simspace 0.3.1__tar.gz → 0.3.2__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {simspace-0.3.1/simspace.egg-info → simspace-0.3.2}/PKG-INFO +4 -6
- {simspace-0.3.1 → simspace-0.3.2}/README.md +4 -6
- {simspace-0.3.1 → simspace-0.3.2}/pyproject.toml +1 -1
- {simspace-0.3.1 → simspace-0.3.2}/setup.py +1 -1
- {simspace-0.3.1 → simspace-0.3.2}/simspace/optimize.py +1 -1
- {simspace-0.3.1 → simspace-0.3.2/simspace.egg-info}/PKG-INFO +4 -6
- {simspace-0.3.1 → simspace-0.3.2}/LICENSE +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/MANIFEST.in +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/setup.cfg +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/simspace/R/.Rprofile +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/simspace/R/SRTsim.R +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/simspace/R/install_r_deps.R +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/simspace/R/renv/activate.R +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/simspace/R/renv.lock +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/simspace/R/scdesign.R +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/simspace/R/splatter.R +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/simspace/R/splatter_fit.R +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/simspace/__init__.py +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/simspace/core.py +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/simspace/initialize/initialize.py +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/simspace/initialize/neighbors.py +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/simspace/niche.py +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/simspace/omics.py +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/simspace/plot.py +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/simspace/spatial.py +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/simspace/util.py +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/simspace.egg-info/SOURCES.txt +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/simspace.egg-info/dependency_links.txt +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/simspace.egg-info/requires.txt +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/simspace.egg-info/top_level.txt +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/tests/test_core.py +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/tests/test_omics.py +0 -0
- {simspace-0.3.1 → simspace-0.3.2}/tests/test_util.py +0 -0
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Metadata-Version: 2.4
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Name: simspace
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Version: 0.3.
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Version: 0.3.2
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Summary: SimSpace: a comprehensive in-silico spatial omics data simulation framework
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Author: Tianxiao Zhao
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License: MIT
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[](https://simspace.readthedocs.io/en/latest/)
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[](https://pypi.org/project/simspace/)
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**SimSpace** is a Python framework for simulating spatial omics data with realistic cellular distributions and tissue organization. Designed for benchmarking spatial analysis methods, SimSpace enables generation of synthetic datasets that preserve spatial autocorrelation, cell-cell interactions, and spatial proximities using a Markov Random Field (MRF) model.
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**SimSpace** is a Python framework for simulating spatial omics data with realistic cellular distributions and tissue organization. Designed for benchmarking spatial analysis methods, SimSpace enables generation of synthetic datasets that preserve spatial autocorrelation, cell-cell interactions, and spatial proximities using a Markov Random Field (MRF) model.
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For full figure reproduction (all analyses and scripts) for the SimSpace manuscript, see: https://github.com/TianxiaoNYU/simspace-reproducibility
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## 📦 Installation
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To install the latest version of SimSpace, we recommend using conda to setup the environment:
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These resources walk through how to configure and run simulations as well as visualize outputs.
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To reproduce the figures in the manuscript, one can find the scripts at [`fig_reproduce/figures.ipynb`](./fig_reproduce/figures.ipynb).
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## 🚀 Quick Start
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Here’s a basic example to simulate a 2D tissue with 3 spatial niches and 8 cell types:
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## 🔗 References
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If you use SimSpace in your work, please cite the work on BioRxiv:
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[Zhao T, Zhang K, Hollenberg M, Zhou W, Fenyo D. SimSpace: a comprehensive in-silico spatial omics data simulation framework. bioRxiv. 2025:2025.07.18.665587.](https://www.biorxiv.org/content/10.1101/2025.07.18.665587)
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[](https://simspace.readthedocs.io/en/latest/)
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[](https://pypi.org/project/simspace/)
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**SimSpace** is a Python framework for simulating spatial omics data with realistic cellular distributions and tissue organization. Designed for benchmarking spatial analysis methods, SimSpace enables generation of synthetic datasets that preserve spatial autocorrelation, cell-cell interactions, and spatial proximities using a Markov Random Field (MRF) model.
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**SimSpace** is a Python framework for simulating spatial omics data with realistic cellular distributions and tissue organization. Designed for benchmarking spatial analysis methods, SimSpace enables generation of synthetic datasets that preserve spatial autocorrelation, cell-cell interactions, and spatial proximities using a Markov Random Field (MRF) model.
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For full figure reproduction (all analyses and scripts) for the SimSpace manuscript, see: https://github.com/TianxiaoNYU/simspace-reproducibility
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## 📦 Installation
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To install the latest version of SimSpace, we recommend using conda to setup the environment:
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These resources walk through how to configure and run simulations as well as visualize outputs.
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To reproduce the figures in the manuscript, one can find the scripts at [`fig_reproduce/figures.ipynb`](./fig_reproduce/figures.ipynb).
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## 🚀 Quick Start
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Here’s a basic example to simulate a 2D tissue with 3 spatial niches and 8 cell types:
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## 🔗 References
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If you use SimSpace in your work, please cite the work on BioRxiv:
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[Zhao T, Zhang K, Hollenberg M, Zhou W, Fenyo D. SimSpace: a comprehensive in-silico spatial omics data simulation framework. bioRxiv. 2025:2025.07.18.665587.](https://www.biorxiv.org/content/10.1101/2025.07.18.665587)
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[Zhao T, Zhang K, Hollenberg M, Zhou W, Fenyo D. SimSpace: a comprehensive in-silico spatial omics data simulation framework. bioRxiv. 2025:2025.07.18.665587.](https://www.biorxiv.org/content/10.1101/2025.07.18.665587)
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setup(
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name="simspace",
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version="0.3.
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version="0.3.2",
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description="SimSpace: a comprehensive in-silico spatial omics data simulation framework",
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long_description=long_description,
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long_description_content_type="text/markdown",
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## Define the Fitness Function, which do the simulation first and then calculate the fitness value
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#### The fitness value is the distance between the simulation result and the experimental data
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def _get_spatial_statistics(simulation, n_state):
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simulation.columns = ['celltype', 'x', 'y', 'celltype_ranked']
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simulation.columns = ['celltype', 'x', 'y', 'niche', 'celltype_ranked']
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tmp = simulation[simulation['celltype'] == -1].index
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simulation = simulation.drop(tmp)
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simulation = simulation.reset_index(drop=True)
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Metadata-Version: 2.4
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Name: simspace
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Version: 0.3.
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Version: 0.3.2
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Summary: SimSpace: a comprehensive in-silico spatial omics data simulation framework
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Author: Tianxiao Zhao
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License: MIT
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[](https://simspace.readthedocs.io/en/latest/)
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[](https://pypi.org/project/simspace/)
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**SimSpace** is a Python framework for simulating spatial omics data with realistic cellular distributions and tissue organization. Designed for benchmarking spatial analysis methods, SimSpace enables generation of synthetic datasets that preserve spatial autocorrelation, cell-cell interactions, and spatial proximities using a Markov Random Field (MRF) model.
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**SimSpace** is a Python framework for simulating spatial omics data with realistic cellular distributions and tissue organization. Designed for benchmarking spatial analysis methods, SimSpace enables generation of synthetic datasets that preserve spatial autocorrelation, cell-cell interactions, and spatial proximities using a Markov Random Field (MRF) model.
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For full figure reproduction (all analyses and scripts) for the SimSpace manuscript, see: https://github.com/TianxiaoNYU/simspace-reproducibility
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35
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## 📦 Installation
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34
36
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To install the latest version of SimSpace, we recommend using conda to setup the environment:
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@@ -94,8 +96,6 @@ To get started with SimSpace, we provide detailed tutorials covering both refere
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These resources walk through how to configure and run simulations as well as visualize outputs.
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To reproduce the figures in the manuscript, one can find the scripts at [`fig_reproduce/figures.ipynb`](./fig_reproduce/figures.ipynb).
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## 🚀 Quick Start
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Here’s a basic example to simulate a 2D tissue with 3 spatial niches and 8 cell types:
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@@ -132,5 +132,3 @@ Developed by Tianxiao Zhao at NYU Grossman School of Medicine. Should you have a
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## 🔗 References
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If you use SimSpace in your work, please cite the work on BioRxiv:
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[Zhao T, Zhang K, Hollenberg M, Zhou W, Fenyo D. SimSpace: a comprehensive in-silico spatial omics data simulation framework. bioRxiv. 2025:2025.07.18.665587.](https://www.biorxiv.org/content/10.1101/2025.07.18.665587)
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