94ec55bd5c13d75a590f82d41ff66e422bc11b1d,scanpy/tools/tsne.py,,tsne,#Any#Any#Any#,26

Before Change

        X = adata["X_pca"]
        sett.m(0, "using X_pca for tSNE")
    else:
        if params["n_pcs"] > 0 and adata.X.shape[1] > params["n_pcs"]:
            sett.m(0, "preprocess using PCA with", params["n_pcs"], "PCs")
            sett.m(0, "--> avoid this by setting n_pcs = 0")
            dpca = pca(adata, n_comps=params["n_pcs"])

After Change

        if n_pcs > 0 and adata.X.shape[1] > n_pcs:
            sett.m(0, "preprocess using PCA with", n_pcs, "PCs")
            sett.m(0, "--> avoid this by setting n_pcs = 0")
            X = pca(adata.X, n_comps=n_pcs)
            adata["X_pca"] = X
        else:
            X = adata.X
    // params for sklearn

Instances