Metadata-Version: 2.1
Name: svgbit
Version: 0.0.15
Summary: UNKNOWN
Home-page: https://github.com/CPenglab/svgbit
Author: CPenglab
Author-email: chengpeng@ynu.edu.cn
License: MIT
Description: # svgbit
        
        ## Installation
        
        Install with `pip`:
        
        ```sh
        pip install svgbit
        ```
        
        ## Usage
        
        ### Command-line interface
        svgbit has a command line version. Just tape
        
        ```sh
        svgbit --help
        ```
        
        after installation, and you may get a short help massage
        
        ```
        usage: svgbit [-h] [--count_transpose] [--coordinate_transpose] [--k K] [--n_svgs N_SVGS]
                      [--n_svg_clusters N_SVG_CLUSTERS] [--he_image HE_IMAGE] [--savedir SAVEDIR]
                      [--cores CORES]
                      count coordinate
        
        Find spatial variable genes for Spatial Trasncriptomics data.
        
        positional arguments:
          count                 path to count matrix file (shape: (spot * gene))
          coordinate            path to coordinate file (shape: (spot * 2))
        
        optional arguments:
          -h, --help            show this help message and exit
          --count_transpose     transpose count matrix if specified
          --coordinate_transpose
                                transpose coordinate file if specified
          --k K                 number of nearest neighbors for KNN network (default: 6)
          --n_svgs N_SVGS       number of SVGs to find clusters (default: 1000)
          --n_svg_clusters N_SVG_CLUSTERS
                                number of SVG clusters to find (default: 8)
          --he_image HE_IMAGE   path to H&E image. Only used for visualization (default: None)
          --savedir SAVEDIR     path to save results (default: .)
          --cores CORES         number of threads to run svgbit (default: 8)
        ```
        
        Follow the introduction and results will save to --savedir. 
        
        ### Python API
        svgbit has a set of python API. You may run svgbit through command line or python.
        We recommend the usage of python API for more feature and full control of your input
        data.
        
        #### Load data
        
        ```python
        import svgbit
        dataset = svgbit.STDataset(
            count_df="Data/count_df.csv",
            coordinate_df="Data/coor_df.csv",
            count_df_kwargs={"index_col": 0, "header": 0},
            coordinate_df_kwargs={"index_col": 0, "header": 0},
        )
        ```
        
        `svgbit.STDataset` also accept `pd.DataFrame`and `np.array` as `count_df` and 
        `coordinate_df`. If `str` or `pathlib.Path` are given, svgbit would try to load
        data with `pandas`.
        
        **Notice**: svgbit assume that the shape of count matrix and coordinate file is 
        (spot * gene) and (spot * 2). Specify `count_transpose` and `coordinate_transpose`
        as `True` when necessary. 
        
        #### Run svgbit with one function
        
        ```python
        svgbit.run(dataset)
        ```
        
        Visit our API reference for further detail.
        
        ## API References
        
        ## Citation
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8.12
Description-Content-Type: text/markdown
