From 9cce50797c8220cca45894f243d0df227698d468 Mon Sep 17 00:00:00 2001 From: Ross DeVito Date: Mon, 21 Aug 2023 17:58:53 -0700 Subject: [PATCH 01/26] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 19ab5c5..ed7be28 100644 --- a/README.md +++ b/README.md @@ -17,6 +17,6 @@ CITRUS, the CIs and Trans inteRaction nUmerical Simulator, is a tool for simulat ```bash git clone https://github.com/gymrek-lab/CITRUS.git -cd CITRUS/ +cd CITRUS pip install . ``` From 010c0733c648492d6da1443a56aec596d48e584c Mon Sep 17 00:00:00 2001 From: Ross DeVito Date: Tue, 29 Aug 2023 13:01:26 -0700 Subject: [PATCH 02/26] Update designing_simulations.md --- doc/designing_simulations.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/designing_simulations.md b/doc/designing_simulations.md index bf1ba7c..08f63bb 100644 --- a/doc/designing_simulations.md +++ b/doc/designing_simulations.md @@ -2,4 +2,5 @@ ## Examples: - * [Linear Additive Phenotype](example_nbs/linear_additive_pheno.ipynb) \ No newline at end of file + * [Linear Additive Phenotype](example_nbs/linear_additive_pheno.ipynb) + * [Complex Phenotype Example 1](example_nbs/complex_pheno_1.ipynb) From cb8d7672f0ee136e12c8e6673c044b46a6fba1b4 Mon Sep 17 00:00:00 2001 From: Ross DeVito Date: Mon, 30 Oct 2023 14:25:46 -0700 Subject: [PATCH 03/26] Update user_guide.md --- doc/user_guide.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/user_guide.md b/doc/user_guide.md index 679e628..2201145 100644 --- a/doc/user_guide.md +++ b/doc/user_guide.md @@ -1,6 +1,6 @@ # CITRUS User Guide -CITRUS, the CIs and Trans inteRaction nUmerical Simulator, is a tool for simulating phenotypes with complex genetic archetectures that go beyond simple models that assume linear, additive contributions of individual SNPs. The goal of this tool is to provide better simulations for benchmarking GWAS/PRS models. +CITRUS, the CIs and Trans inteRaction nUmerical Simulator, is a tool for simulating phenotypes with complex genetic architectures that go beyond simple models that assume linear, additive contributions of individual SNPs. The goal of this tool is to provide better simulations for benchmarking GWAS/PRS models. In CITRUS, simulations are defined by a directed tree-like graph. The directed graph is composed of input nodes, representing genetic variants, and operator nodes, which represent intermediate operations and their resulting values. The edges represent the flow of values from the input nodes to the final operator node, whose resulting value represents the phenotype being simulated. From ee9ec38cb113621fdc5e866ae5d3fd0a1541041a Mon Sep 17 00:00:00 2001 From: Ross DeVito Date: Wed, 12 Jun 2024 22:24:56 -0700 Subject: [PATCH 04/26] Update __init__.py to import shap --- pheno_sim/__init__.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/pheno_sim/__init__.py b/pheno_sim/__init__.py index 0abdcdd..7155733 100644 --- a/pheno_sim/__init__.py +++ b/pheno_sim/__init__.py @@ -16,4 +16,6 @@ from . import heritability_estimation -from . import design_utils \ No newline at end of file +from . import design_utils + +from . import shap From 3ac28aad525a5658cefd95a22e1950c3c0ba55e4 Mon Sep 17 00:00:00 2001 From: RossDeVito Date: Thu, 13 Jun 2024 14:06:42 -0700 Subject: [PATCH 05/26] Start adding filter for which samples to include with SHAP --- cl_tool/cli.py | 2 +- pheno_sim/shap/run_shap.py | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/cl_tool/cli.py b/cl_tool/cli.py index 7da728b..87a0338 100644 --- a/cl_tool/cli.py +++ b/cl_tool/cli.py @@ -231,7 +231,7 @@ def shap( save_config_path: str ): """ - Computes the local and global shapley values of a model. + Computes the local shapley values of a model. """ from pheno_sim import PhenoSimulation from pheno_sim.shap import run_SHAP diff --git a/pheno_sim/shap/run_shap.py b/pheno_sim/shap/run_shap.py index fc2d566..77c1c2f 100644 --- a/pheno_sim/shap/run_shap.py +++ b/pheno_sim/shap/run_shap.py @@ -42,6 +42,8 @@ def run_SHAP( simulation.run_input_step() ) + print(input_df.head()) + # Create SHAP wrapper shap_wrapper = SHAPWrapper(simulation, phenotype, input_df.columns) From bc9dc0ec0ba53921d3136c0e3ed5d1a60566186e Mon Sep 17 00:00:00 2001 From: RossDeVito Date: Thu, 13 Jun 2024 15:19:19 -0700 Subject: [PATCH 06/26] Add sample id subsetting to SHAP --- cl_tool/cli.py | 18 +++++++++++++++++- pheno_sim/shap/run_shap.py | 27 ++++++++++++++++++++------- 2 files changed, 37 insertions(+), 8 deletions(-) diff --git a/cl_tool/cli.py b/cl_tool/cli.py index 87a0338..639112d 100644 --- a/cl_tool/cli.py +++ b/cl_tool/cli.py @@ -203,6 +203,16 @@ def plot(config_file: str, out: str, format: str): " 'input' list and genotypes2.vcf to the second input source)." ) ) +@click.option( + '-i', '--included_samples', + type=str, + default=None, + show_default=True, + help=( + "Path to file containing sample IDs to include in the SHAP analysis. " + "File should contain one sample ID per line." + ) +) @click.option( '-s', '--save_path', type=str, @@ -226,7 +236,8 @@ def plot(config_file: str, out: str, format: str): ) def shap( config_file: str, - genotype_files: str, + genotype_files: str, + included_samples: str, save_path: str, save_config_path: str ): @@ -248,6 +259,11 @@ def shap( for i, path in enumerate(genotype_files): config['input'][i]['file'] = path + # Load optional sample IDs + if included_samples: + with open(included_samples, "r") as f: + included_samples = [line.strip() for line in f] # type: ignore + run_SHAP( simulation, phenotype_key, diff --git a/pheno_sim/shap/run_shap.py b/pheno_sim/shap/run_shap.py index 77c1c2f..64842e4 100644 --- a/pheno_sim/shap/run_shap.py +++ b/pheno_sim/shap/run_shap.py @@ -13,6 +13,7 @@ def run_SHAP( simulation, phenotype: str='phenotype', + included_samples=None, save_path=None, save_config_path=None, ): @@ -29,6 +30,9 @@ def run_SHAP( simulation (PhenoSimulation): PhenoSimulation object. phenotype (str, default 'phenotype'): Phenotype key to use for SHAP values. + included_samples (list, optional): List of sample IDs to compute local + SHAP values for. If None, all samples are included. Defaults + to None. save_path (str, optional): Path to save DataFrame to. Defaults to None. If None, DataFrame is not saved. save_config_path (str, optional): Path to save simulation config to. @@ -42,7 +46,11 @@ def run_SHAP( simulation.run_input_step() ) - print(input_df.head()) + # Create binary mask of columns to keep in included_samples is not None + if included_samples is not None: + mask = [sample in included_samples for sample in simulation.sample_ids] + input_df = input_df.loc[mask] + simulation.sample_ids = simulation.sample_ids[mask] # Create SHAP wrapper shap_wrapper = SHAPWrapper(simulation, phenotype, input_df.columns) @@ -52,7 +60,6 @@ def run_SHAP( shap_wrapper, input_df, algorithm='permutation', - # algorithm='partition', ) # Calculate SHAP values @@ -76,7 +83,7 @@ def run_SHAP( with open(save_config_path, 'w') as f: json.dump(simulation.get_config(), f, indent=4) - # return shap_values, explainer + return shap_values, explainer, input_df if __name__ == '__main__': @@ -91,19 +98,25 @@ def run_SHAP( # genotype files as args. See run_simulation.py for example. simulation = PhenoSimulation.from_JSON_file(sim_config_path) + included = [ + 'HG00099', + 'NA21142' + ] + output = run_SHAP( simulation, phenotype_key, + included_samples=included, save_path='test_shap.csv', save_config_path='test_shap_config.json', ) - print(output) - print(type(output)) + # print(output) + # print(type(output)) - # shap.summary_plot(output) - print(output.shape) + # # shap.summary_plot(output) + # print(output.shape) From f952ddc58eda78df3ce1575cfa3485290618a342 Mon Sep 17 00:00:00 2001 From: RossDeVito Date: Thu, 13 Jun 2024 16:22:51 -0700 Subject: [PATCH 07/26] Update CLI for SHAP --- cl_tool/cli.py | 22 ++-- pheno_sim/shap/test_shap.csv | 3 + pheno_sim/shap/test_shap_config.json | 146 +++++++++++++++++++++++++++ 3 files changed, 164 insertions(+), 7 deletions(-) create mode 100644 pheno_sim/shap/test_shap.csv create mode 100644 pheno_sim/shap/test_shap_config.json diff --git a/cl_tool/cli.py b/cl_tool/cli.py index 639112d..bd225c3 100644 --- a/cl_tool/cli.py +++ b/cl_tool/cli.py @@ -263,10 +263,18 @@ def shap( if included_samples: with open(included_samples, "r") as f: included_samples = [line.strip() for line in f] # type: ignore - - run_SHAP( - simulation, - phenotype_key, - save_path, - save_config_path, - ) + print(included_samples) + run_SHAP( + simulation, + phenotype_key, + included_samples, + save_path, + save_config_path, + ) + else: + run_SHAP( + simulation, + phenotype_key, + save_path, + save_config_path, + ) diff --git a/pheno_sim/shap/test_shap.csv b/pheno_sim/shap/test_shap.csv new file mode 100644 index 0000000..c37b829 --- /dev/null +++ b/pheno_sim/shap/test_shap.csv @@ -0,0 +1,3 @@ +LDLR_upstream_variant*-*a,LDLR_upstream_variant*-*b,LDLR_intron_A_variants*-*a*-*0,LDLR_intron_A_variants*-*a*-*1,LDLR_intron_A_variants*-*b*-*0,LDLR_intron_A_variants*-*b*-*1,LDLR_intron_B_variant*-*a,LDLR_intron_B_variant*-*b,LDLR_missense_variants*-*a*-*0,LDLR_missense_variants*-*a*-*1,LDLR_missense_variants*-*b*-*0,LDLR_missense_variants*-*b*-*1,sample_id +0.0,0.0,0.0,-0.024823906394621995,0.0,0.0,-0.0546808810041348,0.0,0.0,0.0,0.0,0.0,HG00099 +0.0,0.0,0.0,0.024823906394622012,0.0,0.0,0.05468088100413481,0.0,0.0,0.0,0.0,0.0,NA21142 diff --git a/pheno_sim/shap/test_shap_config.json b/pheno_sim/shap/test_shap_config.json new file mode 100644 index 0000000..a6b9408 --- /dev/null +++ b/pheno_sim/shap/test_shap_config.json @@ -0,0 +1,146 @@ +{ + "input": [ + { + "file": "../../pheno_sim_demos/1000_genomes_data/ALL.chr19.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz", + "file_format": "vcf", + "reference_genome": "GRCh37", + "force_bgz": true, + "input_nodes": [ + { + "alias": "LDLR_upstream_variant", + "type": "SNP", + "chr": "19", + "pos": 11197261 + }, + { + "alias": "LDLR_intron_A_variants", + "type": "SNP", + "chr": "19", + "pos": [ + 11202306, + 11206575 + ] + }, + { + "alias": "LDLR_intron_B_variant", + "type": "SNP", + "chr": "19", + "pos": 11216561 + }, + { + "alias": "LDLR_missense_variants", + "type": "SNP", + "chr": "19", + "pos": [ + 11242133, + 11222300 + ] + } + ], + "sample_id_field": "s" + } + ], + "simulation_steps": [ + { + "type": "Constant", + "alias": "LDLR_upstream_variant_beta", + "input_match_size": "LDLR_upstream_variant", + "constant": 0.1 + }, + { + "type": "RandomConstant", + "alias": "LDLR_intron_A_variants_betas", + "input_match_size": "LDLR_intron_A_variants", + "dist_name": "normal", + "dist_kwargs": { + "loc": 0.0, + "scale": 0.25 + }, + "by_feat": true, + "drawn_vals": [ + -0.26573066264122897, + -0.049647812789243864 + ] + }, + { + "type": "RandomConstant", + "alias": "LDLR_intron_B_variant_beta", + "input_match_size": "LDLR_intron_B_variant", + "dist_name": "normal", + "dist_kwargs": { + "loc": -0.05, + "scale": 0.1 + }, + "drawn_vals": [ + 0.10936176200826948 + ] + }, + { + "type": "RandomConstant", + "alias": "LDLR_missense_variants_betas", + "input_match_size": "LDLR_missense_variants", + "dist_name": "normal", + "dist_kwargs": { + "loc": 0.25, + "scale": 0.2 + }, + "by_feat": true, + "drawn_vals": [ + 0.06497350102448105, + 0.2697080565664119 + ] + }, + { + "type": "Product", + "alias": "LDLR_upstream_variant_effect", + "input_aliases": [ + "LDLR_upstream_variant_beta", + "LDLR_upstream_variant" + ] + }, + { + "type": "Product", + "alias": "LDLR_intron_A_variants_effects", + "input_aliases": [ + "LDLR_intron_A_variants_betas", + "LDLR_intron_A_variants" + ] + }, + { + "type": "Product", + "alias": "LDLR_intron_B_variant_effect", + "input_aliases": [ + "LDLR_intron_B_variant_beta", + "LDLR_intron_B_variant" + ] + }, + { + "type": "Product", + "alias": "LDLR_missense_variants_effects", + "input_aliases": [ + "LDLR_missense_variants_betas", + "LDLR_missense_variants" + ] + }, + { + "type": "Concatenate", + "alias": "LDLR_effects_by_haplotype", + "input_aliases": [ + "LDLR_upstream_variant_effect", + "LDLR_intron_A_variants_effects", + "LDLR_intron_B_variant_effect", + "LDLR_missense_variants_effects" + ] + }, + { + "type": "AdditiveCombine", + "alias": "LDLR_effects", + "input_alias": "LDLR_effects_by_haplotype" + }, + { + "type": "SumReduce", + "alias": "phenotype", + "input_alias": "LDLR_effects" + } + ] +} \ No newline at end of file From 2f07b8e3bffccc3c1e1505050815a8318e5a86e0 Mon Sep 17 00:00:00 2001 From: RossDeVito Date: Mon, 17 Jun 2024 10:35:41 -0700 Subject: [PATCH 08/26] Add messages wrt filtering for SHAP CLI --- pheno_sim/shap/run_shap.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/pheno_sim/shap/run_shap.py b/pheno_sim/shap/run_shap.py index 64842e4..9010f40 100644 --- a/pheno_sim/shap/run_shap.py +++ b/pheno_sim/shap/run_shap.py @@ -48,10 +48,17 @@ def run_SHAP( # Create binary mask of columns to keep in included_samples is not None if included_samples is not None: + original_n_samples = len(simulation.sample_ids) mask = [sample in included_samples for sample in simulation.sample_ids] input_df = input_df.loc[mask] simulation.sample_ids = simulation.sample_ids[mask] + # Print number of samples included + print(f"Included {len(simulation.sample_ids)} samples out of {original_n_samples}.") + + if len(simulation.sample_ids) == 0: + raise ValueError("No samples included in SHAP analysis.") + # Create SHAP wrapper shap_wrapper = SHAPWrapper(simulation, phenotype, input_df.columns) From 0df9ec077410a70567839d59095823547e45416c Mon Sep 17 00:00:00 2001 From: RossDeVito Date: Mon, 17 Jun 2024 11:48:34 -0700 Subject: [PATCH 09/26] Remove debugging print --- cl_tool/cli.py | 1 - 1 file changed, 1 deletion(-) diff --git a/cl_tool/cli.py b/cl_tool/cli.py index bd225c3..2b2b62f 100644 --- a/cl_tool/cli.py +++ b/cl_tool/cli.py @@ -263,7 +263,6 @@ def shap( if included_samples: with open(included_samples, "r") as f: included_samples = [line.strip() for line in f] # type: ignore - print(included_samples) run_SHAP( simulation, phenotype_key, From 5e77642d6ea02751b9a4f6068bdaeb608efc89e5 Mon Sep 17 00:00:00 2001 From: Melissa Gymrek Date: Mon, 9 Sep 2024 13:41:30 -0700 Subject: [PATCH 10/26] adding pyproject.toml setup --- {cl_tool => citrus}/__init__.py | 0 {cl_tool => citrus}/cli.py | 0 {cl_tool => citrus}/sim_results/config.json | 0 {cl_tool => citrus}/sim_results/output.csv | 0 .../sim_results/sim_config.json | 0 .../test_configs/simple_sim.json | 0 .../test_configs/simple_sim_rerun.json | 0 dev-env.yml | 13 + noxfile.py | 68 ++ poetry.lock | 765 ++++++++++++++++++ pyproject.toml | 46 ++ 11 files changed, 892 insertions(+) rename {cl_tool => citrus}/__init__.py (100%) rename {cl_tool => citrus}/cli.py (100%) rename {cl_tool => citrus}/sim_results/config.json (100%) rename {cl_tool => citrus}/sim_results/output.csv (100%) rename {cl_tool => citrus}/sim_results/sim_config.json (100%) rename {cl_tool => citrus}/test_configs/simple_sim.json (100%) rename {cl_tool => citrus}/test_configs/simple_sim_rerun.json (100%) create mode 100644 dev-env.yml create mode 100644 noxfile.py create mode 100644 poetry.lock create mode 100644 pyproject.toml diff --git a/cl_tool/__init__.py b/citrus/__init__.py similarity index 100% rename from cl_tool/__init__.py rename to citrus/__init__.py diff --git a/cl_tool/cli.py b/citrus/cli.py similarity index 100% rename from cl_tool/cli.py rename to citrus/cli.py diff --git a/cl_tool/sim_results/config.json b/citrus/sim_results/config.json similarity index 100% rename from cl_tool/sim_results/config.json rename to citrus/sim_results/config.json diff --git a/cl_tool/sim_results/output.csv b/citrus/sim_results/output.csv similarity index 100% rename from cl_tool/sim_results/output.csv rename to citrus/sim_results/output.csv diff --git a/cl_tool/sim_results/sim_config.json b/citrus/sim_results/sim_config.json similarity index 100% rename from cl_tool/sim_results/sim_config.json rename to citrus/sim_results/sim_config.json diff --git a/cl_tool/test_configs/simple_sim.json b/citrus/test_configs/simple_sim.json similarity index 100% rename from cl_tool/test_configs/simple_sim.json rename to citrus/test_configs/simple_sim.json diff --git a/cl_tool/test_configs/simple_sim_rerun.json b/citrus/test_configs/simple_sim_rerun.json similarity index 100% rename from cl_tool/test_configs/simple_sim_rerun.json rename to citrus/test_configs/simple_sim_rerun.json diff --git a/dev-env.yml b/dev-env.yml new file mode 100644 index 0000000..39111db --- /dev/null +++ b/dev-env.yml @@ -0,0 +1,13 @@ +channels: + - conda-forge + - bioconda + - nodefaults +dependencies: + - conda-forge::python=3.8 # the lowest version of python that we formally support + - conda-forge::pip==24.0 + - conda-forge::poetry==1.8.3 # keep in sync with release.yml + - conda-forge::nox==2024.4.15 + - conda-forge::poetry-plugin-export==1.8.0 + - pip: + - nox-poetry==1.0.3 + - poetry-conda==0.1.1 \ No newline at end of file diff --git a/noxfile.py b/noxfile.py new file mode 100644 index 0000000..50772c7 --- /dev/null +++ b/noxfile.py @@ -0,0 +1,68 @@ +"""Nox sessions.""" +import os +from pathlib import Path + +import nox +from nox_poetry import Session +from nox_poetry import session + + +package = "citrus" +python_versions = ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"] +nox.needs_version = ">= 2022.11.21" +nox.options.sessions = ( + "tests", +) + + +cov_cli_args = [ + "--cov=.", + "--cov-report=term-missing", +] + + +def install_handle_python(session): + """ + handle incompatibilities between python and other packages + see https://github.com/cjolowicz/nox-poetry/issues/1116 + """ + # install the latest versions of all dependencies for py3.9+ + # but install the locked versions for < py3.9 to ensure some stability in the CI and + # help us understand when we need to bump our version constraints + if session._session.python in ("3.9", "3.10", "3.11", "3.12"): + session._session.install(".") + else: + session.install(".") + + +# detect whether conda/mamba is installed +if os.getenv("CONDA_EXE"): + conda_cmd = "conda" + if (Path(os.getenv("CONDA_EXE")).parent / "mamba").exists(): + conda_cmd = "mamba" + conda_args = ["-c", "conda-forge"] + + @session(venv_backend=conda_cmd, venv_params=conda_args, python=python_versions) + def tests(session: Session) -> None: + """Run the test suite.""" + session.conda_install( + "numpy", + "pytest", + "pytest-cov", + channel="conda-forge", + ) + install_handle_python(session) + session.run( + "python", "-m", "pytest", *cov_cli_args, *session.posargs + ) + +else: + + @session(python=python_versions) + def tests(session: Session) -> None: + """Run the test suite.""" + session.install("pytest", "pytest-cov") + install_handle_python_numpy(session) + session.run( + "python", "-m", "pytest", *cov_cli_args, *session.posargs + ) \ No newline at end of file diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..a450e8f --- /dev/null +++ b/poetry.lock @@ -0,0 +1,765 @@ +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. + +[[package]] +name = "alabaster" +version = "0.7.13" +description = "A configurable sidebar-enabled Sphinx theme" +optional = false +python-versions = ">=3.6" +files = [ + {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"}, + {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"}, +] + +[[package]] +name = "babel" +version = "2.16.0" +description = "Internationalization utilities" +optional = false +python-versions = ">=3.8" +files = [ + {file = "babel-2.16.0-py3-none-any.whl", hash = "sha256:368b5b98b37c06b7daf6696391c3240c938b37767d4584413e8438c5c435fa8b"}, + {file = "babel-2.16.0.tar.gz", hash = "sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316"}, +] + +[package.dependencies] +pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""} + +[package.extras] +dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] + +[[package]] +name = "certifi" +version = "2024.8.30" +description = "Python package for providing Mozilla's CA Bundle." +optional = false +python-versions = ">=3.6" +files = [ + {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"}, + {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"}, +] + +[[package]] +name = "charset-normalizer" +version = "3.3.2" +description = "The Real First Universal Charset Detector. 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a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..9a5a683 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,46 @@ +[tool.poetry] +name = "citrus" +version = "0.1.0" +description = "CIs and TRans interaction nUmerical Simulator for simulating phenotypes from genotypes" +authors = ["Ross DeVito"] +license = "MIT" +readme = "README.md" +repository = "https://github.com/gymrek-lab/citrus" +homepage = "https://github.com/gymrek-lab/citrus" +documentation = "https://github.com/gymrek-lab/citrus" + +[tool.poetry.dependencies] +python = "^3.8" +click = "^8.1.7" + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" + +[tool.poetry.group.tests.dependencies] +pytest = ">=6.2.0" +pytest-cov = ">=3.0.0" + +[tool.poetry.group.docs.dependencies] +sphinx = ">=3.0.4" +sphinx-rtd-theme = ">=1.0.0" +sphinx-autodoc-typehints = ">=1.12.0" + +[tool.poetry.scripts] +citrus = "citrus.cli:citrus" + +[tool.pytest.ini_options] +addopts = """ +--ignore noxfile.py --doctest-modules +""" + +[tool.coverage.run] +omit = [ + ".nox/*", + "noxfile.py", +] + +[tool.coverage.report] +exclude_lines = [ + "pragma: no cover", +] \ No newline at end of file From 16dd3388b0fbe4120fe146cbe98d8d804b5cab16 Mon Sep 17 00:00:00 2001 From: Melissa Gymrek Date: Mon, 9 Sep 2024 14:51:31 -0700 Subject: [PATCH 11/26] adding example input files --- dev-env.yml | 2 +- example-files/example_gts_chr19.vcf.gz | Bin 0 -> 9149 bytes example-files/example_gts_chr19.vcf.gz.tbi | Bin 0 -> 121 bytes example-files/linear_additive.json | 70 ++++++ poetry.lock | 267 +++++++++++++++++---- pyproject.toml | 4 +- 6 files changed, 297 insertions(+), 46 deletions(-) create mode 100644 example-files/example_gts_chr19.vcf.gz create mode 100644 example-files/example_gts_chr19.vcf.gz.tbi create mode 100644 example-files/linear_additive.json diff --git a/dev-env.yml b/dev-env.yml index 39111db..ed652f3 100644 --- a/dev-env.yml +++ b/dev-env.yml @@ -3,7 +3,7 @@ channels: - bioconda - 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+ { + "type": "Product", + "alias": "chr19:280540:G:A_effect", + "input_aliases": [ + "chr19:280540:G:A_beta", "chr19:280540:G:A" + ] + }, + { + "type": "Product", + "alias": "chr19:523746:C:T_effect", + "input_aliases": [ + "chr19:523746:C:T_beta", "chr19:523746:C:T" + ] + }, + { + "type": "Concatenate", + "alias": "effects_by_haplotype", + "input_aliases": [ + "chr19:280540:G:A_effect", + "chr19:523746:C:T_effect" + ] + }, + { + "type": "AdditiveCombine", + "alias": "effects", + "input_alias": "effects_by_haplotype" + }, + { + "type": "SumReduce", + "alias": "phenotype", + "input_alias": "effects" + } + ] +} \ No newline at end of file diff --git a/poetry.lock b/poetry.lock index a450e8f..d11e84a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -22,9 +22,6 @@ files = [ {file = "babel-2.16.0.tar.gz", hash = "sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316"}, ] -[package.dependencies] -pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""} - 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"pytest-ignore-flaky"] -type = ["pytest-mypy"] - [metadata] lock-version = "2.0" -python-versions = "^3.8" -content-hash = "7848788933445630eae5ee3e53ecc2370b0b5154f3fcb46a5c00cc861b19757d" +python-versions = "^3.10" +content-hash = "e79be590153b40e165a91fd6b010dc34c26c60b77ae20977926349b2c2373c52" diff --git a/pyproject.toml b/pyproject.toml index 9a5a683..89e475f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,8 +10,10 @@ homepage = "https://github.com/gymrek-lab/citrus" documentation = "https://github.com/gymrek-lab/citrus" [tool.poetry.dependencies] -python = "^3.8" +python = "^3.10" click = "^8.1.7" +pandas = "^2.2.2" +scipy = "^1.14.1" [build-system] requires = ["poetry-core"] From 1c03c663454e46763fcb6fa7c183a0e4d4aeb502 Mon Sep 17 00:00:00 2001 From: Melissa Gymrek Date: Mon, 16 Sep 2024 20:34:24 -0700 Subject: [PATCH 12/26] remove colons from node IDs --- README.md | 22 +- dev-env.yml | 3 +- example-files/linear_additive.json | 24 +- poetry.lock | 2653 +++++++++++++++++++++++++--- pyproject.toml | 9 +- setup.py | 29 - 6 files changed, 2495 insertions(+), 245 deletions(-) delete mode 100644 setup.py diff --git a/README.md b/README.md index ed7be28..5b3ccfa 100644 --- a/README.md +++ b/README.md @@ -10,13 +10,31 @@ CITRUS, the CIs and Trans inteRaction nUmerical Simulator, is a tool for simulat [Command Line Interface](doc/cli.md) - ## Installation +For plotting models, you will need to have [graphviz](https://graphviz.org/) installed. + +### With conda + +**TODO - conda install instructions** + +### With pip + +**TODO - pip install instructions** + ### From source +To install from source (only recommended for development), clone the CITRUS repository and checkout the branch you're interested in: + ```bash git clone https://github.com/gymrek-lab/CITRUS.git cd CITRUS -pip install . ``` + +Now, create 1) a conda environment with our development tools and 2) a virtual environment with our dependencies and an editable install of CITRUS: + +``` +conda env create -n citrus -f dev-env.yml +conda run -n citrus poetry install +conda activate citrus +``` \ No newline at end of file diff --git a/dev-env.yml b/dev-env.yml index ed652f3..092f9b8 100644 --- a/dev-env.yml +++ b/dev-env.yml @@ -3,11 +3,12 @@ channels: - bioconda - nodefaults dependencies: - - conda-forge::python=3.10 # the lowest version of python that we formally support + - conda-forge::python=3.11 # the lowest version of python that we formally support - conda-forge::pip==24.0 - conda-forge::poetry==1.8.3 # keep in sync with release.yml - conda-forge::nox==2024.4.15 - conda-forge::poetry-plugin-export==1.8.0 + - anaconda::graphviz==12.1.0 - pip: - nox-poetry==1.0.3 - poetry-conda==0.1.1 \ No newline at end of file diff --git a/example-files/linear_additive.json b/example-files/linear_additive.json index 36d7a15..aad5818 100644 --- a/example-files/linear_additive.json +++ b/example-files/linear_additive.json @@ -7,13 +7,13 @@ "force_bgz": true, "input_nodes": [ { - "alias": "chr19:280540:G:A", + "alias": "chr19_280540_G_A", "type": "SNP", "chr": "19", "pos": 280540 }, { - "alias": "chr19:523746:C:T", + "alias": "chr19_523746_C_T", "type": "SNP", "chr": "19", "pos": [523746] @@ -24,36 +24,36 @@ "simulation_steps": [ { "type": "Constant", - "alias": "chr19:280540:G:A_beta", - "input_match_size": "chr19:280540:G:A", + "alias": "chr19_280540_G_A_beta", + "input_match_size": "chr19_280540_G_A", "constant": 0.1 }, { "type": "Constant", - "alias": "chr19:523746:C:T_beta", - "input_match_size": "chr19:523746:C:T", + "alias": "chr19_523746_C_T_beta", + "input_match_size": "chr19_523746_C_T", "constant": 0.3 }, { "type": "Product", - "alias": "chr19:280540:G:A_effect", + "alias": "chr19_280540_G_A_effect", "input_aliases": [ - "chr19:280540:G:A_beta", "chr19:280540:G:A" + "chr19_280540_G_A_beta", "chr19_280540_G_A" ] }, { "type": "Product", - "alias": "chr19:523746:C:T_effect", + "alias": "chr19_523746_C_T_effect", "input_aliases": [ - 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documentation = "https://github.com/gymrek-lab/citrus" [tool.poetry.dependencies] -python = "^3.10" +python = "^3.11" click = "^8.1.7" pandas = "^2.2.2" -scipy = "^1.14.1" +scipy = "^1.11.4" +shap = "^0.46.0" +hail = "^0.2.132" +tqdm = "^4.66.5" +pydot = "^3.0.1" +scikit-learn = "^1.5.2" [build-system] requires = ["poetry-core"] diff --git a/setup.py b/setup.py deleted file mode 100644 index 6d83c48..0000000 --- a/setup.py +++ /dev/null @@ -1,29 +0,0 @@ -from setuptools import setup, find_packages - -setup( - name="citrus", - version="0.1.0", - description="", - author="Ross DeVito", - author_email="rdevito@ucsd.edu", - packages=find_packages(), - include_package_data=True, - install_requires=[ - "click", - "hail", - "matplotlib", - "numpy", - "pandas", - "pydot", - "scikit-learn", - "scipy", - "seaborn", - "shap", - "tqdm", - ], - entry_points={ - "console_scripts": [ - "citrus = cl_tool.cli:citrus" - ], - }, -) From 9596f72c224753f2c1f3cf8a1d087e9d7ccf06ce Mon Sep 17 00:00:00 2001 From: Melissa Gymrek Date: Mon, 16 Sep 2024 20:43:07 -0700 Subject: [PATCH 13/26] adding test workflow --- .github/workflows/tests.yml | 100 ++++++++++++++++++++++++++++++++++++ noxfile.py | 2 +- 2 files changed, 101 insertions(+), 1 deletion(-) create mode 100644 .github/workflows/tests.yml diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml new file mode 100644 index 0000000..d21b33d --- /dev/null +++ b/.github/workflows/tests.yml @@ -0,0 +1,100 @@ +name: Tests + +on: [pull_request, workflow_call] + +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +jobs: + tests: + name: ${{ matrix.session }} / ${{ matrix.python }} / ${{ matrix.os }} + runs-on: ${{ matrix.os }} + strategy: + fail-fast: false + matrix: + include: + - { python: "3.11", os: "ubuntu-latest", session: "tests" } + - { python: "3.12", os: "ubuntu-latest", session: "tests" } + + env: + NOXSESSION: ${{ matrix.session }} + FORCE_COLOR: "1" + PRE_COMMIT_COLOR: "always" + + steps: + - name: Check out the repository + uses: actions/checkout@v4 + + - name: Setup Mambaforge + uses: conda-incubator/setup-miniconda@v3 + with: + activate-environment: citrus + miniforge-variant: Mambaforge + auto-activate-base: false + miniforge-version: latest + use-mamba: true + + - name: Get Date + id: get-date + run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT + shell: bash + + - name: Cache Conda env + uses: actions/cache@v4 + with: + path: ${{ env.CONDA }}/envs + key: + conda-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-${{ hashFiles('dev-env.yml') }}-${{ env.CACHE_NUMBER }} + env: + # Increase this value to reset cache if dev-env.yml has not changed + CACHE_NUMBER: 0 + id: cache + + - name: Install dev environment + run: + mamba env update -n citrus -f dev-env.yml + if: steps.cache.outputs.cache-hit != 'true' + + - name: Try to build citrus + shell: bash -el {0} + run: | + poetry build --no-ansi + + - name: Check distribution size + if: matrix.session == 'size' + run: | + du -csh dist/* + tar -ztvf dist/*.tar.gz + # check that the generated dist/ directory does not exceed 0.3 MB + # if this check fails, it's because you forgot to list large files in the "exclude" section of our pyproject.toml + # https://python-poetry.org/docs/pyproject/#include-and-exclude + [ $(du -b dist | cut -f1) -lt 300000 ] + + - name: Check code coverage + if: matrix.session == 'coverage' + shell: bash -el {0} + run: | + export NOXSESSION=tests + # check that code coverage is not lower than specific percent + nox --verbose --python=${{ matrix.python }} -- --cov=. --cov-report=term-missing --cov-fail-under=94 + + - name: Run tests with nox + if: matrix.session == 'tests' + shell: bash -el {0} + run: | + nox --verbose --python=${{ matrix.python }} + + large-files: + name: File sizes + runs-on: ubuntu-latest + steps: + - name: Check out the repository + uses: actions/checkout@v4 + + - name: Check for large files + uses: actionsdesk/lfs-warning@v3.2 + with: + token: ${{ secrets.GITHUB_TOKEN }} # Optional + filesizelimit: 500000b + labelName: large-files \ No newline at end of file diff --git a/noxfile.py b/noxfile.py index 50772c7..fc49b92 100644 --- a/noxfile.py +++ b/noxfile.py @@ -8,7 +8,7 @@ package = "citrus" -python_versions = ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"] +python_versions = ["3.11", "3.12"] nox.needs_version = ">= 2022.11.21" nox.options.sessions = ( "tests", From 7f3993e9134782a111915d96653501928c92041d Mon Sep 17 00:00:00 2001 From: Melissa Gymrek Date: Mon, 16 Sep 2024 20:56:46 -0700 Subject: [PATCH 14/26] remov doctests for now --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 65cedf6..7df58f2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -38,7 +38,7 @@ citrus = "citrus.cli:citrus" [tool.pytest.ini_options] addopts = """ ---ignore noxfile.py --doctest-modules +--ignore noxfile.py """ [tool.coverage.run] From e95083062a79b0e5cd8a7c289fbc21d2725ea5d2 Mon Sep 17 00:00:00 2001 From: Melissa Gymrek Date: Mon, 16 Sep 2024 21:03:48 -0700 Subject: [PATCH 15/26] add initial command line tests --- citrus/__init__.py | 6 ++++++ noxfile.py | 5 +++-- poetry.lock | 39 ++++++++++++++++++++++++++++++++++++++- pyproject.toml | 1 + test/cmdline_tests.sh | 30 ++++++++++++++++++++++++++++++ 5 files changed, 78 insertions(+), 3 deletions(-) create mode 100644 test/cmdline_tests.sh diff --git a/citrus/__init__.py b/citrus/__init__.py index e69de29..5aeb0e8 100644 --- a/citrus/__init__.py +++ b/citrus/__init__.py @@ -0,0 +1,6 @@ +from importlib.metadata import version, PackageNotFoundError + +try: + __version__ = version(__name__) +except PackageNotFoundError: + __version__ = "unknown" \ No newline at end of file diff --git a/noxfile.py b/noxfile.py index fc49b92..09646d4 100644 --- a/noxfile.py +++ b/noxfile.py @@ -55,7 +55,7 @@ def tests(session: Session) -> None: session.run( "python", "-m", "pytest", *cov_cli_args, *session.posargs ) - + session.run("./test/cmdline_tests.sh", external=True) else: @session(python=python_versions) @@ -65,4 +65,5 @@ def tests(session: Session) -> None: install_handle_python_numpy(session) session.run( "python", "-m", "pytest", *cov_cli_args, *session.posargs - ) \ No newline at end of file + ) + session.run("./test/cmdline_tests.sh", external=True) \ No newline at end of file diff --git a/poetry.lock b/poetry.lock index de1016e..d5edde3 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1100,6 +1100,24 @@ files = [ {file = "imagesize-1.4.1.tar.gz", hash = "sha256:69150444affb9cb0d5cc5a92b3676f0b2fb7cd9ae39e947a5e11a36b4497cd4a"}, ] +[[package]] +name = "importlib-metadata" +version = "3.10.1" +description = "Read metadata from Python packages" +optional = false +python-versions = ">=3.6" +files = [ + {file = "importlib_metadata-3.10.1-py3-none-any.whl", hash = "sha256:2ec0faae539743ae6aaa84b49a169670a465f7f5d64e6add98388cc29fd1f2f6"}, + {file = "importlib_metadata-3.10.1.tar.gz", hash = "sha256:c9356b657de65c53744046fa8f7358afe0714a1af7d570c00c3835c2d724a7c1"}, +] + +[package.dependencies] +zipp = ">=0.5" + +[package.extras] +docs = ["jaraco.packaging (>=8.2)", "rst.linker (>=1.9)", "sphinx"] +testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pep517", "pyfakefs", "pytest (>=4.6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-flake8", "pytest-mypy"] + [[package]] name = "iniconfig" version = "2.0.0" @@ -3193,7 +3211,26 @@ files = [ idna = ">=2.0" multidict = ">=4.0" +[[package]] +name = "zipp" +version = "3.20.2" +description = "Backport of pathlib-compatible object wrapper for zip files" +optional = false +python-versions = ">=3.8" +files = [ + {file = "zipp-3.20.2-py3-none-any.whl", hash = "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350"}, + {file = "zipp-3.20.2.tar.gz", hash = "sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29"}, +] + +[package.extras] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] +cover = ["pytest-cov"] +doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +enabler = ["pytest-enabler (>=2.2)"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +type = ["pytest-mypy"] + [metadata] lock-version = "2.0" python-versions = "^3.11" -content-hash = "19cb6c7cdaf131e54b6e0008fafeb301aca2ac9060ec1bbb82c5303716679293" +content-hash = "b591372c3286a4484f15d37522f61cee53d7ddc9d2cde6b525e94b031048c01c" diff --git a/pyproject.toml b/pyproject.toml index 7df58f2..98842e7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,6 +19,7 @@ hail = "^0.2.132" tqdm = "^4.66.5" pydot = "^3.0.1" scikit-learn = "^1.5.2" +importlib-metadata = "^3.0.0" [build-system] requires = ["poetry-core"] diff --git a/test/cmdline_tests.sh b/test/cmdline_tests.sh new file mode 100644 index 0000000..b61f3cd --- /dev/null +++ b/test/cmdline_tests.sh @@ -0,0 +1,30 @@ +#!/usr/bin/env bash + +# This script contains command line tests for TRTools utilities + +die() +{ + BASE=$(basename "$0") + echo "$BASE error: $1" >&2 + exit 1 +} + +runcmd_pass() +{ + echo "[runcmd_pass]: $1" + bash -c "$1" >/dev/null 2>&1 || die "Error running: $1" +} + +runcmd_fail() +{ + echo "[runcmd_fail]: $1" + bash -c "$1" >/dev/null 2>&1 && die "Command should have failed: $1" +} + +TMPDIR=$(mktemp -d -t tmp-XXXXXXXXXX) + +echo "Saving tmp files in ${TMPDIR}" + +# Check version +runcmd_pass "citrus --version" +runcmd_pass "python -c 'import citrus; print(citrus.__version__)'" From 7baa20c99cc87bd00dec2e62fc7b9bfcdb7b630d Mon Sep 17 00:00:00 2001 From: Melissa Gymrek Date: Mon, 16 Sep 2024 21:12:12 -0700 Subject: [PATCH 16/26] removing large output file --- citrus/sim_results/output.csv | 2505 --------------------------------- 1 file changed, 2505 deletions(-) delete mode 100644 citrus/sim_results/output.csv diff --git a/citrus/sim_results/output.csv b/citrus/sim_results/output.csv deleted file mode 100644 index 83c3e95..0000000 --- a/citrus/sim_results/output.csv +++ /dev/null @@ -1,2505 +0,0 @@ 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-0,0,0,0,0,1,0,0,0,0,0,0,0.1,0.1,-0.0272961189126802,-0.1348356719374646,-0.0272961189126802,-0.1348356719374646,-0.036289445856674186,-0.036289445856674186,0.1779147282204066,0.00943672391758732,0.1779147282204066,0.00943672391758732,0.0,0.0,-0.0,-0.0,-0.0,-0.1348356719374646,-0.0,-0.0,0.0,0.0,0.0,0.0,0.0,-0.0,-0.0,-0.0,0.0,0.0,0.0,-0.0,-0.1348356719374646,-0.0,0.0,0.0,0.0,-0.0,-0.1348356719374646,-0.0,0.0,0.0,-0.1348356719374646,NA21144 From c64f8243056328c7e7338367f4909084a2cbdb8e Mon Sep 17 00:00:00 2001 From: Melissa Gymrek Date: Mon, 16 Sep 2024 21:14:39 -0700 Subject: [PATCH 17/26] update graphviz in dev env --- dev-env.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dev-env.yml b/dev-env.yml index 092f9b8..30dd150 100644 --- a/dev-env.yml +++ b/dev-env.yml @@ -8,7 +8,7 @@ dependencies: - conda-forge::poetry==1.8.3 # keep in sync with release.yml - conda-forge::nox==2024.4.15 - conda-forge::poetry-plugin-export==1.8.0 - - anaconda::graphviz==12.1.0 + - anaconda::graphviz==2.50.0 - pip: - nox-poetry==1.0.3 - poetry-conda==0.1.1 \ No newline at end of file From b14bcdbf1922e3084d8cf9d65869edbdb045fbd5 Mon Sep 17 00:00:00 2001 From: Melissa Gymrek Date: Mon, 16 Sep 2024 21:18:26 -0700 Subject: [PATCH 18/26] remove test coverage requirement for now --- .github/workflows/tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index d21b33d..9a5d725 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -77,7 +77,7 @@ jobs: run: | export NOXSESSION=tests # check that code coverage is not lower than specific percent - nox --verbose --python=${{ matrix.python }} -- --cov=. --cov-report=term-missing --cov-fail-under=94 + nox --verbose --python=${{ matrix.python }} -- --cov=. --cov-report=term-missing --cov-fail-under=0 # TODO update!! - name: Run tests with nox if: matrix.session == 'tests' From df867efaa27f5f77e0e36d7b164623f47fc19a07 Mon Sep 17 00:00:00 2001 From: Melissa Gymrek Date: Mon, 16 Sep 2024 21:26:23 -0700 Subject: [PATCH 19/26] adding dummy tests --- citrus/tests/__init__.py | 0 citrus/tests/test_citrus.py | 5 +++++ 2 files changed, 5 insertions(+) create mode 100644 citrus/tests/__init__.py create mode 100644 citrus/tests/test_citrus.py diff --git a/citrus/tests/__init__.py b/citrus/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/citrus/tests/test_citrus.py b/citrus/tests/test_citrus.py new file mode 100644 index 0000000..1353c69 --- /dev/null +++ b/citrus/tests/test_citrus.py @@ -0,0 +1,5 @@ +import pytest + +# To check pytest framework is working +def test_dummy(): + assert True \ No newline at end of file From 67969bdd6c03a2b592b708ef7183da4c9d16c33e Mon Sep 17 00:00:00 2001 From: Melissa Gymrek Date: Mon, 16 Sep 2024 21:33:03 -0700 Subject: [PATCH 20/26] update cmdline tests permissions --- test/cmdline_tests.sh | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100644 => 100755 test/cmdline_tests.sh diff --git a/test/cmdline_tests.sh b/test/cmdline_tests.sh old mode 100644 new mode 100755 From 39d5740c89ea3f73f5711777ea826bc415a8705b Mon Sep 17 00:00:00 2001 From: Melissa Gymrek Date: Tue, 24 Sep 2024 19:48:55 -0700 Subject: [PATCH 21/26] minor edits to readme --- README.md | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 5b3ccfa..01ca10c 100644 --- a/README.md +++ b/README.md @@ -2,14 +2,6 @@ CITRUS, the CIs and Trans inteRaction nUmerical Simulator, is a tool for simulating phenotypes with complex genetic archetectures that go beyond simple models that assume linear, additive contributions of individual SNPs. The goal of this tool is to provide better simulations for benchmarking GWAS/PRS models. -## Getting Started - -[User Guide](doc/user_guide.md) - -[Designing Simulations](doc/designing_simulations.md) - -[Command Line Interface](doc/cli.md) - ## Installation For plotting models, you will need to have [graphviz](https://graphviz.org/) installed. @@ -37,4 +29,13 @@ Now, create 1) a conda environment with our development tools and 2) a virtual e conda env create -n citrus -f dev-env.yml conda run -n citrus poetry install conda activate citrus -``` \ No newline at end of file +``` + +## Full documentation + +[User Guide](doc/user_guide.md) + +[Designing Simulations](doc/designing_simulations.md) + +[Command Line Interface](doc/cli.md) + From 1da272c7b4dd564c0c3621eb0b6ba8808862a8ac Mon Sep 17 00:00:00 2001 From: Melissa Gymrek Date: Tue, 24 Sep 2024 19:50:06 -0700 Subject: [PATCH 22/26] minor changes to readme --- README.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/README.md b/README.md index 01ca10c..ae504b6 100644 --- a/README.md +++ b/README.md @@ -31,6 +31,13 @@ conda run -n citrus poetry install conda activate citrus ``` +## Quickstart + +``` +# Visualize a model +citrus plot -c example-files/linear_additive.json +``` + ## Full documentation [User Guide](doc/user_guide.md) From b6f3087ee476e7f73b9367327ff6638ec18aed00 Mon Sep 17 00:00:00 2001 From: Melissa Gymrek Date: Tue, 24 Sep 2024 20:00:00 -0700 Subject: [PATCH 23/26] removing old commented code from plot --- citrus/cli.py | 55 +++++++-------------------------------- pheno_sim/plot.py | 66 +---------------------------------------------- 2 files changed, 11 insertions(+), 110 deletions(-) diff --git a/citrus/cli.py b/citrus/cli.py index 2b2b62f..d6f4cb6 100644 --- a/citrus/cli.py +++ b/citrus/cli.py @@ -1,50 +1,6 @@ """CITRUS command line interface. -See CITRUS/doc/CLI.md for more information. - -This tool can be used to run the simulation based on either: - - 1. A single configuration JSON file that specifies paths to genotype - data files. - - CITRUS_sim -c - - 2. A single configuration JSON file and a list of paths to genotype - data files. The list of paths must be the same length as the - number of input source files in the configuration file (i.e. - the length of the list under the 'input' key in the JSON). Any - paths in the configuration file will be ignored. The -g or - --genotype_files flag can be used to specify the paths to the - genotype files. - - CITRUS_sim -c -g \\ - ... - - CITRUS_sim -c -g - -Output: - - If no additional flags are provided, output will be written to the - current working directory. The output will be a CSV file (output.csv) - containing sample IDs and all corresponding values from the simulation, - and a JSON file (sim_config.json) containing the simulation configuration - (including any random selections made by nodes). - - If the -o or --output_dir flag is provided, if the directory does not - exist it will be created, and the output files will be saved to it. By - default the output files will be named output.csv and sim_config.json, - but these can be changed with the -f or --output_file_name and -j or - --output_config_json flags, respectively. - - Output file will by default be a comma seperated CSV file. Use -t or - --tsv flag to instead save as a tab seperated TSV file. - -Example Usage: - - CITRUS_sim -c config.json -o sim_results/output_dir - - CITRUS_sim -c config.json -g genotype_file_1 genotype_file_2 \\ - -o sim_results/output_dir -t -f my_output.tsv -j my_sim_config.json +See CITRUS/doc/CLI.md and individual tools for more information. """ import click @@ -54,6 +10,9 @@ def citrus(): pass +""" +citrus simulate +""" @citrus.command(no_args_is_help=True) @click.option( '-c', '--config_file', @@ -147,6 +106,9 @@ def simulate( sep="\t" if tsv else "," ) +""" +citrus plot +""" @citrus.command(no_args_is_help=True) @click.option( '-c', '--config_file', @@ -183,6 +145,9 @@ def plot(config_file: str, out: str, format: str): # Create a plot of the model plot.visualize(input_spec=config, filename=out, img_format=format) +""" +citrus shap +""" @citrus.command(no_args_is_help=True) @click.option( '-c', '--config_file', diff --git a/pheno_sim/plot.py b/pheno_sim/plot.py index 68664f1..532ba7b 100644 --- a/pheno_sim/plot.py +++ b/pheno_sim/plot.py @@ -162,68 +162,4 @@ def plot_graph_with_legend(sim_nodes, filename, img_format): y_offset = (img.height - legend.height) // 2 combined.paste(legend, (img.width, y_offset)) - combined.save(filename + '.' + img_format) - - -# if __name__ == '__main__': - -# # dev -# input_spec = '../benchmarking_mlcb/pheno_sim/sim_configs/xor_pheno_1.json' -# filename = '../benchmarking_mlcb/pheno_sim/sim_configs/xor_pheno_1' -# img_format = 'png' - -# # Generate sim object -# sim = PhenoSimulation.from_JSON_file(input_spec) - -# # Add input nodes -# sim_nodes = dict() - -# for input_source in sim.input_runner.input_sources: -# for input_node in input_source.input_nodes: -# sim_nodes[input_node.alias] = CITRUSNode( -# alias=input_node.alias, -# node_type='input', -# class_name=type(input_node).__name__ -# ) - -# # Add operator nodes -# for sim_step in sim.simulation_steps: -# step_alias = sim_step.alias -# step_inputs = sim_step.inputs - -# if isinstance(step_inputs, str): -# step_inputs = [step_inputs] -# elif isinstance(step_inputs, dict): -# step_inputs = list(step_inputs.values()) - -# if isinstance(sim_step, AbstractBaseCombineFunctionNode): -# step_type = 'combine' -# else: -# step_type = 'trans' - -# sim_nodes[step_alias] = CITRUSNode( -# alias=step_alias, -# inputs=step_inputs, -# node_type=step_type, -# class_name=type(sim_step).__name__ -# ) - -# # Identify nodes that are of type 'combine'. -# combine_nodes = [node for node in sim_nodes.values() if node.node_type == 'combine'] - -# # For each combine node, identify its ancestors. -# all_ancestor_nodes = set() -# for combine_node in combine_nodes: -# all_ancestor_nodes.update(get_ancestor_nodes(combine_node, sim_nodes)) - -# # Change the node_type of ancestor nodes which are of type 'trans' to 'cis'. -# for ancestor_node_alias in all_ancestor_nodes: -# if sim_nodes[ancestor_node_alias].node_type == 'trans': -# sim_nodes[ancestor_node_alias].node_type = 'cis' - -# # Print nodes -# for k,v in sim_nodes.items(): -# print(f"{k}:\n\t{str(v)}") - -# # Plot the graph -# plot_graph_with_legend(sim_nodes, filename, img_format) + combined.save(filename + '.' + img_format) \ No newline at end of file From 475278965563688fb8b778b55dc89dea017b1115 Mon Sep 17 00:00:00 2001 From: Melissa Gymrek Date: Tue, 24 Sep 2024 20:47:11 -0700 Subject: [PATCH 24/26] adding docstrings to plot --- citrus/cli.py | 17 +- citrus/plot.py | 234 ++++++++++++++++++ citrus/utils.py | 8 + .../linear_additive_nogenotypes.json | 66 +++++ pheno_sim/plot.py | 165 ------------ 5 files changed, 321 insertions(+), 169 deletions(-) create mode 100644 citrus/plot.py create mode 100644 citrus/utils.py create mode 100644 example-files/linear_additive_nogenotypes.json delete mode 100644 pheno_sim/plot.py diff --git a/citrus/cli.py b/citrus/cli.py index d6f4cb6..51cbbf3 100644 --- a/citrus/cli.py +++ b/citrus/cli.py @@ -4,6 +4,7 @@ """ import click +import sys @click.group() @click.version_option(package_name="citrus", message="%(version)s") @@ -123,27 +124,35 @@ def simulate( help="Output filename (without extension) for saving plot." ) @click.option( - '-f', '--format', + '-f', '--fmt', type=click.Choice(['jpg', 'png', 'svg']), default='png', show_default=True, help="File format and extension for the output plot." ) -def plot(config_file: str, out: str, format: str): +@click.option( + '--verbose', + is_flag=True, + help="Print extra output to the terminal", + default=False +) +def plot(config_file: str, out: str, fmt: str, verbose: str): """ Save a plot of the network defined by the simulation config file. Note: Colors correspond to cis, inheritance, and trans effects """ - from pheno_sim import plot + from . import plot from json import load with open(config_file, "r") as f: config = load(f) # Create a plot of the model - plot.visualize(input_spec=config, filename=out, img_format=format) + retcode = plot.visualize(input_spec=config, filename=out, + img_format=fmt, verbose=verbose) + sys.exit(retcode) """ citrus shap diff --git a/citrus/plot.py b/citrus/plot.py new file mode 100644 index 0000000..38a62a6 --- /dev/null +++ b/citrus/plot.py @@ -0,0 +1,234 @@ +"""Plot simulation as directed graph.""" + +import pydot +from PIL import Image, ImageDraw + +from pheno_sim.pheno_simulation import PhenoSimulation +from pheno_sim.base_nodes import AbstractBaseCombineFunctionNode +from .utils import MSG + +def visualize(input_spec: dict, filename: str, + img_format: str, verbose: bool=False) -> int: + """ + Visualize a phenotype model + + Parameters + ---------- + input_spec : dict + Model configuration + filename : str + Prefix of output filename + img_format : str + Format of output file (jpg, png, or svg}) + verbose : bool + If true, print extra output to terminal + + Returns + ------- + retcode : int + Return code (0 for success) + """ + + # Generate sim object + sim = PhenoSimulation(input_spec) + + # Add input nodes + sim_nodes = dict() + + for input_source in sim.input_runner.input_sources: + for input_node in input_source.input_nodes: + sim_nodes[input_node.alias] = CITRUSNode( + alias=input_node.alias, + node_type='input', + class_name=type(input_node).__name__ + ) + + # Add operator nodes + for sim_step in sim.simulation_steps: + step_alias = sim_step.alias + step_inputs = sim_step.inputs + + if isinstance(step_inputs, str): + step_inputs = [step_inputs] + elif isinstance(step_inputs, dict): + step_inputs = list(step_inputs.values()) + + if isinstance(sim_step, AbstractBaseCombineFunctionNode): + step_type = 'combine' + else: + step_type = 'trans' + + sim_nodes[step_alias] = CITRUSNode( + alias=step_alias, + inputs=step_inputs, + node_type=step_type, + class_name=type(sim_step).__name__ + ) + + # Identify nodes that are of type 'combine'. + combine_nodes = [node for node in sim_nodes.values() if node.node_type == 'combine'] + + # For each combine node, identify its ancestors. + all_ancestor_nodes = set() + for combine_node in combine_nodes: + all_ancestor_nodes.update(get_ancestor_nodes(combine_node, sim_nodes)) + + # Change the node_type of ancestor nodes which are of type 'trans' to 'cis'. + for ancestor_node_alias in all_ancestor_nodes: + if sim_nodes[ancestor_node_alias].node_type == 'trans': + sim_nodes[ancestor_node_alias].node_type = 'cis' + + # Print nodes + if verbose: + for k,v in sim_nodes.items(): + MSG(f"{k}:\n\t{str(v)}") + + # Plot the graph + plot_graph_with_legend(sim_nodes, filename, img_format) + MSG(f"Plot output to {filename}.{img_format}") + + # Return + return 0 + + +class CITRUSNode: + """ + Helper class for plotting. + Represents a single CITRUS model node + + Attributes + ---------- + alias : str + Node alias + inputs : list + Simulation steps input to this node + node_type : str + One of: input, cis, trans, combine + class_name : str + Name of the class of the node + """ + def __init__( + self, + alias, + inputs=[], + node_type=None, + class_name=None + ): + self.alias = alias + self.inputs = inputs + self.node_type = node_type + self.class_name = class_name + + def __str__(self): + return f"alias: {self.alias}\tnode_type: {self.node_type}\tclass_name: {self.class_name}\tinputs: {self.inputs}" + + +def get_ancestor_nodes(node: CITRUSNode, + sim_nodes: dict[str, CITRUSNode]) -> list[CITRUSNode]: + """ + Iteratively get ancestor nodes of a given node. + + Parameters + ---------- + node : CITRUSNode + node to get ancestors of + sim_nodes : dict[str]->CITRUSNode + Dictionary of all nodes + + Returns + ------- + ancestors : list of CITRUSNode + List of nodes that are ancestors of node + """ + ancestors = set() + to_visit = [node] + + while to_visit: + current_node = to_visit.pop() + + # Add the direct parents to the ancestors set + for input_node_alias in current_node.inputs: + # Check if the ancestor is already in the set to avoid cycles + if input_node_alias not in ancestors: + ancestors.add(input_node_alias) + to_visit.append(sim_nodes[input_node_alias]) + + return list(ancestors) + + + +def plot_graph_with_legend(sim_nodes: dict[str, CITRUSNode], + filename: str, img_format: str): + """ + Make the plot from a list of nodes + + Parameters + ---------- + sim_nodes : dict[str]->CITRUSNode + Dictionary of all nodes + filename : str + Prefix of output filename + img_format : str + Format of output file (jpg, png, or svg}) + """ + + # Define a dictionary for colors based on node_type + node_colors = { + 'input': '#FF8C00', # dark orange + 'cis': '#90EE90', # light green + 'trans': '#DEB887', # burly wood (light brown) + 'combine': '#FFF44F' # lemon yellow + } + + # Create a new graph + graph = pydot.Dot(graph_type='digraph', rankdir='UD', ranksep='0.5') + + # Add nodes with their respective colors + for node in sim_nodes.values(): + label = f"{node.alias}\n<{node.class_name}>" + graph.add_node(pydot.Node(node.alias, label=label, style="filled", fillcolor=node_colors[node.node_type])) + + # Add edges based on the inputs of each node + for node in sim_nodes.values(): + for input_node in node.inputs: + graph.add_edge(pydot.Edge(input_node, node.alias)) + + # Save graph to file + graph.write(filename + '.' + img_format, format=img_format) + + # Adding a legend using PIL + img = Image.open(filename + '.' + img_format) + legend = Image.new('RGB', (250, 100), (255, 255, 255)) + + # Draw the legend + for index, (label, color) in enumerate(node_colors.items()): + d = ImageDraw.Draw(legend) + d.rectangle([10, 10 + index * 25, 30, 30 + index * 25], fill=color) + d.text((40, 10 + index * 25), label, fill=(0, 0, 0)) + + # Scale up the legend by any desired factor + scale_factor = 2.0 + scaled_width = int(legend.width * scale_factor) + scaled_height = int(legend.height * scale_factor) + legend = legend.resize( + (scaled_width, scaled_height), + resample=Image.BICUBIC + ) + + # Trim whitespace: Here we'll crop out 40% from the right, adjust as needed + crop_percentage = 0.5 + cropped_width = int(scaled_width * (1 - crop_percentage)) + legend = legend.crop((0, 0, cropped_width, scaled_height)) + + # Combine original image and legend + total_width = img.width + legend.width + max_height = max(img.height, legend.height) + + combined = Image.new('RGB', (total_width, max_height), 'white') + combined.paste(img, (0, 0)) + + # Center the legend vertically + y_offset = (img.height - legend.height) // 2 + combined.paste(legend, (img.width, y_offset)) + + combined.save(filename + '.' + img_format) \ No newline at end of file diff --git a/citrus/utils.py b/citrus/utils.py new file mode 100644 index 0000000..3a52884 --- /dev/null +++ b/citrus/utils.py @@ -0,0 +1,8 @@ +""" +Utility functions +""" + +import sys + +def MSG(msg: str): + sys.stderr.write("[CITRUS]: " + msg.strip() +"\n") \ No newline at end of file diff --git a/example-files/linear_additive_nogenotypes.json b/example-files/linear_additive_nogenotypes.json new file mode 100644 index 0000000..d43a80d --- /dev/null +++ b/example-files/linear_additive_nogenotypes.json @@ -0,0 +1,66 @@ +{ + "input": [ + { + "input_nodes": [ + { + "alias": "chr19_280540_G_A", + "type": "SNP", + "chr": "19", + "pos": 280540 + }, + { + "alias": "chr19_523746_C_T", + "type": "SNP", + "chr": "19", + "pos": [523746] + } + ] + } + ], + "simulation_steps": [ + { + "type": "Constant", + "alias": "chr19_280540_G_A_beta", + "input_match_size": "chr19_280540_G_A", + "constant": 0.1 + }, + { + "type": "Constant", + "alias": "chr19_523746_C_T_beta", + "input_match_size": "chr19_523746_C_T", + "constant": 0.3 + }, + { + "type": "Product", + "alias": "chr19_280540_G_A_effect", + "input_aliases": [ + "chr19_280540_G_A_beta", "chr19_280540_G_A" + ] + }, + { + "type": "Product", + "alias": "chr19_523746_C_T_effect", + "input_aliases": [ + "chr19_523746_C_T_beta", "chr19_523746_C_T" + ] + }, + { + "type": "Concatenate", + "alias": "effects_by_haplotype", + "input_aliases": [ + "chr19_280540_G_A_effect", + "chr19_523746_C_T_effect" + ] + }, + { + "type": "AdditiveCombine", + "alias": "effects", + "input_alias": "effects_by_haplotype" + }, + { + "type": "SumReduce", + "alias": "phenotype", + "input_alias": "effects" + } + ] +} \ No newline at end of file diff --git a/pheno_sim/plot.py b/pheno_sim/plot.py deleted file mode 100644 index 532ba7b..0000000 --- a/pheno_sim/plot.py +++ /dev/null @@ -1,165 +0,0 @@ -"""Plot simulation as directed graph.""" - -import pydot -from PIL import Image, ImageDraw - -from pheno_sim.pheno_simulation import PhenoSimulation -from pheno_sim.base_nodes import AbstractBaseCombineFunctionNode - - -def visualize(input_spec: dict, filename: str, img_format: str): - # Generate sim object - sim = PhenoSimulation(input_spec) - - # Add input nodes - sim_nodes = dict() - - for input_source in sim.input_runner.input_sources: - for input_node in input_source.input_nodes: - sim_nodes[input_node.alias] = CITRUSNode( - alias=input_node.alias, - node_type='input', - class_name=type(input_node).__name__ - ) - - # Add operator nodes - for sim_step in sim.simulation_steps: - step_alias = sim_step.alias - step_inputs = sim_step.inputs - - if isinstance(step_inputs, str): - step_inputs = [step_inputs] - elif isinstance(step_inputs, dict): - step_inputs = list(step_inputs.values()) - - if isinstance(sim_step, AbstractBaseCombineFunctionNode): - step_type = 'combine' - else: - step_type = 'trans' - - sim_nodes[step_alias] = CITRUSNode( - alias=step_alias, - inputs=step_inputs, - node_type=step_type, - class_name=type(sim_step).__name__ - ) - - # Identify nodes that are of type 'combine'. - combine_nodes = [node for node in sim_nodes.values() if node.node_type == 'combine'] - - # For each combine node, identify its ancestors. - all_ancestor_nodes = set() - for combine_node in combine_nodes: - all_ancestor_nodes.update(get_ancestor_nodes(combine_node, sim_nodes)) - - # Change the node_type of ancestor nodes which are of type 'trans' to 'cis'. - for ancestor_node_alias in all_ancestor_nodes: - if sim_nodes[ancestor_node_alias].node_type == 'trans': - sim_nodes[ancestor_node_alias].node_type = 'cis' - - # Print nodes - for k,v in sim_nodes.items(): - print(f"{k}:\n\t{str(v)}") - - # Plot the graph - plot_graph_with_legend(sim_nodes, filename, img_format) - - -class CITRUSNode: - - def __init__( - self, - alias, - inputs=[], - node_type=None, - class_name=None - ): - self.alias = alias - self.inputs = inputs - self.node_type = node_type - self.class_name = class_name - - def __str__(self): - return f"alias: {self.alias}\tnode_type: {self.node_type}\tclass_name: {self.class_name}\tinputs: {self.inputs}" - - -def get_ancestor_nodes(node, sim_nodes): - """Iteratively get ancestor nodes of a given node.""" - ancestors = set() - to_visit = [node] - - while to_visit: - current_node = to_visit.pop() - - # Add the direct parents to the ancestors set - for input_node_alias in current_node.inputs: - # Check if the ancestor is already in the set to avoid cycles - if input_node_alias not in ancestors: - ancestors.add(input_node_alias) - to_visit.append(sim_nodes[input_node_alias]) - - return list(ancestors) - - - -def plot_graph_with_legend(sim_nodes, filename, img_format): - # Define a dictionary for colors based on node_type - node_colors = { - 'input': '#FF8C00', # dark orange - 'cis': '#90EE90', # light green - 'trans': '#DEB887', # burly wood (light brown) - 'combine': '#FFF44F' # lemon yellow - } - - # Create a new graph - graph = pydot.Dot(graph_type='digraph', rankdir='UD', ranksep='0.5') - - # Add nodes with their respective colors - for node in sim_nodes.values(): - label = f"{node.alias}\n<{node.class_name}>" - graph.add_node(pydot.Node(node.alias, label=label, style="filled", fillcolor=node_colors[node.node_type])) - - # Add edges based on the inputs of each node - for node in sim_nodes.values(): - for input_node in node.inputs: - graph.add_edge(pydot.Edge(input_node, node.alias)) - - # Save graph to file - graph.write(filename + '.' + img_format, format=img_format) - - # Adding a legend using PIL - img = Image.open(filename + '.' + img_format) - legend = Image.new('RGB', (250, 100), (255, 255, 255)) - - # Draw the legend - for index, (label, color) in enumerate(node_colors.items()): - d = ImageDraw.Draw(legend) - d.rectangle([10, 10 + index * 25, 30, 30 + index * 25], fill=color) - d.text((40, 10 + index * 25), label, fill=(0, 0, 0)) - - # Scale up the legend by any desired factor - scale_factor = 2.0 - scaled_width = int(legend.width * scale_factor) - scaled_height = int(legend.height * scale_factor) - legend = legend.resize( - (scaled_width, scaled_height), - resample=Image.BICUBIC - ) - - # Trim whitespace: Here we'll crop out 40% from the right, adjust as needed - crop_percentage = 0.5 - cropped_width = int(scaled_width * (1 - crop_percentage)) - legend = legend.crop((0, 0, cropped_width, scaled_height)) - - # Combine original image and legend - total_width = img.width + legend.width - max_height = max(img.height, legend.height) - - combined = Image.new('RGB', (total_width, max_height), 'white') - combined.paste(img, (0, 0)) - - # Center the legend vertically - y_offset = (img.height - legend.height) // 2 - combined.paste(legend, (img.width, y_offset)) - - combined.save(filename + '.' + img_format) \ No newline at end of file From 176fa7e36fb3712a91298043678b05058da6aadf Mon Sep 17 00:00:00 2001 From: Melissa Gymrek Date: Tue, 24 Sep 2024 20:58:31 -0700 Subject: [PATCH 25/26] updating readme --- README.md | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index ae504b6..866cd9f 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,16 @@ # CITRUS🍊: A phenotype simulation tool with the flexibility to model complex interactions -CITRUS, the CIs and Trans inteRaction nUmerical Simulator, is a tool for simulating phenotypes with complex genetic archetectures that go beyond simple models that assume linear, additive contributions of individual SNPs. The goal of this tool is to provide better simulations for benchmarking GWAS/PRS models. +CITRUS, the CIs and Trans inteRaction nUmerical Simulator, is a collection of tools for simulating phenotypes with complex genetic architectures that go beyond simple models that assume linear, additive contributions of individual SNPs. The goal of CITRUS is to provide better simulations for benchmarking GWAS/PRS models. -## Installation +The key component of CITRUS is the ability to specify custom models relating genotypes to phenotypes. See the [user Guide](doc/user_guide.md) for details on specifying models. Example models are provided in `example-files/`. + +CITRUS provides multiple command line utilities for performing and analyzing simulations: -For plotting models, you will need to have [graphviz](https://graphviz.org/) installed. +* [citrus simulate](doc/cli.md#simulate): Perform a simulation using a given model +* [citrus plot](doc/cli.md#plot): Visualize a phenotype model +* [citrus shap](doc/cli.md#shap): Generate SHAP values for a model + +## Installation ### With conda @@ -31,6 +37,8 @@ conda run -n citrus poetry install conda activate citrus ``` +Note, for plotting models, you will need to have [graphviz](https://graphviz.org/) installed. + ## Quickstart ``` @@ -40,9 +48,10 @@ citrus plot -c example-files/linear_additive.json ## Full documentation +[Command Line Interface](doc/cli.md) + [User Guide](doc/user_guide.md) [Designing Simulations](doc/designing_simulations.md) -[Command Line Interface](doc/cli.md) From a63163a655600cf25d4490f3383aa3d9c2db102d Mon Sep 17 00:00:00 2001 From: Melissa Gymrek Date: Tue, 24 Sep 2024 20:59:43 -0700 Subject: [PATCH 26/26] updating readme --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 866cd9f..86d6b28 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ CITRUS, the CIs and Trans inteRaction nUmerical Simulator, is a collection of tools for simulating phenotypes with complex genetic architectures that go beyond simple models that assume linear, additive contributions of individual SNPs. The goal of CITRUS is to provide better simulations for benchmarking GWAS/PRS models. -The key component of CITRUS is the ability to specify custom models relating genotypes to phenotypes. See the [user Guide](doc/user_guide.md) for details on specifying models. Example models are provided in `example-files/`. +The key component of CITRUS is the ability to specify custom models relating genotypes to phenotypes. See the [designing simulations](doc/designing_simulations.md) for details on specifying models. Example models are provided in `example-files/`. CITRUS provides multiple command line utilities for performing and analyzing simulations: