SCUBA_core.py 文件源码

def PCA_analysis(data, mode, cell_stages = None):
    """Principal Component Analysis.
    """

    assert mode in {'pca', 'pca2'}

    mean_shifter = StandardScaler(with_std = False)

    if mode == 'pca':
        pca = PCA(min(data.shape))
        projected_data = pca.fit_transform(data)
        projected_data = pca.fit_transform(mean_shifter.fit_transform(data))
        components = pca.components_
    else:
        assert isinstance(cell_stages, np.ndarray)

        idx = np.where(cell_stages == np.max(cell_stages))[0]

        pca = PCA(min(idx.size, data.shape[1]))
        pca.fit(mean_shifter.fit_transform(data[idx]))
        components = pca.components_
        projected_data = np.dot(data, components.T)

    return components, projected_data