Partition-Assisted Clustering and Multiple Alignments of Networks

aggregateData | Aggregates results from the clustering and merging step. |

annotateClades | Creates annotation matrix for the clades in aggregated... |

annotationMatrix_withSubpopProp | Adds subpopulation proportion for the annotation matrix for... |

BSPLeaveCenter | Finds N Leaf centers in the data |

constellationPlot | Makes constellation plot, in which the centroids are clusters... |

fmeasure | F-measure Calculation |

getAverageSpreadOf2SubpopClades | Calculate the (global) average spread of subpopulations in... |

getExtraneousCladeSubpopulations | Calculates subpopulations in clades (with two or more... |

getRepresentativeNetworks | Representative Networks |

heatmapInput | Creates the matrix that can be easily plotted with a heatmap... |

JaccardSM | Calculates the Jaccard similarity matrix. |

MAN | Creates network alignments using network constructed from... |

MINetwork_matrix_topEdges | Mutual information network connection matrix generation... |

MINetworkPlot_topEdges | Plots mutual information network (mrnet algorithm) connection... |

MINetwork_simplified_topEdges | Outputs the vectorized summary of a network based on the... |

outputNetworks_topEdges_matrix | Wrapper to output the mutual information networks for... |

outputRepresentativeNetworks_topEdges | Outputs the representative/clade networks (plots and summary... |

PAC | Partition Assisted Clustering PAC 1) utilizes dsp or bsp-ll... |

recordWithinClusterSpread | Calculates the within cluster spread |

refineSubpopulationLabels | Refines the subpopulation labels from PAC using network... |

renamePrunedSubpopulations | Prune away specified subpopulations in clades that are far... |

runElbowPointAnalysis | Runs elbow point analysis to find the practical optimal... |

samplePass | Run PAC for Specified Samples |

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