annotationMatrix_withSubpopProp
Adds subpopulation proportion for the annotation matrix for the clades
Plots mutual information network (mrnet algorithm) connection using the parmigene package. Mutual information calculated with infotheo package.
Calculates the Jaccard similarity matrix.
getAverageSpreadOf2SubpopClades
Calculate the (global) average spread of subpopulations in clades with 2 subpopulations on the constellation plot.
refineSubpopulationLabels
Refines the subpopulation labels from PAC using network alignment and small subpopulation information. Outputs a new set of files containing the representative labels.
recordWithinClusterSpread
Calculates the within cluster spread
getExtraneousCladeSubpopulations
Calculates subpopulations in clades (with two or more subpopulations) that are too far away from other subpopulations (within the same clade) on the constellation plot; these far away subpopulations should be pruned away from the original clades.
getRepresentativeNetworks
Representative Networks
Creates the matrix that can be easily plotted with a heatmap function available in an R package
Aggregates results from the clustering and merging step.
outputRepresentativeNetworks_topEdges
Outputs the representative/clade networks (plots and summary vectors) for subpopulations with size larger than a desired threshold. Saves the networks and the data matrices without the smaller subpopulations.
outputNetworks_topEdges_matrix
Wrapper to output the mutual information networks for subpopulations with size larger than a desired threshold.
Run PAC for Specified Samples
F-measure Calculation
Makes constellation plot, in which the centroids are clusters are embedded in the t-SNE 2D plane and the cross-sample relationships are plotted as lines connecting related sample clusters (clades).
Runs elbow point analysis to find the practical optimal number of clades to output. Outputs the average within sample cluster spread for all samples and the elbow point analysis plot with loess line fitted through the results.
renamePrunedSubpopulations
Prune away specified subpopulations in clades that are far away.
Creates annotation matrix for the clades in aggregated format. The matrix contains average signals of each dimension for each clade in each sample
MINetwork_matrix_topEdges
Mutual information network connection matrix generation (mrnet algorithm) using the parmigene package. Mutual information calculated with infotheo package.
Partition Assisted Clustering
PAC 1) utilizes dsp or bsp-ll to recursively partition the data space and 2) applies a short round of kmeans style postprocessing to efficiently output clustered labels of data points.
Finds N Leaf centers in the data
MINetwork_simplified_topEdges
Outputs the vectorized summary of a network based on the number of edges connected to a node
Creates network alignments using network constructed from subpopulations after PAC