├── .github └── workflows │ └── python-package.yml ├── .gitignore ├── CHANGELOG.md ├── CONTRIBUTING.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── data ├── lisi_lisi.tsv.gz ├── lisi_metadata.tsv.gz ├── lisi_x.tsv.gz ├── pbmc_3500_meta.tsv.gz ├── pbmc_3500_pcs.tsv.gz └── pbmc_3500_pcs_harmonized.tsv.gz ├── harmonypy ├── __init__.py ├── harmony.py └── lisi.py ├── pyproject.toml └── tests ├── __init__.py ├── test_harmony.py └── test_lisi.py /.github/workflows/python-package.yml: -------------------------------------------------------------------------------- 1 | # This workflow will install Python dependencies, run tests and lint with a variety of Python versions 2 | # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python 3 | 4 | name: pytest 5 | 6 | on: 7 | push: 8 | branches: [ "master" ] 9 | pull_request: 10 | branches: [ "master" ] 11 | 12 | jobs: 13 | build: 14 | 15 | runs-on: ubuntu-20.04 16 | strategy: 17 | fail-fast: false 18 | matrix: 19 | python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"] 20 | 21 | steps: 22 | - uses: actions/checkout@v3 23 | - name: Set up Python ${{ matrix.python-version }} 24 | uses: actions/setup-python@v3 25 | with: 26 | python-version: ${{ matrix.python-version }} 27 | - name: Install dependencies 28 | run: | 29 | python -m pip install --upgrade pip build 30 | python -m pip install flake8 pytest 31 | python -m build 32 | pip install -e . 33 | - name: Lint with flake8 34 | run: | 35 | # stop the build if there are Python syntax errors or undefined names 36 | flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics 37 | # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide 38 | flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics 39 | - name: Test with pytest 40 | run: | 41 | pytest 42 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # Byte-compiled / optimized / DLL files 2 | __pycache__/ 3 | *.py[cod] 4 | *$py.class 5 | 6 | # C extensions 7 | *.so 8 | 9 | # Distribution / packaging 10 | .Python 11 | build/ 12 | develop-eggs/ 13 | dist/ 14 | downloads/ 15 | eggs/ 16 | .eggs/ 17 | lib/ 18 | lib64/ 19 | parts/ 20 | sdist/ 21 | var/ 22 | wheels/ 23 | pip-wheel-metadata/ 24 | share/python-wheels/ 25 | *.egg-info/ 26 | .installed.cfg 27 | *.egg 28 | MANIFEST 29 | 30 | # PyInstaller 31 | # Usually these files are written by a python script from a template 32 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 33 | *.manifest 34 | *.spec 35 | 36 | # Installer logs 37 | pip-log.txt 38 | pip-delete-this-directory.txt 39 | 40 | # Unit test / coverage reports 41 | htmlcov/ 42 | .tox/ 43 | .nox/ 44 | .coverage 45 | .coverage.* 46 | .cache 47 | nosetests.xml 48 | coverage.xml 49 | *.cover 50 | *.py,cover 51 | .hypothesis/ 52 | .pytest_cache/ 53 | 54 | # Translations 55 | *.mo 56 | *.pot 57 | 58 | # Django stuff: 59 | *.log 60 | local_settings.py 61 | db.sqlite3 62 | db.sqlite3-journal 63 | 64 | # Flask stuff: 65 | instance/ 66 | .webassets-cache 67 | 68 | # Scrapy stuff: 69 | .scrapy 70 | 71 | # Sphinx documentation 72 | docs/_build/ 73 | 74 | # PyBuilder 75 | target/ 76 | 77 | # Jupyter Notebook 78 | .ipynb_checkpoints 79 | 80 | # IPython 81 | profile_default/ 82 | ipython_config.py 83 | 84 | # pyenv 85 | .python-version 86 | 87 | # pipenv 88 | # According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. 89 | # However, in case of collaboration, if having platform-specific dependencies or dependencies 90 | # having no cross-platform support, pipenv may install dependencies that don't work, or not 91 | # install all needed dependencies. 92 | #Pipfile.lock 93 | 94 | # PEP 582; used by e.g. github.com/David-OConnor/pyflow 95 | __pypackages__/ 96 | 97 | # Celery stuff 98 | celerybeat-schedule 99 | celerybeat.pid 100 | 101 | # SageMath parsed files 102 | *.sage.py 103 | 104 | # Environments 105 | .env 106 | .venv 107 | env/ 108 | venv/ 109 | ENV/ 110 | env.bak/ 111 | venv.bak/ 112 | 113 | # Spyder project settings 114 | .spyderproject 115 | .spyproject 116 | 117 | # Rope project settings 118 | .ropeproject 119 | 120 | # mkdocs documentation 121 | /site 122 | 123 | # mypy 124 | .mypy_cache/ 125 | .dmypy.json 126 | dmypy.json 127 | 128 | # Pyre type checker 129 | .pyre/ 130 | 131 | # Data files 132 | *.gz 133 | *.swp 134 | -------------------------------------------------------------------------------- /CHANGELOG.md: -------------------------------------------------------------------------------- 1 | # 0.0.10 - 2024-07-04 2 | 3 | - Migrate to hatch to ease development and include multiple authors. 4 | - Add @johnarevalo to the author list. 5 | 6 | # 0.0.9 - 2022-11-23 7 | 8 | - Stop excluding `README.md` from the build, because setup.py depends on this 9 | file. 10 | 11 | # 0.0.8 - 2022-11-22 12 | 13 | - Replace `scipy.cluster.vq.kmeans2` with the faster function 14 | `sklearn.cluster.KMeans`. Thanks to @johnarevalo for providing details about 15 | the running time with both functions in PR #20. 16 | 17 | # 0.0.6 - 2022-02-02 18 | 19 | - Replace `scipy.cluster.vq.kmeans` with `scipy.cluster.vq.kmeans2` to address 20 | issue #10 where we learned that kmeans does not always return k centroids, 21 | but kmeans2 does return k centroids. Thanks to @onionpork and @DennisPost10 22 | for reporting this. 23 | 24 | # 0.0.5 - 2020-08-11 25 | 26 | - Expose `max_iter_harmony` as a new top-level argument, in addition to the 27 | previously exposed `max_iter_kmeans`. This more closely resembles the 28 | original interface in the harmony R package. Thanks to @pinin4fjords 29 | for pull request #8 30 | 31 | # 0.0.4 - 2020-03-02 32 | 33 | - Fix a bug in the LISI code that sometimes causes computation to break. Thanks 34 | to @tariqdaouda for reporting it in issue #1 35 | 36 | - Fix a bug that prevents controlling the number of iterations. Thanks to 37 | @liboxun for reporting it in issue #3 38 | 39 | - Fix a bug causing slightly different results than expected. Thanks to 40 | @bli25broad for pull request #2 41 | 42 | - Add support for multiple categorical batch variables. 43 | 44 | # 0.0.3 - 2019-12-26 45 | 46 | - Speed up the Harmony algorithm. It should now be as fast as the R package. 47 | 48 | # 0.0.2 - 2019-12-20 49 | 50 | - Add Local Inverse Simpson Index (LISI) functions from the lisi R package. 51 | 52 | 53 | # 0.0.1 - 2019-12-19 54 | 55 | - Initial release. Code ported directly from the harmony R package. 56 | 57 | -------------------------------------------------------------------------------- /CONTRIBUTING.md: -------------------------------------------------------------------------------- 1 | We use [hatch] to develop harmonypy. 2 | 3 | Copy the harmonypy code to your computer: 4 | 5 | ``` 6 | git clone https://github.com/slowkow/harmonpy 7 | ``` 8 | 9 | Then change to the newly created directory: 10 | 11 | ``` 12 | cd harmonypy 13 | ``` 14 | 15 | Install hatch: 16 | 17 | ``` 18 | pipx install hatch 19 | ``` 20 | 21 | Create a new environment just for harmonypy: 22 | 23 | ``` 24 | hatch env create 25 | ``` 26 | 27 | Once we have hatch and an environment, then we can enter a new shell: 28 | 29 | ``` 30 | hatch shell 31 | ``` 32 | 33 | In this environment, we can run tests: 34 | 35 | ``` 36 | hatch test 37 | ``` 38 | 39 | And we can also build the files needed for PyPI: 40 | 41 | ``` 42 | hatch build 43 | ``` 44 | 45 | We should double-check that the contents of the `.tar.gz` file do not include any files we do not want to publish: 46 | 47 | ``` 48 | tar tvf dist/harmonypy-0.0.10.tar.gz 49 | -rw-r--r-- 0 0 0 97 Feb 1 2020 harmonypy-0.0.10/harmonypy/__init__.py 50 | -rw-r--r-- 0 0 0 12783 Feb 1 2020 harmonypy-0.0.10/harmonypy/harmony.py 51 | -rw-r--r-- 0 0 0 4559 Feb 1 2020 harmonypy-0.0.10/harmonypy/lisi.py 52 | -rw-r--r-- 0 0 0 1824 Feb 1 2020 harmonypy-0.0.10/.gitignore 53 | -rw-r--r-- 0 0 0 35149 Feb 1 2020 harmonypy-0.0.10/LICENSE 54 | -rw-r--r-- 0 0 0 3126 Feb 1 2020 harmonypy-0.0.10/README.md 55 | -rw-r--r-- 0 0 0 1026 Feb 1 2020 harmonypy-0.0.10/pyproject.toml 56 | ``` 57 | 58 | When we're ready, we can publish to PyPI: 59 | 60 | ``` 61 | hatch publish 62 | ``` 63 | 64 | [hatch]: https://hatch.pypa.io 65 | 66 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. By contrast, 15 | the GNU General Public License is intended to guarantee your freedom to 16 | share and change all versions of a program--to make sure it remains free 17 | software for all its users. We, the Free Software Foundation, use the 18 | GNU General Public License for most of our software; it applies also to 19 | any other work released this way by its authors. You can apply it to 20 | your programs, too. 21 | 22 | When we speak of free software, we are referring to freedom, not 23 | price. Our General Public Licenses are designed to make sure that you 24 | have the freedom to distribute copies of free software (and charge for 25 | them if you wish), that you receive source code or can get it if you 26 | want it, that you can change the software or use pieces of it in new 27 | free programs, and that you know you can do these things. 28 | 29 | To protect your rights, we need to prevent others from denying you 30 | these rights or asking you to surrender the rights. Therefore, you have 31 | certain responsibilities if you distribute copies of the software, or if 32 | you modify it: responsibilities to respect the freedom of others. 33 | 34 | For example, if you distribute copies of such a program, whether 35 | gratis or for a fee, you must pass on to the recipients the same 36 | freedoms that you received. You must make sure that they, too, receive 37 | or can get the source code. And you must show them these terms so they 38 | know their rights. 39 | 40 | Developers that use the GNU GPL protect your rights with two steps: 41 | (1) assert copyright on the software, and (2) offer you this License 42 | giving you legal permission to copy, distribute and/or modify it. 43 | 44 | For the developers' and authors' protection, the GPL clearly explains 45 | that there is no warranty for this free software. For both users' and 46 | authors' sake, the GPL requires that modified versions be marked as 47 | changed, so that their problems will not be attributed erroneously to 48 | authors of previous versions. 49 | 50 | Some devices are designed to deny users access to install or run 51 | modified versions of the software inside them, although the manufacturer 52 | can do so. This is fundamentally incompatible with the aim of 53 | protecting users' freedom to change the software. The systematic 54 | pattern of such abuse occurs in the area of products for individuals to 55 | use, which is precisely where it is most unacceptable. Therefore, we 56 | have designed this version of the GPL to prohibit the practice for those 57 | products. If such problems arise substantially in other domains, we 58 | stand ready to extend this provision to those domains in future versions 59 | of the GPL, as needed to protect the freedom of users. 60 | 61 | Finally, every program is threatened constantly by software patents. 62 | States should not allow patents to restrict development and use of 63 | software on general-purpose computers, but in those that do, we wish to 64 | avoid the special danger that patents applied to a free program could 65 | make it effectively proprietary. To prevent this, the GPL assures that 66 | patents cannot be used to render the program non-free. 67 | 68 | The precise terms and conditions for copying, distribution and 69 | modification follow. 70 | 71 | TERMS AND CONDITIONS 72 | 73 | 0. Definitions. 74 | 75 | "This License" refers to version 3 of the GNU General Public License. 76 | 77 | "Copyright" also means copyright-like laws that apply to other kinds of 78 | works, such as semiconductor masks. 79 | 80 | "The Program" refers to any copyrightable work licensed under this 81 | License. Each licensee is addressed as "you". "Licensees" and 82 | "recipients" may be individuals or organizations. 83 | 84 | To "modify" a work means to copy from or adapt all or part of the work 85 | in a fashion requiring copyright permission, other than the making of an 86 | exact copy. The resulting work is called a "modified version" of the 87 | earlier work or a work "based on" the earlier work. 88 | 89 | A "covered work" means either the unmodified Program or a work based 90 | on the Program. 91 | 92 | To "propagate" a work means to do anything with it that, without 93 | permission, would make you directly or secondarily liable for 94 | infringement under applicable copyright law, except executing it on a 95 | computer or modifying a private copy. Propagation includes copying, 96 | distribution (with or without modification), making available to the 97 | public, and in some countries other activities as well. 98 | 99 | To "convey" a work means any kind of propagation that enables other 100 | parties to make or receive copies. Mere interaction with a user through 101 | a computer network, with no transfer of a copy, is not conveying. 102 | 103 | An interactive user interface displays "Appropriate Legal Notices" 104 | to the extent that it includes a convenient and prominently visible 105 | feature that (1) displays an appropriate copyright notice, and (2) 106 | tells the user that there is no warranty for the work (except to the 107 | extent that warranties are provided), that licensees may convey the 108 | work under this License, and how to view a copy of this License. If 109 | the interface presents a list of user commands or options, such as a 110 | menu, a prominent item in the list meets this criterion. 111 | 112 | 1. Source Code. 113 | 114 | The "source code" for a work means the preferred form of the work 115 | for making modifications to it. "Object code" means any non-source 116 | form of a work. 117 | 118 | A "Standard Interface" means an interface that either is an official 119 | standard defined by a recognized standards body, or, in the case of 120 | interfaces specified for a particular programming language, one that 121 | is widely used among developers working in that language. 122 | 123 | The "System Libraries" of an executable work include anything, other 124 | than the work as a whole, that (a) is included in the normal form of 125 | packaging a Major Component, but which is not part of that Major 126 | Component, and (b) serves only to enable use of the work with that 127 | Major Component, or to implement a Standard Interface for which an 128 | implementation is available to the public in source code form. A 129 | "Major Component", in this context, means a major essential component 130 | (kernel, window system, and so on) of the specific operating system 131 | (if any) on which the executable work runs, or a compiler used to 132 | produce the work, or an object code interpreter used to run it. 133 | 134 | The "Corresponding Source" for a work in object code form means all 135 | the source code needed to generate, install, and (for an executable 136 | work) run the object code and to modify the work, including scripts to 137 | control those activities. However, it does not include the work's 138 | System Libraries, or general-purpose tools or generally available free 139 | programs which are used unmodified in performing those activities but 140 | which are not part of the work. For example, Corresponding Source 141 | includes interface definition files associated with source files for 142 | the work, and the source code for shared libraries and dynamically 143 | linked subprograms that the work is specifically designed to require, 144 | such as by intimate data communication or control flow between those 145 | subprograms and other parts of the work. 146 | 147 | The Corresponding Source need not include anything that users 148 | can regenerate automatically from other parts of the Corresponding 149 | Source. 150 | 151 | The Corresponding Source for a work in source code form is that 152 | same work. 153 | 154 | 2. Basic Permissions. 155 | 156 | All rights granted under this License are granted for the term of 157 | copyright on the Program, and are irrevocable provided the stated 158 | conditions are met. This License explicitly affirms your unlimited 159 | permission to run the unmodified Program. The output from running a 160 | covered work is covered by this License only if the output, given its 161 | content, constitutes a covered work. This License acknowledges your 162 | rights of fair use or other equivalent, as provided by copyright law. 163 | 164 | You may make, run and propagate covered works that you do not 165 | convey, without conditions so long as your license otherwise remains 166 | in force. You may convey covered works to others for the sole purpose 167 | of having them make modifications exclusively for you, or provide you 168 | with facilities for running those works, provided that you comply with 169 | the terms of this License in conveying all material for which you do 170 | not control copyright. Those thus making or running the covered works 171 | for you must do so exclusively on your behalf, under your direction 172 | and control, on terms that prohibit them from making any copies of 173 | your copyrighted material outside their relationship with you. 174 | 175 | Conveying under any other circumstances is permitted solely under 176 | the conditions stated below. Sublicensing is not allowed; section 10 177 | makes it unnecessary. 178 | 179 | 3. Protecting Users' Legal Rights From Anti-Circumvention Law. 180 | 181 | No covered work shall be deemed part of an effective technological 182 | measure under any applicable law fulfilling obligations under article 183 | 11 of the WIPO copyright treaty adopted on 20 December 1996, or 184 | similar laws prohibiting or restricting circumvention of such 185 | measures. 186 | 187 | When you convey a covered work, you waive any legal power to forbid 188 | circumvention of technological measures to the extent such circumvention 189 | is effected by exercising rights under this License with respect to 190 | the covered work, and you disclaim any intention to limit operation or 191 | modification of the work as a means of enforcing, against the work's 192 | users, your or third parties' legal rights to forbid circumvention of 193 | technological measures. 194 | 195 | 4. Conveying Verbatim Copies. 196 | 197 | You may convey verbatim copies of the Program's source code as you 198 | receive it, in any medium, provided that you conspicuously and 199 | appropriately publish on each copy an appropriate copyright notice; 200 | keep intact all notices stating that this License and any 201 | non-permissive terms added in accord with section 7 apply to the code; 202 | keep intact all notices of the absence of any warranty; and give all 203 | recipients a copy of this License along with the Program. 204 | 205 | You may charge any price or no price for each copy that you convey, 206 | and you may offer support or warranty protection for a fee. 207 | 208 | 5. Conveying Modified Source Versions. 209 | 210 | You may convey a work based on the Program, or the modifications to 211 | produce it from the Program, in the form of source code under the 212 | terms of section 4, provided that you also meet all of these conditions: 213 | 214 | a) The work must carry prominent notices stating that you modified 215 | it, and giving a relevant date. 216 | 217 | b) The work must carry prominent notices stating that it is 218 | released under this License and any conditions added under section 219 | 7. This requirement modifies the requirement in section 4 to 220 | "keep intact all notices". 221 | 222 | c) You must license the entire work, as a whole, under this 223 | License to anyone who comes into possession of a copy. This 224 | License will therefore apply, along with any applicable section 7 225 | additional terms, to the whole of the work, and all its parts, 226 | regardless of how they are packaged. This License gives no 227 | permission to license the work in any other way, but it does not 228 | invalidate such permission if you have separately received it. 229 | 230 | d) If the work has interactive user interfaces, each must display 231 | Appropriate Legal Notices; however, if the Program has interactive 232 | interfaces that do not display Appropriate Legal Notices, your 233 | work need not make them do so. 234 | 235 | A compilation of a covered work with other separate and independent 236 | works, which are not by their nature extensions of the covered work, 237 | and which are not combined with it such as to form a larger program, 238 | in or on a volume of a storage or distribution medium, is called an 239 | "aggregate" if the compilation and its resulting copyright are not 240 | used to limit the access or legal rights of the compilation's users 241 | beyond what the individual works permit. Inclusion of a covered work 242 | in an aggregate does not cause this License to apply to the other 243 | parts of the aggregate. 244 | 245 | 6. Conveying Non-Source Forms. 246 | 247 | You may convey a covered work in object code form under the terms 248 | of sections 4 and 5, provided that you also convey the 249 | machine-readable Corresponding Source under the terms of this License, 250 | in one of these ways: 251 | 252 | a) Convey the object code in, or embodied in, a physical product 253 | (including a physical distribution medium), accompanied by the 254 | Corresponding Source fixed on a durable physical medium 255 | customarily used for software interchange. 256 | 257 | b) Convey the object code in, or embodied in, a physical product 258 | (including a physical distribution medium), accompanied by a 259 | written offer, valid for at least three years and valid for as 260 | long as you offer spare parts or customer support for that product 261 | model, to give anyone who possesses the object code either (1) a 262 | copy of the Corresponding Source for all the software in the 263 | product that is covered by this License, on a durable physical 264 | medium customarily used for software interchange, for a price no 265 | more than your reasonable cost of physically performing this 266 | conveying of source, or (2) access to copy the 267 | Corresponding Source from a network server at no charge. 268 | 269 | c) Convey individual copies of the object code with a copy of the 270 | written offer to provide the Corresponding Source. This 271 | alternative is allowed only occasionally and noncommercially, and 272 | only if you received the object code with such an offer, in accord 273 | with subsection 6b. 274 | 275 | d) Convey the object code by offering access from a designated 276 | place (gratis or for a charge), and offer equivalent access to the 277 | Corresponding Source in the same way through the same place at no 278 | further charge. You need not require recipients to copy the 279 | Corresponding Source along with the object code. If the place to 280 | copy the object code is a network server, the Corresponding Source 281 | may be on a different server (operated by you or a third party) 282 | that supports equivalent copying facilities, provided you maintain 283 | clear directions next to the object code saying where to find the 284 | Corresponding Source. Regardless of what server hosts the 285 | Corresponding Source, you remain obligated to ensure that it is 286 | available for as long as needed to satisfy these requirements. 287 | 288 | e) Convey the object code using peer-to-peer transmission, provided 289 | you inform other peers where the object code and Corresponding 290 | Source of the work are being offered to the general public at no 291 | charge under subsection 6d. 292 | 293 | A separable portion of the object code, whose source code is excluded 294 | from the Corresponding Source as a System Library, need not be 295 | included in conveying the object code work. 296 | 297 | A "User Product" is either (1) a "consumer product", which means any 298 | tangible personal property which is normally used for personal, family, 299 | or household purposes, or (2) anything designed or sold for incorporation 300 | into a dwelling. In determining whether a product is a consumer product, 301 | doubtful cases shall be resolved in favor of coverage. For a particular 302 | product received by a particular user, "normally used" refers to a 303 | typical or common use of that class of product, regardless of the status 304 | of the particular user or of the way in which the particular user 305 | actually uses, or expects or is expected to use, the product. A product 306 | is a consumer product regardless of whether the product has substantial 307 | commercial, industrial or non-consumer uses, unless such uses represent 308 | the only significant mode of use of the product. 309 | 310 | "Installation Information" for a User Product means any methods, 311 | procedures, authorization keys, or other information required to install 312 | and execute modified versions of a covered work in that User Product from 313 | a modified version of its Corresponding Source. The information must 314 | suffice to ensure that the continued functioning of the modified object 315 | code is in no case prevented or interfered with solely because 316 | modification has been made. 317 | 318 | If you convey an object code work under this section in, or with, or 319 | specifically for use in, a User Product, and the conveying occurs as 320 | part of a transaction in which the right of possession and use of the 321 | User Product is transferred to the recipient in perpetuity or for a 322 | fixed term (regardless of how the transaction is characterized), the 323 | Corresponding Source conveyed under this section must be accompanied 324 | by the Installation Information. But this requirement does not apply 325 | if neither you nor any third party retains the ability to install 326 | modified object code on the User Product (for example, the work has 327 | been installed in ROM). 328 | 329 | The requirement to provide Installation Information does not include a 330 | requirement to continue to provide support service, warranty, or updates 331 | for a work that has been modified or installed by the recipient, or for 332 | the User Product in which it has been modified or installed. Access to a 333 | network may be denied when the modification itself materially and 334 | adversely affects the operation of the network or violates the rules and 335 | protocols for communication across the network. 336 | 337 | Corresponding Source conveyed, and Installation Information provided, 338 | in accord with this section must be in a format that is publicly 339 | documented (and with an implementation available to the public in 340 | source code form), and must require no special password or key for 341 | unpacking, reading or copying. 342 | 343 | 7. Additional Terms. 344 | 345 | "Additional permissions" are terms that supplement the terms of this 346 | License by making exceptions from one or more of its conditions. 347 | Additional permissions that are applicable to the entire Program shall 348 | be treated as though they were included in this License, to the extent 349 | that they are valid under applicable law. If additional permissions 350 | apply only to part of the Program, that part may be used separately 351 | under those permissions, but the entire Program remains governed by 352 | this License without regard to the additional permissions. 353 | 354 | When you convey a copy of a covered work, you may at your option 355 | remove any additional permissions from that copy, or from any part of 356 | it. (Additional permissions may be written to require their own 357 | removal in certain cases when you modify the work.) You may place 358 | additional permissions on material, added by you to a covered work, 359 | for which you have or can give appropriate copyright permission. 360 | 361 | Notwithstanding any other provision of this License, for material you 362 | add to a covered work, you may (if authorized by the copyright holders of 363 | that material) supplement the terms of this License with terms: 364 | 365 | a) Disclaiming warranty or limiting liability differently from the 366 | terms of sections 15 and 16 of this License; or 367 | 368 | b) Requiring preservation of specified reasonable legal notices or 369 | author attributions in that material or in the Appropriate Legal 370 | Notices displayed by works containing it; or 371 | 372 | c) Prohibiting misrepresentation of the origin of that material, or 373 | requiring that modified versions of such material be marked in 374 | reasonable ways as different from the original version; or 375 | 376 | d) Limiting the use for publicity purposes of names of licensors or 377 | authors of the material; or 378 | 379 | e) Declining to grant rights under trademark law for use of some 380 | trade names, trademarks, or service marks; or 381 | 382 | f) Requiring indemnification of licensors and authors of that 383 | material by anyone who conveys the material (or modified versions of 384 | it) with contractual assumptions of liability to the recipient, for 385 | any liability that these contractual assumptions directly impose on 386 | those licensors and authors. 387 | 388 | All other non-permissive additional terms are considered "further 389 | restrictions" within the meaning of section 10. If the Program as you 390 | received it, or any part of it, contains a notice stating that it is 391 | governed by this License along with a term that is a further 392 | restriction, you may remove that term. If a license document contains 393 | a further restriction but permits relicensing or conveying under this 394 | License, you may add to a covered work material governed by the terms 395 | of that license document, provided that the further restriction does 396 | not survive such relicensing or conveying. 397 | 398 | If you add terms to a covered work in accord with this section, you 399 | must place, in the relevant source files, a statement of the 400 | additional terms that apply to those files, or a notice indicating 401 | where to find the applicable terms. 402 | 403 | Additional terms, permissive or non-permissive, may be stated in the 404 | form of a separately written license, or stated as exceptions; 405 | the above requirements apply either way. 406 | 407 | 8. Termination. 408 | 409 | You may not propagate or modify a covered work except as expressly 410 | provided under this License. Any attempt otherwise to propagate or 411 | modify it is void, and will automatically terminate your rights under 412 | this License (including any patent licenses granted under the third 413 | paragraph of section 11). 414 | 415 | However, if you cease all violation of this License, then your 416 | license from a particular copyright holder is reinstated (a) 417 | provisionally, unless and until the copyright holder explicitly and 418 | finally terminates your license, and (b) permanently, if the copyright 419 | holder fails to notify you of the violation by some reasonable means 420 | prior to 60 days after the cessation. 421 | 422 | Moreover, your license from a particular copyright holder is 423 | reinstated permanently if the copyright holder notifies you of the 424 | violation by some reasonable means, this is the first time you have 425 | received notice of violation of this License (for any work) from that 426 | copyright holder, and you cure the violation prior to 30 days after 427 | your receipt of the notice. 428 | 429 | Termination of your rights under this section does not terminate the 430 | licenses of parties who have received copies or rights from you under 431 | this License. If your rights have been terminated and not permanently 432 | reinstated, you do not qualify to receive new licenses for the same 433 | material under section 10. 434 | 435 | 9. Acceptance Not Required for Having Copies. 436 | 437 | You are not required to accept this License in order to receive or 438 | run a copy of the Program. Ancillary propagation of a covered work 439 | occurring solely as a consequence of using peer-to-peer transmission 440 | to receive a copy likewise does not require acceptance. However, 441 | nothing other than this License grants you permission to propagate or 442 | modify any covered work. These actions infringe copyright if you do 443 | not accept this License. Therefore, by modifying or propagating a 444 | covered work, you indicate your acceptance of this License to do so. 445 | 446 | 10. Automatic Licensing of Downstream Recipients. 447 | 448 | Each time you convey a covered work, the recipient automatically 449 | receives a license from the original licensors, to run, modify and 450 | propagate that work, subject to this License. You are not responsible 451 | for enforcing compliance by third parties with this License. 452 | 453 | An "entity transaction" is a transaction transferring control of an 454 | organization, or substantially all assets of one, or subdividing an 455 | organization, or merging organizations. If propagation of a covered 456 | work results from an entity transaction, each party to that 457 | transaction who receives a copy of the work also receives whatever 458 | licenses to the work the party's predecessor in interest had or could 459 | give under the previous paragraph, plus a right to possession of the 460 | Corresponding Source of the work from the predecessor in interest, if 461 | the predecessor has it or can get it with reasonable efforts. 462 | 463 | You may not impose any further restrictions on the exercise of the 464 | rights granted or affirmed under this License. For example, you may 465 | not impose a license fee, royalty, or other charge for exercise of 466 | rights granted under this License, and you may not initiate litigation 467 | (including a cross-claim or counterclaim in a lawsuit) alleging that 468 | any patent claim is infringed by making, using, selling, offering for 469 | sale, or importing the Program or any portion of it. 470 | 471 | 11. Patents. 472 | 473 | A "contributor" is a copyright holder who authorizes use under this 474 | License of the Program or a work on which the Program is based. The 475 | work thus licensed is called the contributor's "contributor version". 476 | 477 | A contributor's "essential patent claims" are all patent claims 478 | owned or controlled by the contributor, whether already acquired or 479 | hereafter acquired, that would be infringed by some manner, permitted 480 | by this License, of making, using, or selling its contributor version, 481 | but do not include claims that would be infringed only as a 482 | consequence of further modification of the contributor version. For 483 | purposes of this definition, "control" includes the right to grant 484 | patent sublicenses in a manner consistent with the requirements of 485 | this License. 486 | 487 | Each contributor grants you a non-exclusive, worldwide, royalty-free 488 | patent license under the contributor's essential patent claims, to 489 | make, use, sell, offer for sale, import and otherwise run, modify and 490 | propagate the contents of its contributor version. 491 | 492 | In the following three paragraphs, a "patent license" is any express 493 | agreement or commitment, however denominated, not to enforce a patent 494 | (such as an express permission to practice a patent or covenant not to 495 | sue for patent infringement). To "grant" such a patent license to a 496 | party means to make such an agreement or commitment not to enforce a 497 | patent against the party. 498 | 499 | If you convey a covered work, knowingly relying on a patent license, 500 | and the Corresponding Source of the work is not available for anyone 501 | to copy, free of charge and under the terms of this License, through a 502 | publicly available network server or other readily accessible means, 503 | then you must either (1) cause the Corresponding Source to be so 504 | available, or (2) arrange to deprive yourself of the benefit of the 505 | patent license for this particular work, or (3) arrange, in a manner 506 | consistent with the requirements of this License, to extend the patent 507 | license to downstream recipients. "Knowingly relying" means you have 508 | actual knowledge that, but for the patent license, your conveying the 509 | covered work in a country, or your recipient's use of the covered work 510 | in a country, would infringe one or more identifiable patents in that 511 | country that you have reason to believe are valid. 512 | 513 | If, pursuant to or in connection with a single transaction or 514 | arrangement, you convey, or propagate by procuring conveyance of, a 515 | covered work, and grant a patent license to some of the parties 516 | receiving the covered work authorizing them to use, propagate, modify 517 | or convey a specific copy of the covered work, then the patent license 518 | you grant is automatically extended to all recipients of the covered 519 | work and works based on it. 520 | 521 | A patent license is "discriminatory" if it does not include within 522 | the scope of its coverage, prohibits the exercise of, or is 523 | conditioned on the non-exercise of one or more of the rights that are 524 | specifically granted under this License. You may not convey a covered 525 | work if you are a party to an arrangement with a third party that is 526 | in the business of distributing software, under which you make payment 527 | to the third party based on the extent of your activity of conveying 528 | the work, and under which the third party grants, to any of the 529 | parties who would receive the covered work from you, a discriminatory 530 | patent license (a) in connection with copies of the covered work 531 | conveyed by you (or copies made from those copies), or (b) primarily 532 | for and in connection with specific products or compilations that 533 | contain the covered work, unless you entered into that arrangement, 534 | or that patent license was granted, prior to 28 March 2007. 535 | 536 | Nothing in this License shall be construed as excluding or limiting 537 | any implied license or other defenses to infringement that may 538 | otherwise be available to you under applicable patent law. 539 | 540 | 12. No Surrender of Others' Freedom. 541 | 542 | If conditions are imposed on you (whether by court order, agreement or 543 | otherwise) that contradict the conditions of this License, they do not 544 | excuse you from the conditions of this License. If you cannot convey a 545 | covered work so as to satisfy simultaneously your obligations under this 546 | License and any other pertinent obligations, then as a consequence you may 547 | not convey it at all. For example, if you agree to terms that obligate you 548 | to collect a royalty for further conveying from those to whom you convey 549 | the Program, the only way you could satisfy both those terms and this 550 | License would be to refrain entirely from conveying the Program. 551 | 552 | 13. Use with the GNU Affero General Public License. 553 | 554 | Notwithstanding any other provision of this License, you have 555 | permission to link or combine any covered work with a work licensed 556 | under version 3 of the GNU Affero General Public License into a single 557 | combined work, and to convey the resulting work. The terms of this 558 | License will continue to apply to the part which is the covered work, 559 | but the special requirements of the GNU Affero General Public License, 560 | section 13, concerning interaction through a network will apply to the 561 | combination as such. 562 | 563 | 14. Revised Versions of this License. 564 | 565 | The Free Software Foundation may publish revised and/or new versions of 566 | the GNU General Public License from time to time. Such new versions will 567 | be similar in spirit to the present version, but may differ in detail to 568 | address new problems or concerns. 569 | 570 | Each version is given a distinguishing version number. If the 571 | Program specifies that a certain numbered version of the GNU General 572 | Public License "or any later version" applies to it, you have the 573 | option of following the terms and conditions either of that numbered 574 | version or of any later version published by the Free Software 575 | Foundation. If the Program does not specify a version number of the 576 | GNU General Public License, you may choose any version ever published 577 | by the Free Software Foundation. 578 | 579 | If the Program specifies that a proxy can decide which future 580 | versions of the GNU General Public License can be used, that proxy's 581 | public statement of acceptance of a version permanently authorizes you 582 | to choose that version for the Program. 583 | 584 | Later license versions may give you additional or different 585 | permissions. However, no additional obligations are imposed on any 586 | author or copyright holder as a result of your choosing to follow a 587 | later version. 588 | 589 | 15. Disclaimer of Warranty. 590 | 591 | THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY 592 | APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT 593 | HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY 594 | OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, 595 | THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR 596 | PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM 597 | IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF 598 | ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 599 | 600 | 16. Limitation of Liability. 601 | 602 | IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING 603 | WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS 604 | THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY 605 | GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE 606 | USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF 607 | DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD 608 | PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), 609 | EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF 610 | SUCH DAMAGES. 611 | 612 | 17. Interpretation of Sections 15 and 16. 613 | 614 | If the disclaimer of warranty and limitation of liability provided 615 | above cannot be given local legal effect according to their terms, 616 | reviewing courts shall apply local law that most closely approximates 617 | an absolute waiver of all civil liability in connection with the 618 | Program, unless a warranty or assumption of liability accompanies a 619 | copy of the Program in return for a fee. 620 | 621 | END OF TERMS AND CONDITIONS 622 | 623 | How to Apply These Terms to Your New Programs 624 | 625 | If you develop a new program, and you want it to be of the greatest 626 | possible use to the public, the best way to achieve this is to make it 627 | free software which everyone can redistribute and change under these terms. 628 | 629 | To do so, attach the following notices to the program. It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | 635 | Copyright (C) 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | include README.md 2 | prune data* 3 | prune tests* 4 | exclude MANIFEST.in 5 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | harmonypy 2 | ========= 3 | 4 | [![Latest PyPI Version][pb]][pypi] [![PyPI Downloads][db]][pypi] [![tests][gb]][yml] [![DOI](https://zenodo.org/badge/229105533.svg)](https://zenodo.org/badge/latestdoi/229105533) 5 | 6 | [gb]: https://github.com/slowkow/harmonypy/actions/workflows/python-package.yml/badge.svg 7 | [yml]: https://github.com/slowkow/harmonypy/actions/workflows/python-package.yml 8 | [pb]: https://img.shields.io/pypi/v/harmonypy.svg 9 | [pypi]: https://pypi.org/project/harmonypy/ 10 | 11 | [db]: https://img.shields.io/pypi/dm/harmonypy?label=pypi%20downloads 12 | 13 | Harmony is an algorithm for integrating multiple high-dimensional datasets. 14 | 15 | harmonypy is a port of the [harmony] R package by [Ilya Korsunsky]. 16 | 17 | Example 18 | ------- 19 | 20 |

21 | 22 |

23 | 24 | This animation shows the Harmony alignment of three single-cell RNA-seq datasets from different donors. 25 | 26 | [→ How to make this animation.](https://slowkow.com/notes/harmony-animation/) 27 | 28 | Installation 29 | ------------ 30 | 31 | This package has been tested with Python 3.7. 32 | 33 | Use [pip] to install: 34 | 35 | ```bash 36 | pip install harmonypy 37 | ``` 38 | 39 | Usage 40 | ----- 41 | 42 | Here is a brief example using the data that comes with the R package: 43 | 44 | ```python 45 | # Load data 46 | import pandas as pd 47 | 48 | meta_data = pd.read_csv("data/meta.tsv.gz", sep = "\t") 49 | vars_use = ['dataset'] 50 | 51 | # meta_data 52 | # 53 | # cell_id dataset nGene percent_mito cell_type 54 | # 0 half_TGAAATTGGTCTAG half 3664 0.017722 jurkat 55 | # 1 half_GCGATATGCTGATG half 3858 0.029228 t293 56 | # 2 half_ATTTCTCTCACTAG half 4049 0.015966 jurkat 57 | # 3 half_CGTAACGACGAGAG half 3443 0.020379 jurkat 58 | # 4 half_ACGCCTTGTTTACC half 2813 0.024774 t293 59 | # .. ... ... ... ... ... 60 | # 295 t293_TTACGTACGACACT t293 4152 0.033997 t293 61 | # 296 t293_TAGAATTGTTGGTG t293 3097 0.021769 t293 62 | # 297 t293_CGGATAACACCACA t293 3157 0.020411 t293 63 | # 298 t293_GGTACTGAGTCGAT t293 2685 0.027846 t293 64 | # 299 t293_ACGCTGCTTCTTAC t293 3513 0.021240 t293 65 | 66 | data_mat = pd.read_csv("data/pcs.tsv.gz", sep = "\t") 67 | data_mat = np.array(data_mat) 68 | 69 | # data_mat[:5,:5] 70 | # 71 | # array([[ 0.0071695 , -0.00552724, -0.0036281 , -0.00798025, 0.00028931], 72 | # [-0.011333 , 0.00022233, -0.00073589, -0.00192452, 0.0032624 ], 73 | # [ 0.0091214 , -0.00940727, -0.00106816, -0.0042749 , -0.00029096], 74 | # [ 0.00866286, -0.00514987, -0.0008989 , -0.00821785, -0.00126997], 75 | # [-0.00953977, 0.00222714, -0.00374373, -0.00028554, 0.00063737]]) 76 | 77 | # meta_data.shape # 300 cells, 5 variables 78 | # (300, 5) 79 | # 80 | # data_mat.shape # 300 cells, 20 PCs 81 | # (300, 20) 82 | 83 | # Run Harmony 84 | import harmonypy as hm 85 | ho = hm.run_harmony(data_mat, meta_data, vars_use) 86 | 87 | # Write the adjusted PCs to a new file. 88 | res = pd.DataFrame(ho.Z_corr) 89 | res.columns = ['X{}'.format(i + 1) for i in range(res.shape[1])] 90 | res.to_csv("data/adj.tsv.gz", sep = "\t", index = False) 91 | ``` 92 | 93 | [harmony]: https://github.com/immunogenomics/harmony 94 | [Ilya Korsunsky]: https://github.com/ilyakorsunsky 95 | [pip]: https://pip.readthedocs.io/ 96 | 97 | -------------------------------------------------------------------------------- /data/lisi_lisi.tsv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/slowkow/harmonypy/6daf80d794e65b0a4da2ccba8369b5eb4b3f5ca4/data/lisi_lisi.tsv.gz -------------------------------------------------------------------------------- /data/lisi_metadata.tsv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/slowkow/harmonypy/6daf80d794e65b0a4da2ccba8369b5eb4b3f5ca4/data/lisi_metadata.tsv.gz -------------------------------------------------------------------------------- /data/lisi_x.tsv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/slowkow/harmonypy/6daf80d794e65b0a4da2ccba8369b5eb4b3f5ca4/data/lisi_x.tsv.gz -------------------------------------------------------------------------------- /data/pbmc_3500_meta.tsv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/slowkow/harmonypy/6daf80d794e65b0a4da2ccba8369b5eb4b3f5ca4/data/pbmc_3500_meta.tsv.gz -------------------------------------------------------------------------------- /data/pbmc_3500_pcs.tsv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/slowkow/harmonypy/6daf80d794e65b0a4da2ccba8369b5eb4b3f5ca4/data/pbmc_3500_pcs.tsv.gz -------------------------------------------------------------------------------- /data/pbmc_3500_pcs_harmonized.tsv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/slowkow/harmonypy/6daf80d794e65b0a4da2ccba8369b5eb4b3f5ca4/data/pbmc_3500_pcs_harmonized.tsv.gz -------------------------------------------------------------------------------- /harmonypy/__init__.py: -------------------------------------------------------------------------------- 1 | from .harmony import Harmony, run_harmony 2 | from .lisi import compute_lisi 3 | 4 | __version__ = '0.0.10' 5 | -------------------------------------------------------------------------------- /harmonypy/harmony.py: -------------------------------------------------------------------------------- 1 | # harmonypy - A data alignment algorithm. 2 | # Copyright (C) 2018 Ilya Korsunsky 3 | # 2019 Kamil Slowikowski 4 | # 5 | # This program is free software: you can redistribute it and/or modify 6 | # it under the terms of the GNU General Public License as published by 7 | # the Free Software Foundation, either version 3 of the License, or 8 | # (at your option) any later version. 9 | # 10 | # This program is distributed in the hope that it will be useful, 11 | # but WITHOUT ANY WARRANTY; without even the implied warranty of 12 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 13 | # GNU General Public License for more details. 14 | # 15 | # You should have received a copy of the GNU General Public License 16 | # along with this program. If not, see . 17 | 18 | from functools import partial 19 | import pandas as pd 20 | import numpy as np 21 | from sklearn.cluster import KMeans 22 | import logging 23 | 24 | # create logger 25 | logger = logging.getLogger('harmonypy') 26 | logger.setLevel(logging.DEBUG) 27 | ch = logging.StreamHandler() 28 | ch.setLevel(logging.DEBUG) 29 | formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s') 30 | ch.setFormatter(formatter) 31 | logger.addHandler(ch) 32 | 33 | # from IPython.core.debugger import set_trace 34 | 35 | def run_harmony( 36 | data_mat: np.ndarray, 37 | meta_data: pd.DataFrame, 38 | vars_use, 39 | theta = None, 40 | lamb = None, 41 | sigma = 0.1, 42 | nclust = None, 43 | tau = 0, 44 | block_size = 0.05, 45 | max_iter_harmony = 10, 46 | max_iter_kmeans = 20, 47 | epsilon_cluster = 1e-5, 48 | epsilon_harmony = 1e-4, 49 | plot_convergence = False, 50 | verbose = True, 51 | reference_values = None, 52 | cluster_prior = None, 53 | random_state = 0, 54 | cluster_fn = 'kmeans' 55 | ): 56 | """Run Harmony. 57 | """ 58 | 59 | # theta = None 60 | # lamb = None 61 | # sigma = 0.1 62 | # nclust = None 63 | # tau = 0 64 | # block_size = 0.05 65 | # epsilon_cluster = 1e-5 66 | # epsilon_harmony = 1e-4 67 | # plot_convergence = False 68 | # verbose = True 69 | # reference_values = None 70 | # cluster_prior = None 71 | # random_state = 0 72 | # cluster_fn = 'kmeans'. Also accepts a callable object with data, num_clusters parameters 73 | 74 | N = meta_data.shape[0] 75 | if data_mat.shape[1] != N: 76 | data_mat = data_mat.T 77 | 78 | assert data_mat.shape[1] == N, \ 79 | "data_mat and meta_data do not have the same number of cells" 80 | 81 | if nclust is None: 82 | nclust = np.min([np.round(N / 30.0), 100]).astype(int) 83 | 84 | if type(sigma) is float and nclust > 1: 85 | sigma = np.repeat(sigma, nclust) 86 | 87 | if isinstance(vars_use, str): 88 | vars_use = [vars_use] 89 | 90 | phi = pd.get_dummies(meta_data[vars_use]).to_numpy().T 91 | phi_n = meta_data[vars_use].describe().loc['unique'].to_numpy().astype(int) 92 | 93 | if theta is None: 94 | theta = np.repeat([1] * len(phi_n), phi_n) 95 | elif isinstance(theta, float) or isinstance(theta, int): 96 | theta = np.repeat([theta] * len(phi_n), phi_n) 97 | elif len(theta) == len(phi_n): 98 | theta = np.repeat([theta], phi_n) 99 | 100 | assert len(theta) == np.sum(phi_n), \ 101 | "each batch variable must have a theta" 102 | 103 | if lamb is None: 104 | lamb = np.repeat([1] * len(phi_n), phi_n) 105 | elif isinstance(lamb, float) or isinstance(lamb, int): 106 | lamb = np.repeat([lamb] * len(phi_n), phi_n) 107 | elif len(lamb) == len(phi_n): 108 | lamb = np.repeat([lamb], phi_n) 109 | 110 | assert len(lamb) == np.sum(phi_n), \ 111 | "each batch variable must have a lambda" 112 | 113 | # Number of items in each category. 114 | N_b = phi.sum(axis = 1) 115 | # Proportion of items in each category. 116 | Pr_b = N_b / N 117 | 118 | if tau > 0: 119 | theta = theta * (1 - np.exp(-(N_b / (nclust * tau)) ** 2)) 120 | 121 | lamb_mat = np.diag(np.insert(lamb, 0, 0)) 122 | 123 | phi_moe = np.vstack((np.repeat(1, N), phi)) 124 | 125 | np.random.seed(random_state) 126 | 127 | ho = Harmony( 128 | data_mat, phi, phi_moe, Pr_b, sigma, theta, max_iter_harmony, max_iter_kmeans, 129 | epsilon_cluster, epsilon_harmony, nclust, block_size, lamb_mat, verbose, 130 | random_state, cluster_fn 131 | ) 132 | 133 | return ho 134 | 135 | class Harmony(object): 136 | def __init__( 137 | self, Z, Phi, Phi_moe, Pr_b, sigma, 138 | theta, max_iter_harmony, max_iter_kmeans, 139 | epsilon_kmeans, epsilon_harmony, K, block_size, 140 | lamb, verbose, random_state=None, cluster_fn='kmeans' 141 | ): 142 | self.Z_corr = np.array(Z) 143 | self.Z_orig = np.array(Z) 144 | 145 | self.Z_cos = self.Z_orig / self.Z_orig.max(axis=0) 146 | self.Z_cos = self.Z_cos / np.linalg.norm(self.Z_cos, ord=2, axis=0) 147 | 148 | self.Phi = Phi 149 | self.Phi_moe = Phi_moe 150 | self.N = self.Z_corr.shape[1] 151 | self.Pr_b = Pr_b 152 | self.B = self.Phi.shape[0] # number of batch variables 153 | self.d = self.Z_corr.shape[0] 154 | self.window_size = 3 155 | self.epsilon_kmeans = epsilon_kmeans 156 | self.epsilon_harmony = epsilon_harmony 157 | 158 | self.lamb = lamb 159 | self.sigma = sigma 160 | self.sigma_prior = sigma 161 | self.block_size = block_size 162 | self.K = K # number of clusters 163 | self.max_iter_harmony = max_iter_harmony 164 | self.max_iter_kmeans = max_iter_kmeans 165 | self.verbose = verbose 166 | self.theta = theta 167 | 168 | self.objective_harmony = [] 169 | self.objective_kmeans = [] 170 | self.objective_kmeans_dist = [] 171 | self.objective_kmeans_entropy = [] 172 | self.objective_kmeans_cross = [] 173 | self.kmeans_rounds = [] 174 | 175 | self.allocate_buffers() 176 | if cluster_fn == 'kmeans': 177 | cluster_fn = partial(Harmony._cluster_kmeans, random_state=random_state) 178 | self.init_cluster(cluster_fn) 179 | self.harmonize(self.max_iter_harmony, self.verbose) 180 | 181 | def result(self): 182 | return self.Z_corr 183 | 184 | def allocate_buffers(self): 185 | self._scale_dist = np.zeros((self.K, self.N)) 186 | self.dist_mat = np.zeros((self.K, self.N)) 187 | self.O = np.zeros((self.K, self.B)) 188 | self.E = np.zeros((self.K, self.B)) 189 | self.W = np.zeros((self.B + 1, self.d)) 190 | self.Phi_Rk = np.zeros((self.B + 1, self.N)) 191 | 192 | @staticmethod 193 | def _cluster_kmeans(data, K, random_state): 194 | # Start with cluster centroids 195 | logger.info("Computing initial centroids with sklearn.KMeans...") 196 | model = KMeans(n_clusters=K, init='k-means++', 197 | n_init=10, max_iter=25, random_state=random_state) 198 | model.fit(data) 199 | km_centroids, km_labels = model.cluster_centers_, model.labels_ 200 | logger.info("sklearn.KMeans initialization complete.") 201 | return km_centroids 202 | 203 | def init_cluster(self, cluster_fn): 204 | self.Y = cluster_fn(self.Z_cos.T, self.K).T 205 | # (1) Normalize 206 | self.Y = self.Y / np.linalg.norm(self.Y, ord=2, axis=0) 207 | # (2) Assign cluster probabilities 208 | self.dist_mat = 2 * (1 - np.dot(self.Y.T, self.Z_cos)) 209 | self.R = -self.dist_mat 210 | self.R = self.R / self.sigma[:,None] 211 | self.R -= np.max(self.R, axis = 0) 212 | self.R = np.exp(self.R) 213 | self.R = self.R / np.sum(self.R, axis = 0) 214 | # (3) Batch diversity statistics 215 | self.E = np.outer(np.sum(self.R, axis=1), self.Pr_b) 216 | self.O = np.inner(self.R , self.Phi) 217 | self.compute_objective() 218 | # Save results 219 | self.objective_harmony.append(self.objective_kmeans[-1]) 220 | 221 | def compute_objective(self): 222 | kmeans_error = np.sum(np.multiply(self.R, self.dist_mat)) 223 | # Entropy 224 | _entropy = np.sum(safe_entropy(self.R) * self.sigma[:,np.newaxis]) 225 | # Cross Entropy 226 | x = (self.R * self.sigma[:,np.newaxis]) 227 | y = np.tile(self.theta[:,np.newaxis], self.K).T 228 | z = np.log((self.O + 1) / (self.E + 1)) 229 | w = np.dot(y * z, self.Phi) 230 | _cross_entropy = np.sum(x * w) 231 | # Save results 232 | self.objective_kmeans.append(kmeans_error + _entropy + _cross_entropy) 233 | self.objective_kmeans_dist.append(kmeans_error) 234 | self.objective_kmeans_entropy.append(_entropy) 235 | self.objective_kmeans_cross.append(_cross_entropy) 236 | 237 | def harmonize(self, iter_harmony=10, verbose=True): 238 | converged = False 239 | for i in range(1, iter_harmony + 1): 240 | if verbose: 241 | logger.info("Iteration {} of {}".format(i, iter_harmony)) 242 | # STEP 1: Clustering 243 | self.cluster() 244 | # STEP 2: Regress out covariates 245 | # self.moe_correct_ridge() 246 | self.Z_cos, self.Z_corr, self.W, self.Phi_Rk = moe_correct_ridge( 247 | self.Z_orig, self.Z_cos, self.Z_corr, self.R, self.W, self.K, 248 | self.Phi_Rk, self.Phi_moe, self.lamb 249 | ) 250 | # STEP 3: Check for convergence 251 | converged = self.check_convergence(1) 252 | if converged: 253 | if verbose: 254 | logger.info( 255 | "Converged after {} iteration{}" 256 | .format(i, 's' if i > 1 else '') 257 | ) 258 | break 259 | if verbose and not converged: 260 | logger.info("Stopped before convergence") 261 | return 0 262 | 263 | def cluster(self): 264 | # Z_cos has changed 265 | # R is assumed to not have changed 266 | # Update Y to match new integrated data 267 | self.dist_mat = 2 * (1 - np.dot(self.Y.T, self.Z_cos)) 268 | for i in range(self.max_iter_kmeans): 269 | # print("kmeans {}".format(i)) 270 | # STEP 1: Update Y 271 | self.Y = np.dot(self.Z_cos, self.R.T) 272 | self.Y = self.Y / np.linalg.norm(self.Y, ord=2, axis=0) 273 | # STEP 2: Update dist_mat 274 | self.dist_mat = 2 * (1 - np.dot(self.Y.T, self.Z_cos)) 275 | # STEP 3: Update R 276 | self.update_R() 277 | # STEP 4: Check for convergence 278 | self.compute_objective() 279 | if i > self.window_size: 280 | converged = self.check_convergence(0) 281 | if converged: 282 | break 283 | self.kmeans_rounds.append(i) 284 | self.objective_harmony.append(self.objective_kmeans[-1]) 285 | return 0 286 | 287 | def update_R(self): 288 | self._scale_dist = -self.dist_mat 289 | self._scale_dist = self._scale_dist / self.sigma[:,None] 290 | self._scale_dist -= np.max(self._scale_dist, axis=0) 291 | self._scale_dist = np.exp(self._scale_dist) 292 | # Update cells in blocks 293 | update_order = np.arange(self.N) 294 | np.random.shuffle(update_order) 295 | n_blocks = np.ceil(1 / self.block_size).astype(int) 296 | blocks = np.array_split(update_order, n_blocks) 297 | for b in blocks: 298 | # STEP 1: Remove cells 299 | self.E -= np.outer(np.sum(self.R[:,b], axis=1), self.Pr_b) 300 | self.O -= np.dot(self.R[:,b], self.Phi[:,b].T) 301 | # STEP 2: Recompute R for removed cells 302 | self.R[:,b] = self._scale_dist[:,b] 303 | self.R[:,b] = np.multiply( 304 | self.R[:,b], 305 | np.dot( 306 | np.power((self.E + 1) / (self.O + 1), self.theta), 307 | self.Phi[:,b] 308 | ) 309 | ) 310 | self.R[:,b] = self.R[:,b] / np.linalg.norm(self.R[:,b], ord=1, axis=0) 311 | # STEP 3: Put cells back 312 | self.E += np.outer(np.sum(self.R[:,b], axis=1), self.Pr_b) 313 | self.O += np.dot(self.R[:,b], self.Phi[:,b].T) 314 | return 0 315 | 316 | def check_convergence(self, i_type): 317 | obj_old = 0.0 318 | obj_new = 0.0 319 | # Clustering, compute new window mean 320 | if i_type == 0: 321 | okl = len(self.objective_kmeans) 322 | for i in range(self.window_size): 323 | obj_old += self.objective_kmeans[okl - 2 - i] 324 | obj_new += self.objective_kmeans[okl - 1 - i] 325 | if abs(obj_old - obj_new) / abs(obj_old) < self.epsilon_kmeans: 326 | return True 327 | return False 328 | # Harmony 329 | if i_type == 1: 330 | obj_old = self.objective_harmony[-2] 331 | obj_new = self.objective_harmony[-1] 332 | if (obj_old - obj_new) / abs(obj_old) < self.epsilon_harmony: 333 | return True 334 | return False 335 | return True 336 | 337 | 338 | def safe_entropy(x: np.array): 339 | y = np.multiply(x, np.log(x)) 340 | y[~np.isfinite(y)] = 0.0 341 | return y 342 | 343 | def moe_correct_ridge(Z_orig, Z_cos, Z_corr, R, W, K, Phi_Rk, Phi_moe, lamb): 344 | Z_corr = Z_orig.copy() 345 | for i in range(K): 346 | Phi_Rk = np.multiply(Phi_moe, R[i,:]) 347 | x = np.dot(Phi_Rk, Phi_moe.T) + lamb 348 | W = np.dot(np.dot(np.linalg.inv(x), Phi_Rk), Z_orig.T) 349 | W[0,:] = 0 # do not remove the intercept 350 | Z_corr -= np.dot(W.T, Phi_Rk) 351 | Z_cos = Z_corr / np.linalg.norm(Z_corr, ord=2, axis=0) 352 | return Z_cos, Z_corr, W, Phi_Rk 353 | 354 | -------------------------------------------------------------------------------- /harmonypy/lisi.py: -------------------------------------------------------------------------------- 1 | # LISI - The Local Inverse Simpson Index 2 | # Copyright (C) 2018 Ilya Korsunsky 3 | # 2019 Kamil Slowikowski 4 | # 5 | # This program is free software: you can redistribute it and/or modify 6 | # it under the terms of the GNU General Public License as published by 7 | # the Free Software Foundation, either version 3 of the License, or 8 | # (at your option) any later version. 9 | # 10 | # This program is distributed in the hope that it will be useful, 11 | # but WITHOUT ANY WARRANTY; without even the implied warranty of 12 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 13 | # GNU General Public License for more details. 14 | # 15 | # You should have received a copy of the GNU General Public License 16 | # along with this program. If not, see . 17 | 18 | import numpy as np 19 | import pandas as pd 20 | from sklearn.neighbors import NearestNeighbors 21 | from typing import Iterable 22 | 23 | 24 | def compute_lisi( 25 | X: np.array, 26 | metadata: pd.DataFrame, 27 | label_colnames: Iterable[str], 28 | perplexity: float=30 29 | ): 30 | """Compute the Local Inverse Simpson Index (LISI) for each column in metadata. 31 | 32 | LISI is a statistic computed for each item (row) in the data matrix X. 33 | 34 | The following example may help to interpret the LISI values. 35 | 36 | Suppose one of the columns in metadata is a categorical variable with 3 categories. 37 | 38 | - If LISI is approximately equal to 3 for an item in the data matrix, 39 | that means that the item is surrounded by neighbors from all 3 40 | categories. 41 | 42 | - If LISI is approximately equal to 1, then the item is surrounded by 43 | neighbors from 1 category. 44 | 45 | The LISI statistic is useful to evaluate whether multiple datasets are 46 | well-integrated by algorithms such as Harmony [1]. 47 | 48 | [1]: Korsunsky et al. 2019 doi: 10.1038/s41592-019-0619-0 49 | """ 50 | n_cells = metadata.shape[0] 51 | n_labels = len(label_colnames) 52 | # We need at least 3 * n_neigbhors to compute the perplexity 53 | knn = NearestNeighbors(n_neighbors = perplexity * 3, algorithm = 'kd_tree').fit(X) 54 | distances, indices = knn.kneighbors(X) 55 | # Don't count yourself 56 | indices = indices[:,1:] 57 | distances = distances[:,1:] 58 | # Save the result 59 | lisi_df = np.zeros((n_cells, n_labels)) 60 | for i, label in enumerate(label_colnames): 61 | labels = pd.Categorical(metadata[label]) 62 | n_categories = len(labels.categories) 63 | simpson = compute_simpson(distances.T, indices.T, labels, n_categories, perplexity) 64 | lisi_df[:,i] = 1 / simpson 65 | return lisi_df 66 | 67 | 68 | def compute_simpson( 69 | distances: np.ndarray, 70 | indices: np.ndarray, 71 | labels: pd.Categorical, 72 | n_categories: int, 73 | perplexity: float, 74 | tol: float=1e-5 75 | ): 76 | n = distances.shape[1] 77 | P = np.zeros(distances.shape[0]) 78 | simpson = np.zeros(n) 79 | logU = np.log(perplexity) 80 | # Loop through each cell. 81 | for i in range(n): 82 | beta = 1 83 | betamin = -np.inf 84 | betamax = np.inf 85 | # Compute Hdiff 86 | P = np.exp(-distances[:,i] * beta) 87 | P_sum = np.sum(P) 88 | if P_sum == 0: 89 | H = 0 90 | P = np.zeros(distances.shape[0]) 91 | else: 92 | H = np.log(P_sum) + beta * np.sum(distances[:,i] * P) / P_sum 93 | P = P / P_sum 94 | Hdiff = H - logU 95 | n_tries = 50 96 | for t in range(n_tries): 97 | # Stop when we reach the tolerance 98 | if abs(Hdiff) < tol: 99 | break 100 | # Update beta 101 | if Hdiff > 0: 102 | betamin = beta 103 | if not np.isfinite(betamax): 104 | beta *= 2 105 | else: 106 | beta = (beta + betamax) / 2 107 | else: 108 | betamax = beta 109 | if not np.isfinite(betamin): 110 | beta /= 2 111 | else: 112 | beta = (beta + betamin) / 2 113 | # Compute Hdiff 114 | P = np.exp(-distances[:,i] * beta) 115 | P_sum = np.sum(P) 116 | if P_sum == 0: 117 | H = 0 118 | P = np.zeros(distances.shape[0]) 119 | else: 120 | H = np.log(P_sum) + beta * np.sum(distances[:,i] * P) / P_sum 121 | P = P / P_sum 122 | Hdiff = H - logU 123 | # distancesefault value 124 | if H == 0: 125 | simpson[i] = -1 126 | # Simpson's index 127 | for label_category in labels.categories: 128 | ix = indices[:,i] 129 | q = labels[ix] == label_category 130 | if np.any(q): 131 | P_sum = np.sum(P[q]) 132 | simpson[i] += P_sum * P_sum 133 | return simpson 134 | 135 | -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- 1 | [build-system] 2 | requires = ["hatchling"] 3 | build-backend = "hatchling.build" 4 | 5 | [project] 6 | name = "harmonypy" 7 | dynamic = ["version"] 8 | description = "A data integration algorithm." 9 | readme = "README.md" 10 | license = "" 11 | requires-python = ">=3.6" 12 | authors = [ 13 | { name = "Kamil Slowikowski", orcid = "0000-0002-2843-6370", email = "kslowikowski@gmail.com" }, 14 | { name = "John Arevalo", orcid = "0000-0002-1138-5036", email = "johnarevalo@gmail.com" } 15 | ] 16 | classifiers = [ 17 | "Development Status :: 3 - Alpha", 18 | "Intended Audience :: Science/Research", 19 | "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)", 20 | "Natural Language :: English", 21 | "Operating System :: OS Independent", 22 | "Programming Language :: Python :: 3", 23 | "Topic :: Scientific/Engineering :: Bio-Informatics", 24 | ] 25 | dependencies = [ 26 | "numpy", 27 | "pandas", 28 | "scikit-learn", 29 | "scipy", 30 | ] 31 | 32 | [project.urls] 33 | Homepage = "https://github.com/slowkow/harmonypy" 34 | 35 | [tool.hatch.version] 36 | path = "harmonypy/__init__.py" 37 | 38 | [tool.hatch.build.targets.sdist] 39 | include = [ 40 | "/harmonypy", 41 | ] 42 | 43 | [tool.hatch.envs.test] 44 | dependencies = [ 45 | "pytest" 46 | ] 47 | -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/slowkow/harmonypy/6daf80d794e65b0a4da2ccba8369b5eb4b3f5ca4/tests/__init__.py -------------------------------------------------------------------------------- /tests/test_harmony.py: -------------------------------------------------------------------------------- 1 | # vprof -c p tests/test_harmony.py 2 | from time import time 3 | 4 | import numpy as np 5 | import pandas as pd 6 | from scipy.cluster.vq import kmeans2 7 | from scipy.stats import pearsonr 8 | import sys 9 | 10 | import harmonypy as hm 11 | 12 | 13 | def test_run_harmony(): 14 | 15 | meta_data = pd.read_csv("data/pbmc_3500_meta.tsv.gz", sep="\t") 16 | data_mat = pd.read_csv("data/pbmc_3500_pcs.tsv.gz", sep="\t") 17 | 18 | start = time() 19 | ho = hm.run_harmony(data_mat, meta_data, ['donor']) 20 | end = time() 21 | print("{:.2f} seconds elapsed".format(end - start)) 22 | 23 | res = pd.DataFrame(ho.Z_corr).T 24 | res.columns = ['PC{}'.format(i + 1) for i in range(res.shape[1])] 25 | # res.to_csv("data/pbmc_3500_pcs_harmonized_python.tsv.gz", sep = "\t", index = False) 26 | 27 | harm = pd.read_csv("data/pbmc_3500_pcs_harmonized.tsv.gz", sep="\t") 28 | 29 | cors = [] 30 | for i in range(res.shape[1]): 31 | cors.append(pearsonr(res.iloc[:, i].values, harm.iloc[:, i].values)) 32 | print([np.round(x[0], 3) for x in cors]) 33 | 34 | # Correlation between test PCs and observed PCs is high 35 | assert np.all(np.array([x[0] for x in cors]) >= 0.9) 36 | 37 | 38 | def test_random_seed(): 39 | meta_data = pd.read_csv("data/pbmc_3500_meta.tsv.gz", sep="\t") 40 | data_mat = pd.read_csv("data/pbmc_3500_pcs.tsv.gz", sep="\t") 41 | 42 | def run(random_state): 43 | ho = hm.run_harmony(data_mat, 44 | meta_data, ['donor'], 45 | max_iter_harmony=2, 46 | max_iter_kmeans=2, 47 | random_state=random_state) 48 | return ho.Z_corr 49 | 50 | # Assert same results when random_state is set. 51 | np.testing.assert_allclose(run(42), run(42)) 52 | 53 | # Assert different values when random_state is None. Absolute differences 54 | # in multiple runs are usually > 2000 55 | assert np.abs(run(None) - run(None)).sum() > 1000 56 | 57 | 58 | def test_cluster_fn(): 59 | meta_data = pd.read_csv("data/pbmc_3500_meta.tsv.gz", sep="\t") 60 | data_mat = pd.read_csv("data/pbmc_3500_pcs.tsv.gz", sep="\t") 61 | 62 | if sys.version_info.major == 3 and sys.version_info.minor == 6: 63 | return 64 | 65 | def cluster_fn(data, K): 66 | centroid, label = kmeans2(data, K, minit='++', seed=0) 67 | return centroid 68 | 69 | def run(cluster_fn): 70 | ho = hm.run_harmony(data_mat, 71 | meta_data, ['donor'], 72 | max_iter_harmony=2, 73 | max_iter_kmeans=2, 74 | cluster_fn=cluster_fn) 75 | return ho.Z_corr 76 | 77 | # Assert same results when random_state is set. 78 | np.testing.assert_equal(run(cluster_fn), run(cluster_fn)) 79 | 80 | -------------------------------------------------------------------------------- /tests/test_lisi.py: -------------------------------------------------------------------------------- 1 | import harmonypy as hm 2 | import pandas as pd 3 | import numpy as np 4 | 5 | def test_lisi(): 6 | 7 | X = pd.read_csv("data/lisi_x.tsv.gz", sep = "\t") 8 | metadata = pd.read_csv("data/lisi_metadata.tsv.gz", sep = "\t") 9 | label_colnames = metadata.columns 10 | perplexity = 30 11 | 12 | lisi = hm.compute_lisi(X, metadata, label_colnames, perplexity) 13 | 14 | lisi_test = pd.read_csv("data/lisi_lisi.tsv.gz", sep="\t") 15 | lisi_test = lisi_test.iloc[:,-2:].to_numpy() 16 | 17 | assert np.allclose(lisi, lisi_test) 18 | 19 | # def timereps(reps, func): 20 | # from time import time 21 | # start = time() 22 | # for i in range(0, reps): 23 | # func() 24 | # end = time() 25 | # return (end - start) / reps 26 | # 27 | # # 0.3 seconds per loop (too slow) 28 | # timereps(10, lambda: hm.compute_lisi(X, metadata, label_colnames, perplexity)) 29 | # 30 | # 31 | # # Try https://github.com/rkern/line_profiler 32 | --------------------------------------------------------------------------------