After running CEFCON_obj.preprocess(), only one lineage can be found, with the name all

[Zstark11]

import cefcon as cf
import matplotlib.pyplot as plt
import warnings
import scanpy as sc
warnings.filterwarnings("ignore")

adata = sc.read("IT-blood-NSX-CD8.h5ad")
prior_network = cf.datasets.load_human_prior_interaction_network(dataset='nichenet')
data = cf.data_preparation(adata, prior_network)

The result is:

Start data preparation

[0] - Data loading and preprocessing...
Consider the input data with 1 lineages:
  Lineage - all:
    73 extra edges (Spearman correlation > 0.6) are added into the prior gene interaction network.
    Total number of edges: 97346.
    n_genes × n_cells = 2142 × 7091

My anndata data structure is:

AnnData object with n_obs × n_vars = 7091 × 3000
    obs: 'V_pseudotime', 'D_pseudotime', 'batch', 'nUMIs', 'mito_perc', 'detected_genes', 'cell_complexity', 'n_genes', 'doublet_score', 'predicted_doublet', 'passing_mt', 'passing_nUMIs', 'passing_ngenes', 'leiden_res1', 'scsa_celltype_cellmarker-1', 'major_celltype', '_scvi_batch', '_scvi_labels', 'condition', 'scCODA_sample_id', 'major_celltype_combined', 'S_pseudotime', 'pt_via'
    var: 'gene_ids', 'mt', 'n_cells', 'percent_cells', 'robust', 'highly_variable_rank', 'means', 'variances', 'variances_norm', 'highly_variable_nbatches', 'highly_variable_features'
    uns: '_scvi_manager_uuid', '_scvi_uuid', 'batch_colors', 'dea_leiden_res1', 'dea_leiden_res1-combined', 'dea_leiden_resMo', 'dendrogram_leiden_res1', 'dendrogram_major_celltype', 'dendrogram_major_celltype_combined', 'diffmap_evals', 'draw_graph', 'expected_values', 'hvg', 'iroot', 'layers_counts', 'leiden_res1', 'leiden_res1_colors', 'log1p', 'major_celltype_colors', 'major_celltype_combined_colors', 'major_celltype_combined_sizes', 'neighbors', 'paga', 'paga_graph', 'pca', 'rank_genes_groups', 'roe_results', 'scaled|original|cum_sum_eigenvalues', 'scaled|original|pca_var_ratios', 'scrublet', 'scsa_celltype_cellmarker-1_colors', 'sig_roe_results', 'tsne', 'umap'
    obsm: 'X_diffmap', 'X_draw_graph_fa', 'X_draw_graph_fr', 'X_harmony', 'X_mde_harmony', 'X_mde_pca', 'X_mde_scANVI', 'X_mde_scVI', 'X_pca', 'X_scANVI', 'X_scVI', 'X_tsne', 'X_umap', 'scaled|original|X_pca'
    layers: 'lognorm'
    obsp: 'connectivities', 'distances'

Why can I only find 1 Lineage, and it's named all?

[Zstark11]

Later, I can also recognize a lineage after importing an anndata object without a pseudotime, and the name is all

AnnData object with n_obs × n_vars = 12791 × 3000
    obs: 'batch', 'nUMIs', 'mito_perc', 'detected_genes', 'cell_complexity', 'n_genes', 'doublet_score', 'predicted_doublet', 'passing_mt', 'passing_nUMIs', 'passing_ngenes', 'leiden_res1', 'scsa_celltype_cellmarker-1', 'major_celltype', '_scvi_batch', '_scvi_labels', 'condition', 'scCODA_sample_id', 'leiden_NK', 'NK_celltype'
    var: 'gene_ids', 'mt', 'n_cells', 'percent_cells', 'robust', 'highly_variable_rank', 'means', 'variances', 'variances_norm', 'highly_variable_nbatches', 'highly_variable_features'
    uns: '_scvi_manager_uuid', '_scvi_uuid', 'batch_colors', 'dea_leiden_res1', 'dea_leiden_resMo', 'dendrogram_leiden_res1', 'dendrogram_major_celltype', 'expected_values', 'hvg', 'layers_counts', 'leiden_NK', 'leiden_NK_colors', 'leiden_res1', 'leiden_res1_colors', 'log1p', 'major_celltype_colors', 'neighbors', 'pca', 'rank_genes_groups', 'roe_results', 'scaled|original|cum_sum_eigenvalues', 'scaled|original|pca_var_ratios', 'scrublet', 'scsa_celltype_cellmarker-1_colors', 'sig_roe_results', 'tsne', 'umap'
    obsm: 'X_harmony', 'X_mde_harmony', 'X_mde_pca', 'X_mde_scANVI', 'X_mde_scVI', 'X_pca', 'X_scANVI', 'X_scVI', 'X_tsne', 'X_umap', 'scaled|original|X_pca'
    varm: 'PCs', 'scaled|original|pca_loadings'
    layers: 'counts', 'lognorm', 'scaled'
    obsp: 'connectivities', 'distances'

data = cf.data_preparation(adata, prior_network)

Start data preparation

[0] - Data loading and preprocessing...
Consider the input data with 1 lineages:
  Lineage - all:
    6 extra edges (Spearman correlation > 0.6) are added into the prior gene interaction network.
    Total number of edges: 97279.
    n_genes × n_cells = 2142 × 12791

I wonder how cf.data_preparation identify the pseudotime in anndata