svgbit 0.1.0

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svgbit

Installation

Install with pip:

pip install svgbit

Usage

Command-line interface

svgbit has a command line version. Just tape

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

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.DataFrameand 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

svgbit.run(dataset)

Visit our API reference for further detail.

API References

Citation