scTenifoldXct 0.1.0__tar.gz

sctenifoldxct-0.1.0/.dockerignore

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+**/__pycache__
+**/.venv
+**/.classpath
+**/.dockerignore
+**/.env
+**/.git
+**/.gitignore
+**/.project
+**/.settings
+**/.toolstarget
+**/.vs
+**/.vscode
+**/*.*proj.user
+**/*.dbmdl
+**/*.jfm
+**/bin
+**/charts
+**/docker-compose*
+**/compose*
+**/Dockerfile*
+**/node_modules
+**/npm-debug.log
+**/obj
+**/secrets.dev.yaml
+**/values.dev.yaml
+README.md

sctenifoldxct-0.1.0/.github/workflows/testing.yml

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+name: Python package
+
+on:
+  push:
+    branches:
+      - dev
+  pull_request:
+    branches: 
+      - master
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 pytest
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Test with pytest
+        run: |
+          pytest
+          

sctenifoldxct-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# scTenifoldXct
+scTenifoldXct/*.pyc
+tutorials/*
+!tutorials/*.ipynb

sctenifoldxct-0.1.0/Dockerfile

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+FROM python:3.8-slim
+
+# Keeps Python from generating .pyc files in the container
+ENV PYTHONDONTWRITEBYTECODE=1
+
+# Turns off buffering for easier container logging
+ENV PYTHONUNBUFFERED=1
+
+# Install pip requirements
+COPY requirements.txt .
+RUN python -m pip install --no-cache-dir -r requirements.txt
+
+WORKDIR /app
+COPY ./scTenifoldXct /app/scTenifoldXct
+COPY ./tutorials /app/tutorials
+
+# Creates a non-root user with an explicit UID and adds permission to access the /app folder
+RUN adduser -u 5678 --disabled-password --gecos "" appuser && chown -R appuser /app
+USER appuser
+
+# During debugging, this entry point will be overridden.
+CMD ["sh"]

sctenifoldxct-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2022 Yongjian Yang
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

sctenifoldxct-0.1.0/MANIFEST.in

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+recursive-include scTenifoldXct *.csv
+exclude scTenifoldXct/_deprecated.py
+exclude scTenifoldXct/_functional.py

sctenifoldxct-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: scTenifoldXct
+Version: 0.1.0
+Summary: scTenifoldXct
+Home-page: https://github.com/cailab-tamu/scTenifoldXct
+Author: Yongjian Yang, TAMU
+Author-email: yjyang027@tamu.edu
+License: MIT
+Keywords: neural network,embedding,manifold-learning,computational-biology,single-cell,cell-cell interaction,gene regulatroy network,visualization
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: anndata
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: python_igraph
+Requires-Dist: ray
+Requires-Dist: scanpy
+Requires-Dist: scipy
+Requires-Dist: statsmodels
+Requires-Dist: torch
+Requires-Dist: tqdm
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: summary
+
+# scTenifoldXct
+a semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs via manifold learning <br> 
+<span style="color:red;">New!</span> Data has been added. Feel free to explore and use it. <br>
+<span style="color:red;">New!</span> A standalone UI has been added. [Give it a try!](https://sctenifold.streamlit.app/)
+[[Paper]](https://doi.org/10.1016/j.cels.2023.01.004)
+<br/>
+<p align="center">
+    <img src="LS_git.jpeg" alt="drawing" width="300"/>
+</p>
+<br/>
+
+### Install Dependencies
+We suggest first intall dependencies of scTenifoldXct with `conda`:
+```shell
+git clone https://github.com/cailab-tamu/scTenifoldXct.git
+cd scTenifoldXct
+conda env create -f environment.yml
+conda activate scTenifold
+```
+
+### Install scTenifoldXct
+Install scTenifoldXct with `pip`:
+```shell
+pip install git+https://github.com/cailab-tamu/scTenifoldXct.git 
+```
+
+or install it manually from source:
+```shell
+pip install .
+```
+
+### Usages
+
+#### Quick Start
+The following code runs scTenifoldXct on an example data set in the tutorials:
+```python
+import scanpy as sc
+import scTenifoldXct as st
+
+adata = sc.read_h5ad('data/adata_short_example.h5ad') # load data
+xct = st.scTenifoldXct(data = adata, # an AnnData 
+                    source_celltype = 'Inflam. FIB', # sender cell type
+                    target_celltype = 'Inflam. DC', # receiver cell type
+                    obs_label = 'ident', # colname in adata.obs indicating cell types
+                    rebuild_GRN = True, # whether to build GRNs
+                    GRN_file_dir = 'Net_example_dev',  # folder path to GRNs
+                    verbose = True, # whether to verbose the processing
+                    n_cpus = -1) # CPU multiprocessing, -1 to use all
+emb = xct.get_embeds(train = True) # Manifold alignment to project data to low-dimensional embeddings
+xct_pairs = xct.null_test() # non-parametric test to get significant interactions
+print(xct_pairs)
+```
+
+### Tutorial
+We have included two tutorial notebooks on scTenifoldXct usage and results visualization.
+
+Single-sample interaction analysis:<br> https://github.com/cailab-tamu/scTenifoldXct/blob/master/tutorials/tutorial-short_example.ipynb <br>
+Two-sample differential interaction analysis:<br> https://github.com/cailab-tamu/scTenifoldXct/blob/master/tutorials/tutorial-merge_short_example.ipynb 
+<br/>
+
+### Run scTenifoldXct from command-line by `Docker`
+scTenifoldXct provides command-line utilities for users who are not familiar with Python.<br>
+A Docker image of scTenifoldXct can be built from the repository. The Docker image has all required packages and databases included. 
+
+```shell
+docker build -t sctenifold .
+docker run -it --name xct --shm-size=8gb sctenifold
+```
+If successful, a Bash terminal will be present in the newly created container.<br>
+An example for running single-sample analysis:
+```shell
+python -m scTenifoldXct.core tutorials/data/adata_short_example.h5ad \
+--rebuild \
+-s "Inflam. FIB" \
+-r "Inflam. DC" \
+--n_cpus 8 \
+-v
+```
+For runnning two-sample analysis:
+```shell
+python -m scTenifoldXct.merge tutorials/data/adata_merge_example.h5ad \
+NormalvsTumor N T \
+--rebuild \
+-s "B cells" \
+-r "Fibroblasts" \
+--n_cpus 8 \
+-v
+```
+Users should copy their own data to the container for their analyses. 
+
+When analysis completes, hit Ctrl + p and Ctrl + q to detach from the container and then copy the result to the host:
+```shell
+docker cp xct:/app/xct_results/ .
+```
+
+

sctenifoldxct-0.1.0/README.md

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+# scTenifoldXct
+a semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs via manifold learning <br> 
+<span style="color:red;">New!</span> Data has been added. Feel free to explore and use it. <br>
+<span style="color:red;">New!</span> A standalone UI has been added. [Give it a try!](https://sctenifold.streamlit.app/)
+[[Paper]](https://doi.org/10.1016/j.cels.2023.01.004)
+<br/>
+<p align="center">
+    <img src="LS_git.jpeg" alt="drawing" width="300"/>
+</p>
+<br/>
+
+### Install Dependencies
+We suggest first intall dependencies of scTenifoldXct with `conda`:
+```shell
+git clone https://github.com/cailab-tamu/scTenifoldXct.git
+cd scTenifoldXct
+conda env create -f environment.yml
+conda activate scTenifold
+```
+
+### Install scTenifoldXct
+Install scTenifoldXct with `pip`:
+```shell
+pip install git+https://github.com/cailab-tamu/scTenifoldXct.git 
+```
+
+or install it manually from source:
+```shell
+pip install .
+```
+
+### Usages
+
+#### Quick Start
+The following code runs scTenifoldXct on an example data set in the tutorials:
+```python
+import scanpy as sc
+import scTenifoldXct as st
+
+adata = sc.read_h5ad('data/adata_short_example.h5ad') # load data
+xct = st.scTenifoldXct(data = adata, # an AnnData 
+                    source_celltype = 'Inflam. FIB', # sender cell type
+                    target_celltype = 'Inflam. DC', # receiver cell type
+                    obs_label = 'ident', # colname in adata.obs indicating cell types
+                    rebuild_GRN = True, # whether to build GRNs
+                    GRN_file_dir = 'Net_example_dev',  # folder path to GRNs
+                    verbose = True, # whether to verbose the processing
+                    n_cpus = -1) # CPU multiprocessing, -1 to use all
+emb = xct.get_embeds(train = True) # Manifold alignment to project data to low-dimensional embeddings
+xct_pairs = xct.null_test() # non-parametric test to get significant interactions
+print(xct_pairs)
+```
+
+### Tutorial
+We have included two tutorial notebooks on scTenifoldXct usage and results visualization.
+
+Single-sample interaction analysis:<br> https://github.com/cailab-tamu/scTenifoldXct/blob/master/tutorials/tutorial-short_example.ipynb <br>
+Two-sample differential interaction analysis:<br> https://github.com/cailab-tamu/scTenifoldXct/blob/master/tutorials/tutorial-merge_short_example.ipynb 
+<br/>
+
+### Run scTenifoldXct from command-line by `Docker`
+scTenifoldXct provides command-line utilities for users who are not familiar with Python.<br>
+A Docker image of scTenifoldXct can be built from the repository. The Docker image has all required packages and databases included. 
+
+```shell
+docker build -t sctenifold .
+docker run -it --name xct --shm-size=8gb sctenifold
+```
+If successful, a Bash terminal will be present in the newly created container.<br>
+An example for running single-sample analysis:
+```shell
+python -m scTenifoldXct.core tutorials/data/adata_short_example.h5ad \
+--rebuild \
+-s "Inflam. FIB" \
+-r "Inflam. DC" \
+--n_cpus 8 \
+-v
+```
+For runnning two-sample analysis:
+```shell
+python -m scTenifoldXct.merge tutorials/data/adata_merge_example.h5ad \
+NormalvsTumor N T \
+--rebuild \
+-s "B cells" \
+-r "Fibroblasts" \
+--n_cpus 8 \
+-v
+```
+Users should copy their own data to the container for their analyses. 
+
+When analysis completes, hit Ctrl + p and Ctrl + q to detach from the container and then copy the result to the host:
+```shell
+docker cp xct:/app/xct_results/ .
+```
+
+

sctenifoldxct-0.1.0/data/README.md

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+* The example datasets used in the tutorial have been uploaded. 
+* The lesional skin dataset is available at [GoogleDrive](https://drive.google.com/file/d/1pNnjwES7ahMrC6OcdQMxNkAnG_5a7Gwy/view?usp=drive_link). 
+* Additional datasets may be provided upon request.

sctenifoldxct-0.1.0/environment.yml

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+channels:
+- conda-forge
+dependencies:
+- python~=3.9.6
+- pip>=22.0.4
+- pycairo>=1.21.0
+- anndata>=0.7.4
+- numpy>=1.17.0
+- matplotlib-base>=3.1.2
+- pandas>=0.21
+- scipy>=1.4
+- seaborn
+- h5py>=3
+- tqdm
+- scikit-learn>=0.22
+- statsmodels~=0.13.1
+- patsy
+- networkx>=2.3
+- natsort
+- joblib
+- numba>=0.41.0
+- umap-learn>=0.3.10
+- packaging
+- setuptools-scm
+- black>=20.8b1
+- docutils
+- sphinx<4.2,>=4.1
+- sphinx_rtd_theme>=0.3.1
+- python-igraph~=0.9.8
+- leidenalg
+- louvain!=0.6.2,>=0.6
+# - scikit-misc~=0.1.4
+- pytest>=4.4
+- pytest-nunit
+- dask-core!=2.17.0
+- fsspec
+- zappy
+- zarr
+- profimp
+- flit-core
+- ipywidgets
+- pip:
+  - flit
+  - session-info
+  # - bbknn
+  - scanpydoc<0.7.6,>=0.7.4
+  # - harmonypy
+  # - magic-impute>=2.0
+  # - cudf
+  # - cuml
+  # - cugraph
+  # - scanorama
+  # - scrublet
+  - torch>=1.8.0
+  - scikit-misc>=0.1.3
+  - scanpy>=1.7.2
+  - ray # https://docs.ray.io/en/latest/ray-overview/installation.html
+  - notebook
+name: scTenifold
+

sctenifoldxct-0.1.0/requirements.txt

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+scipy
+matplotlib
+numpy
+statsmodels
+torch
+pandas
+python_igraph
+scanpy
+anndata
+ray
+tqdm

sctenifoldxct-0.1.0/scTenifoldXct/__init__.py

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+from .version import __version__ # scTenifoldXct.__version__
+from scTenifoldXct.core import scTenifoldXct
+from scTenifoldXct.visualization import get_Xct_pairs, plot_XNet
+from scTenifoldXct.merge import merge_scTenifoldXct

sctenifoldxct-0.1.0/scTenifoldXct/cko.py

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+from typing import List, Union
+import anndata
+
+
+def get_cko_data(data: anndata.AnnData, cko_gene_names: Union[List[str], str]) -> anndata.AnnData:
+    """
+    Get the adata with the cko genes.
+    """
+    cko_gene_names = [cko_gene_names.lower()] if isinstance(cko_gene_names, str) else [gene.lower() for gene in cko_gene_names]
+    data.var_names = data.var_names.str.lower()
+    gene_index = [data.var_names.get_loc(gene_name) for gene_name in cko_gene_names]
+    data.X[:, gene_index] = 0.
+    print(f"CKO genes {cko_gene_names} are set")
+    
+    return data