Man pages for Albluca/ElPiGraph.R
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 |
