Elastic principal graph construction

accuracyComplexityPlot | Accuracy-Complexity plot |

AddNode2Node | Adds a node to each graph node |

AdjustByConstant | Adjust elastic matrix by dividing the values of lambda and mu... |

ApplyOptimalGraphGrammarOpeation | Application of the grammar operation. This in an internal... |

BranchingDimension | Produce a multidimensional dimension matrix |

circle_data | Points on a circle |

CollapseBrances | Filter "small" branches |

CollapseCliques | Filter cliques |

CompareOnBranches | Compare feature values over different branches |

computeElasticPrincipalCircle | Conscruct a princial elastic circle |

computeElasticPrincipalCurve | Construct a princial elastic curve |

computeElasticPrincipalGraph | Regularize data and construct a principal elastic graph |

computeElasticPrincipalGraphWithGrammars | Conscruct a princial graph with the specified grammar |

computeElasticPrincipalTree | Conscruct a princial elastic tree |

ComputeRelativeChangeOfNodePositions | Estimates the relative difference between two node... |

ComputeSpringLaplacianMatrix | Compute the Laplacian matrix |

ConstructGraph | Generate an igraph object from a ElPiGraph structure |

curve_data | Points on a curve |

DecodeElasticMatrix | Converts ElasticMatrix into a set of edges and vectors of... |

DistanceOnGraph | Compute "on the graph" distance |

EdgeCatAssociation | Title |

ElPrincGraph | Core function to construct a principal elestic graph |

Encode2ElasticMatrix | Create an Elastic matrix from a set of edges |

ExploreNei | Interactivelly look at data |

ExtendLeaves | Extend leaves with additional nodes |

FindAssocited | Find the points associted with the final ElPiGraph structure |

fineTuneBR | Expand the nodes around a branching point |

generateInitialConfiguration | Produce an initial graph with a given structure |

GenertateConsensusGraph | Obtain a consens tree from bootstrapped data |

GetBranches | Return a data frame summarizing the branching structure |

getPrimitiveGraphStructureBarCode | Title |

GetProjectionUncertainty | Compute projection-associted uncertainty |

getPseudotime | Compute the pseudotime associted with a path |

GetSubGraph | Extract a subgraph with a given topology from a graph |

GrowLeaves | Extend the leaves of a graph |

GrowPath | Grow a branching path using walkers |

hello | Hello, World! |

InferTrimRadius | Title |

InizializeWalkers | Initialize a group of 'walkers' |

MakeUniformElasticMatrix | Create a uniform elastic matrix from a set of edges |

MeasureSmoothness | Measure smoothness of the differnt feature of the data |

PartitionData | Assign data points to a set of nodes |

plotMSDEnergyPlot | Plot the MSD VS Energy plot |

PlotPG | Plot data and principal graph(s) |

plotPieNet | Plot a graph with pie chart associated with each node |

PlotShiny | Auxiliary function used by the shiny interface |

PrimitiveElasticGraphEmbedment | Function fitting a primitive elastic graph to the data |

project_point_onto_edge | Title |

project_point_onto_graph | Project data points on the precipal graph |

RearrangePlot | Interactivelly modify data |

RemoveNodesbyIDs | Title |

ReportOnPrimitiveGraphEmbedment | Title |

ShiftBranching | Move branching nodes to areas with higher point density |

tree_data | Points on a tree |

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