8ed1ab_0
- typing-extensions=4.7.1=hd8ed1ab_0
- typing_extensions=4.7.1=pyha770c72_0
- tzdata=2023c=h71feb2d_0
- umap-learn=0.5.3=py39hf3d152e_1
- urllib3=2.0.4=pyhd8ed1ab_0
- wheel=0.41.2=pyhd8ed1ab_0
- xz=5.2.6=h166bdaf_0
- pip:
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- bokeh==2.4.3
- certifi==2022.9.24
- charset-normalizer==2.1.1
- click==8.1.3
- cloudpickle==2.2.0
- colorcet==3.0.1
- contourpy==1.0.5
- cycler==0.11.0
- dask==2022.10.0
- datashader==0.14.2
- datashape==0.5.2
- distributed==2022.10.0
- fonttools==4.37.4
- fsspec==2022.8.2
- heapdict==1.0.1
- holoviews==1.15.1
- idna==3.4
- imageio==2.22.2
- importlib-metadata==5.0.0
- jinja2==3.1.2
- kiwisolver==1.4.4
- locket==1.0.0
- markdown==3.4.1
- markupsafe==2.1.1
- matplotlib==3.6.1
- msgpack==1.0.4
- multipledispatch==0.6.0
- networkx==2.8.7
- packaging==21.3
- panel==0.14.0
- param==1.12.2
- partd==1.3.0
- pillow==9.2.0
- psutil==5.9.2
- pyct==0.4.8
- pyparsing==3.0.9
- pyviz-comms==2.2.1
- pywavelets==1.4.1
- pyyaml==6.0
- requests==2.28.1
- scikit-image==0.19.3
- seaborn==0.12.0
- sortedcontainers==2.4.0
- tblib==1.7.0
- tifffile==2022.10.10
- toolz==0.12.0
- tornado==6.1
- typing-extensions==4.4.0
- urllib3==1.26.12
- webencodings==0.5.1
- xarray==2022.10.0
- zict==2.2.0
- zipp==3.9.0
prefix: /nobackup/lab_bock/users/sreichl/snakemake_conda/513c3eece9f3e16ab23d4213ff2b9ab8_
- bleach==6.0.0
- bokeh==3.2.2
- click==8.1.7
- cloudpickle==2.2.1
- colorcet==3.0.1
- contourpy==1.1.0
- cycler==0.11.0
- dask==2023.8.1
- datashader==0.15.2
- datashape==0.5.2
- fonttools==4.42.1
- fsspec==2023.6.0
- holoviews==1.17.1
- imageio==2.31.2
- importlib-metadata==6.8.0
- importlib-resources==6.0.1
- jinja2==3.1.2
- kiwisolver==1.4.5
- lazy-loader==0.3
- linkify-it-py==2.0.2
- locket==1.0.0
- markdown==3.4.4
- markdown-it-py==3.0.0
- markupsafe==2.1.3
- matplotlib==3.7.2
- mdit-py-plugins==0.4.0
- mdurl==0.1.2
- multipledispatch==1.0.0
- networkx==3.1
- panel==1.2.1
- param==1.13.0
- partd==1.4.0
- pillow==10.0.0
- pyct==0.5.0
- pyparsing==3.0.9
- pyviz-comms==3.0.0
- pywavelets==1.4.1
- pyyaml==6.0.1
- scikit-image==0.21.0
- seaborn==0.12.2
- tifffile==2023.8.25
- toolz==0.12.0
- tornado==6.3.3
- uc-micro-py==1.0.2
- webencodings==0.5.1
- xarray==2023.8.0
- xyzservices==2023.7.0
- zipp==3.16.2
prefix:
/nobackup/lab_bock/users/sreichl/snakemake_conda/f15966d832bbab56c59bf1689176d51f_
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