CellScope.cs.Visualization

CellScope.cs. Visualization (fea : np.ndarray, Visualization_Method : str = “UMAP”)

The Visualization function generates a two-dimensional representation of high-dimensional data, offering UMAP [MMH18], PCA [AW10], and t-SNE [VH08] as available visualization methods.

Parameters

• fea (np.ndarray):

  The result from either the first or second Manifold Fitting step, with dimensions (num_cell, num_Selected_Gene).

• Visualization_Method (str, optional, default=”UMAP”):

  The method used for visualizing the data. The default is UMAP, but available options include PCA, tSNE, and UMAP.

Return

• Y (ndarray):

  A matrix of size (n_cell, 2), representing the visualization result with two-dimensional coordinates for each cell.