clustering_utils

Functions

clustering_of_correlation_matrix(...)	Function for hierarchical clustering of the correlation matrix
plot_dendrogram(dissimilarity_matrix, reactions, group_map)	Function that plots the dendrogram from hierarchical clustering

Module Contents

clustering_utils.clustering_of_correlation_matrix(correlation_matrix: numpy.typing.NDArray[numpy.float64], reactions: List, linkage: str = 'ward', t: float = 4.0, correction: bool = True) → Tuple[numpy.typing.NDArray[numpy.float64], numpy.typing.NDArray[numpy.float64], List[List]]

Function for hierarchical clustering of the correlation matrix

Keyword arguments: correlation_matrix (NDArray[np.float64]) – A numpy 2D array of a correlation matrix reactions (List) – A list with the corresponding reactions (must be in accordance with the correlation matrix) linkage (str) – linkage defines the type of linkage. Available linkage types are: single, average, complete, ward. t (float) – A threshold that defines a threshold that cuts the dendrogram at a specific height and produces clusters correction (bool) – A boolean variable that if True converts the values of the the correlation matrix to absolute values.

Returns: Tuple[NDArray[np.float64], NDArray[np.float64], List[List]]

dissimilarity_matrix (NDArray[np.float64]) – The dissimilarity matrix calculated from the given correlation matrix labels (NDArray[np.float64]) – Integer labels corresponding to clusters clusters (List[List]) – Nested list containing reaction IDs grouped based on their cluster labels

clustering_utils.plot_dendrogram(dissimilarity_matrix: numpy.typing.NDArray[numpy.float64], reactions: List, group_map: dict, linkage: str = 'ward', t: float = 4.0, label_fontsize: int = 10, height: int = 600, width: int = 1000, show_labels: bool = True, title: str = '')

Function that plots the dendrogram from hierarchical clustering

Keyword arguments: dissimilarity_matrix (NDArray[np.float64]) – The dissimilarity matrix calculated from the clustering_of_correlation_matrix function reactions (List) – List with reactions IDs group_map (Dict) – Dictionary mapping reactions to pathways linkage (str) – linkage defines the type of linkage. Available linkage types are: single, average, complete, ward. t (float) – A threshold that defines a threshold that cuts the dendrogram at a specific height label_fontsize (int) – Size for the plotted labels (reaction IDs) height (int) – Defines the height of the plot width (int) – Defines the width of the plot show_labels (bool) – Boolean variable that if True labels are shown in the x-axis title (str) – Title for the plot