diff --git a/requirements-dev.lock b/requirements-dev.lock index 6c44cfb..02a0f3e 100644 --- a/requirements-dev.lock +++ b/requirements-dev.lock @@ -5,106 +5,307 @@ # pre: false # features: [] # all-features: false +# with-sources: false +# generate-hashes: false +# universal: false -e file:. anndata==0.10.9 + # via doubletdetection + # via parafac2 + # via scanpy + # via spatialpf2 annoy==1.17.3 + # via pacmap array-api-compat==1.8 + # via anndata asttokens==2.4.1 + # via stack-data certifi==2024.8.30 + # via requests charset-normalizer==3.3.2 + # via requests click==8.1.7 + # via dask cloudpickle==3.0.0 + # via dask colorcet==3.1.0 + # via datashader comm==0.2.2 + # via ipywidgets contourpy==1.3.0 + # via matplotlib coverage==7.6.1 + # via pytest-cov cupy-cuda12x==13.3.0 + # via parafac2 cycler==0.12.1 + # via matplotlib dask==2024.9.0 + # via dask-expr + # via datashader + # via spatialpf2 dask-expr==1.1.14 + # via dask datashader==0.16.3 + # via spatialpf2 decorator==5.1.1 + # via ipython doubletdetection==4.2 + # via spatialpf2 executing==2.1.0 + # via stack-data fastrlock==0.8.2 + # via cupy-cuda12x fonttools==4.53.1 + # via matplotlib fsspec==2024.9.0 + # via dask h5py==3.11.0 + # via anndata + # via scanpy idna==3.10 + # via requests igraph==0.11.6 + # via leidenalg + # via louvain importlib-metadata==8.5.0 + # via dask iniconfig==2.0.0 + # via pytest ipython==8.27.0 + # via ipywidgets ipywidgets==8.1.5 + # via doubletdetection jedi==0.19.1 + # via ipython joblib==1.4.2 + # via pynndescent + # via scanpy + # via scikit-learn jupyterlab-widgets==3.0.13 + # via ipywidgets kiwisolver==1.4.7 + # via matplotlib legacy-api-wrap==1.4 + # via scanpy leidenalg==0.10.2 + # via doubletdetection + # via phenograph llvmlite==0.43.0 + # via numba + # via pynndescent locket==1.0.0 + # via partd louvain==0.8.2 + # via doubletdetection matplotlib==3.9.2 + # via doubletdetection + # via scanpy + # via seaborn + # via spatialpf2 + # via tlviz matplotlib-inline==0.1.7 + # via ipython multipledispatch==1.0.0 + # via datashader natsort==8.4.0 + # via anndata + # via scanpy networkx==3.3 + # via scanpy + # via spatialpf2 nodeenv==1.9.1 + # via pyright numba==0.60.0 + # via datashader + # via pacmap + # via pynndescent + # via scanpy + # via umap-learn numpy==1.26.4 + # via anndata + # via contourpy + # via cupy-cuda12x + # via dask + # via datashader + # via doubletdetection + # via h5py + # via matplotlib + # via numba + # via pacmap + # via pandas + # via parafac2 + # via patsy + # via phenograph + # via pyarrow + # via scanpy + # via scikit-learn + # via scipy + # via seaborn + # via spatialpf2 + # via statsmodels + # via tensorly + # via tlviz + # via umap-learn + # via xarray packaging==24.1 + # via anndata + # via dask + # via datashader + # via matplotlib + # via pytest + # via scanpy + # via statsmodels + # via xarray pacmap==0.7.3 + # via parafac2 + # via spatialpf2 pandas==2.2.2 + # via anndata + # via dask + # via dask-expr + # via datashader + # via doubletdetection + # via scanpy + # via seaborn + # via spatialpf2 + # via statsmodels + # via tlviz + # via xarray parafac2 @ git+https://github.com/meyer-lab/parafac2.git@793f8ad06791ffcc698105d80941774741722574 + # via spatialpf2 param==2.1.1 + # via datashader + # via pyct parso==0.8.4 + # via jedi partd==1.4.2 + # via dask patsy==0.5.6 + # via scanpy + # via statsmodels pexpect==4.9.0 + # via ipython phenograph==1.5.7 + # via doubletdetection pillow==10.4.0 + # via datashader + # via matplotlib pluggy==1.5.0 + # via pytest prompt-toolkit==3.0.47 + # via ipython psutil==6.0.0 + # via phenograph ptyprocess==0.7.0 + # via pexpect pure-eval==0.2.3 + # via stack-data pyarrow==17.0.0 + # via dask-expr pyct==0.5.0 + # via datashader pygments==2.18.0 + # via ipython pynndescent==0.5.13 + # via scanpy + # via umap-learn pyparsing==3.1.4 + # via matplotlib pyright==1.1.380 pytest==8.3.3 + # via pytest-cov pytest-cov==5.0.0 python-dateutil==2.9.0.post0 + # via matplotlib + # via pandas pytz==2024.2 + # via pandas pyyaml==6.0.2 + # via dask requests==2.32.3 + # via datashader + # via tlviz scanpy==1.10.2 + # via doubletdetection + # via spatialpf2 scikit-learn==1.5.2 + # via pacmap + # via parafac2 + # via phenograph + # via pynndescent + # via scanpy + # via spatialpf2 + # via umap-learn scipy==1.14.1 + # via anndata + # via datashader + # via doubletdetection + # via parafac2 + # via phenograph + # via pynndescent + # via scanpy + # via scikit-learn + # via statsmodels + # via tensorly + # via tlviz + # via umap-learn seaborn==0.13.2 + # via scanpy session-info==1.0.0 + # via scanpy +setuptools==75.1.0 + # via phenograph + # via spatialpf2 six==1.16.0 + # via asttokens + # via patsy + # via python-dateutil stack-data==0.6.3 + # via ipython statsmodels==0.14.3 + # via scanpy + # via tlviz stdlib-list==0.10.0 + # via session-info tensorly==0.8.1 + # via parafac2 + # via spatialpf2 texttable==1.7.0 + # via igraph threadpoolctl==3.5.0 + # via scikit-learn tlviz==0.1.1 + # via spatialpf2 toolz==0.12.1 + # via dask + # via datashader + # via partd tqdm==4.66.5 + # via doubletdetection + # via parafac2 + # via scanpy + # via umap-learn traitlets==5.14.3 + # via comm + # via ipython + # via ipywidgets + # via matplotlib-inline typing-extensions==4.12.2 + # via ipython tzdata==2024.1 + # via pandas umap-learn==0.5.6 + # via scanpy urllib3==2.2.3 + # via requests wcwidth==0.2.13 + # via prompt-toolkit widgetsnbextension==4.0.13 + # via ipywidgets xarray==2024.9.0 + # via datashader + # via tlviz zipp==3.20.2 -# The following packages are considered to be unsafe in a requirements file: -setuptools==75.1.0 + # via importlib-metadata diff --git a/requirements.lock b/requirements.lock index 35906cb..a70d000 100644 --- a/requirements.lock +++ b/requirements.lock @@ -5,99 +5,294 @@ # pre: false # features: [] # all-features: false +# with-sources: false +# generate-hashes: false +# universal: false -e file:. anndata==0.10.9 + # via doubletdetection + # via parafac2 + # via scanpy + # via spatialpf2 annoy==1.17.3 + # via pacmap array-api-compat==1.8 + # via anndata asttokens==2.4.1 + # via stack-data certifi==2024.8.30 + # via requests charset-normalizer==3.3.2 + # via requests click==8.1.7 + # via dask cloudpickle==3.0.0 + # via dask colorcet==3.1.0 + # via datashader comm==0.2.2 + # via ipywidgets contourpy==1.3.0 + # via matplotlib cupy-cuda12x==13.3.0 + # via parafac2 cycler==0.12.1 + # via matplotlib dask==2024.9.0 + # via dask-expr + # via datashader + # via spatialpf2 dask-expr==1.1.14 + # via dask datashader==0.16.3 + # via spatialpf2 decorator==5.1.1 + # via ipython doubletdetection==4.2 + # via spatialpf2 executing==2.1.0 + # via stack-data fastrlock==0.8.2 + # via cupy-cuda12x fonttools==4.53.1 + # via matplotlib fsspec==2024.9.0 + # via dask h5py==3.11.0 + # via anndata + # via scanpy idna==3.10 + # via requests igraph==0.11.6 + # via leidenalg + # via louvain importlib-metadata==8.5.0 + # via dask ipython==8.27.0 + # via ipywidgets ipywidgets==8.1.5 + # via doubletdetection jedi==0.19.1 + # via ipython joblib==1.4.2 + # via pynndescent + # via scanpy + # via scikit-learn jupyterlab-widgets==3.0.13 + # via ipywidgets kiwisolver==1.4.7 + # via matplotlib legacy-api-wrap==1.4 + # via scanpy leidenalg==0.10.2 + # via doubletdetection + # via phenograph llvmlite==0.43.0 + # via numba + # via pynndescent locket==1.0.0 + # via partd louvain==0.8.2 + # via doubletdetection matplotlib==3.9.2 + # via doubletdetection + # via scanpy + # via seaborn + # via spatialpf2 + # via tlviz matplotlib-inline==0.1.7 + # via ipython multipledispatch==1.0.0 + # via datashader natsort==8.4.0 + # via anndata + # via scanpy networkx==3.3 + # via scanpy + # via spatialpf2 numba==0.60.0 + # via datashader + # via pacmap + # via pynndescent + # via scanpy + # via umap-learn numpy==1.26.4 + # via anndata + # via contourpy + # via cupy-cuda12x + # via dask + # via datashader + # via doubletdetection + # via h5py + # via matplotlib + # via numba + # via pacmap + # via pandas + # via parafac2 + # via patsy + # via phenograph + # via pyarrow + # via scanpy + # via scikit-learn + # via scipy + # via seaborn + # via spatialpf2 + # via statsmodels + # via tensorly + # via tlviz + # via umap-learn + # via xarray packaging==24.1 + # via anndata + # via dask + # via datashader + # via matplotlib + # via scanpy + # via statsmodels + # via xarray pacmap==0.7.3 + # via parafac2 + # via spatialpf2 pandas==2.2.2 + # via anndata + # via dask + # via dask-expr + # via datashader + # via doubletdetection + # via scanpy + # via seaborn + # via spatialpf2 + # via statsmodels + # via tlviz + # via xarray parafac2 @ git+https://github.com/meyer-lab/parafac2.git@793f8ad06791ffcc698105d80941774741722574 + # via spatialpf2 param==2.1.1 + # via datashader + # via pyct parso==0.8.4 + # via jedi partd==1.4.2 + # via dask patsy==0.5.6 + # via scanpy + # via statsmodels pexpect==4.9.0 + # via ipython phenograph==1.5.7 + # via doubletdetection pillow==10.4.0 + # via datashader + # via matplotlib prompt-toolkit==3.0.47 + # via ipython psutil==6.0.0 + # via phenograph ptyprocess==0.7.0 + # via pexpect pure-eval==0.2.3 + # via stack-data pyarrow==17.0.0 + # via dask-expr pyct==0.5.0 + # via datashader pygments==2.18.0 + # via ipython pynndescent==0.5.13 + # via scanpy + # via umap-learn pyparsing==3.1.4 + # via matplotlib python-dateutil==2.9.0.post0 + # via matplotlib + # via pandas pytz==2024.2 + # via pandas pyyaml==6.0.2 + # via dask requests==2.32.3 + # via datashader + # via tlviz scanpy==1.10.2 + # via doubletdetection + # via spatialpf2 scikit-learn==1.5.2 + # via pacmap + # via parafac2 + # via phenograph + # via pynndescent + # via scanpy + # via spatialpf2 + # via umap-learn scipy==1.14.1 + # via anndata + # via datashader + # via doubletdetection + # via parafac2 + # via phenograph + # via pynndescent + # via scanpy + # via scikit-learn + # via statsmodels + # via tensorly + # via tlviz + # via umap-learn seaborn==0.13.2 + # via scanpy session-info==1.0.0 + # via scanpy +setuptools==75.1.0 + # via phenograph + # via spatialpf2 six==1.16.0 + # via asttokens + # via patsy + # via python-dateutil stack-data==0.6.3 + # via ipython statsmodels==0.14.3 + # via scanpy + # via tlviz stdlib-list==0.10.0 + # via session-info tensorly==0.8.1 + # via parafac2 + # via spatialpf2 texttable==1.7.0 + # via igraph threadpoolctl==3.5.0 + # via scikit-learn tlviz==0.1.1 + # via spatialpf2 toolz==0.12.1 + # via dask + # via datashader + # via partd tqdm==4.66.5 + # via doubletdetection + # via parafac2 + # via scanpy + # via umap-learn traitlets==5.14.3 + # via comm + # via ipython + # via ipywidgets + # via matplotlib-inline typing-extensions==4.12.2 + # via ipython tzdata==2024.1 + # via pandas umap-learn==0.5.6 + # via scanpy urllib3==2.2.3 + # via requests wcwidth==0.2.13 + # via prompt-toolkit widgetsnbextension==4.0.13 + # via ipywidgets xarray==2024.9.0 + # via datashader + # via tlviz zipp==3.20.2 -# The following packages are considered to be unsafe in a requirements file: -setuptools==75.1.0 + # via importlib-metadata diff --git a/spatialpf2/imports.py b/spatialpf2/imports.py index a71c5bf..a5b0ed1 100644 --- a/spatialpf2/imports.py +++ b/spatialpf2/imports.py @@ -63,3 +63,10 @@ def import_HTAN() -> anndata.AnnData: X = anndata.concat(data, merge="same", label="Condition") return prepare_dataset(X, "Condition", geneThreshold=0.1) + +def import_scRNAseq() -> anndata.AnnData: + "Imports scRNA-seq data" + + X = anndata.read_h5ad("/opt/extra-storage/CRC/Heiser/VUMC_HTAN_DIS_EPI_V2.h5ad") + + return X \ No newline at end of file