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. 2025 Jul 25;11:e2986. doi: 10.7717/peerj-cs.2986

Table 1. Complete configuration flags of TaGra.

Option Description Default value
input_dataframe Path to the input DataFrame. *mandatory*
output_directory Path to the folder where the results will be collected. results/
preprocessed_filename Filename of the preprocessed DataFrame. None
graph_filename Filename of the graph file. None
numeric_columns List of columns to be treated as numeric. None
categorical_columns List of columns to be treated as categorical. [ ]
target_columns Column to be used as the target variable for coloring the graph and neighborhood statistics. [ ]
ignore_columns List of columns to ignore during preprocessing. [ ]
unknown_column_action Action to take on columns not specified as numeric, categorical, or ignored. “infer”
numeric_threshold Threshold for determining if a column is numeric. 0.05
numeric_scaling Method for scaling numeric columns. “standard”
categorical_encoding Method for encoding categorical columns. “one-hot”
nan_action Action to take on NaN values. “infer”
nan_threshold Threshold for dropping columns based on NaN ratio. 0.5
verbose Flag for detailed output. True
overwrite Overwrite or not the previous output. False
manifold_method Method for manifold learning on numeric columns. None
manifold_dimension Number of dimensions for manifold learning output. None
method Method for creating the graph. “knn”
k Number of neighbors for KNN graph creation. 5
distance_threshold Threshold for distance-based graph creation. None
similarity_threshold Threshold for similarity-based graph creation. None
neigh_prob_path Filename for neighborhood probability statistics. “neigh_prob.txt”
degree_distribution_filename Filename for the degree distribution plot. “degree.png”
community_filename Filename for the community composition histogram. “communities.png”
graph_visualization_filename Filename for the graph visualization. “graph.png”
prob_heatmap_filename Filename for the neighborhood probability heatmap. “neigh_prob_heatmap.png”
network_metrics_filename Filename for the other network metrics. None (will be displayed in terminal)