GrowLeaves: Extend the leaves of a graph

Description Usage Arguments Value Examples

View source: R/topologies.R

Description

This function is a wrapper to the computeElasticPrincipalGraph function that construct the appropriate initial graph and grammars when increasing the nume number around the branching point

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
GrowLeaves(X, NumNodes, NumEdges = Inf, InitNodes = 2, Lambda = 0.01,
  Mu = 0.1, InitNodePositions, InitEdges = NULL, ElasticMatrix = NULL,
  MaxSteps = 100, MaxNumberOfIterations = 10, TrimmingRadius = Inf,
  eps = 0.01, Do_PCA = TRUE, AdjustVect = NULL, CenterData = TRUE,
  ComputeMSEP = TRUE, verbose = FALSE, ShowTimer = FALSE,
  ReduceDimension = NULL, drawAccuracyComplexity = TRUE,
  drawPCAView = TRUE, drawEnergy = TRUE, n.cores = 1, MinParOP = 20,
  ClusType = "Sock", nReps = 1, Subsets = list(), ProbPoint = 1,
  Mode = 1, FinalEnergy = "Base", alpha = 0, beta = 0,
  FastSolve = FALSE, ICOver = NULL, DensityRadius = NULL,
  AvoidSolitary = FALSE, EmbPointProb = 1, ParallelRep = FALSE,
  SampleIC = TRUE, AdjustElasticMatrix = NULL,
  AdjustElasticMatrix.Initial = NULL, Lambda.Initial = NULL,
  Mu.Initial = NULL, ...)

Arguments

X

numerical 2D matrix, the n-by-m matrix with the position of n m-dimensional points

NumNodes

integer, the number of nodes of the principal graph

NumEdges

integer, the maximum nulber of edges

InitNodes

integer, number of points to include in the initial graph

Lambda

real, the lambda parameter used the compute the elastic energy

Mu

real, the lambda parameter used the compute the elastic energy

InitNodePositions

numerical 2D matrix, the k-by-m matrix with k m-dimensional positions of the nodes in the initial step

InitEdges

numerical 2D matrix, the e-by-2 matrix with e end-points of the edges connecting the nodes

ElasticMatrix

numerical 2D matrix, the k-by-k elastic matrix

MaxNumberOfIterations

integer, maximum number of steps to embed the nodes in the data

TrimmingRadius

real, maximal distance of point from a node to affect its embedment

eps

real, minimal relative change in the position of the nodes to stop embedment

Do_PCA

boolean, should data and initial node positions be PCA trnasformed?

AdjustVect

boolean vector keeping track of the nodes for which the elasticity parameters have been adjusted. When true for a node its elasticity parameters will not be adjusted.

CenterData

boolean, should data and initial node positions be centered?

ComputeMSEP

boolean, should MSEP be computed when building the report?

verbose

boolean, should debugging information be reported?

ShowTimer

boolean, should the time to construct the graph be computed and reported for each step?

ReduceDimension

integer vector, vector of principal components to retain when performing dimensionality reduction. If NULL all the components will be used

drawAccuracyComplexity

boolean, should the accuracy VS complexity plot be reported?

drawPCAView

boolean, should a 2D plot of the points and pricipal curve be dranw for the final configuration?

drawEnergy

boolean, should changes of evergy VS the number of nodes be reported?

n.cores

either an integer (indicating the number of cores to used for the creation of a cluster) or cluster structure returned, e.g., by makeCluster. If a cluster structure is used, all the nodes must contains X (this is done using clusterExport)'

MinParOP

integer, the minimum number of operations to use parallel computation

ClusType

string, the type of cluster to use. It can gbe either "Sock" or "Fork". Currently fork clustering only works in Linux

nReps

integer, number of replica of the construction

Subsets

list of column names (or column number). When specified a principal curve will be computed for each of the subsets specified.

ProbPoint

real between 0 and 1, probability of inclusing of a single point for each computation

Mode

integer, the energy computation mode

FinalEnergy

string indicating the final elastic emergy associated with the configuration. Currently it can be "Base" or "Penalized"

alpha

positive numeric, the value of the alpha parameter of the penalized elastic energy

beta

positive numeric, the value of the beta parameter of the penalized elastic energy

FastSolve

boolean, should FastSolve be used when fitting the points to the data?

ICOver

string, initial condition overlap mode. This can be used to alter the default behaviour for the initial configuration of the principal curve.

DensityRadius

numeric, the radius used to estimate local density. This need to be set when ICOver is equal to "Density"

AvoidSolitary

boolean, should configurations with "solitary nodes", i.e., nodes without associted points be discarded?

EmbPointProb

numeric between 0 and 1. If less than 1 point will be sampled at each iteration. EmbPointProb indicates the probability of using each points. This is an *experimental* feature, which may helps speeding up the computation if a large number of points is present.

ParallelRep
SampleIC

boolean, should the initial configuration be considered on the sampled points when applicable?

AdjustElasticMatrix

a penalization function to adjust the elastic matrices after a configuration has been chosen (e.g., AdjustByConstant). If NULL (the default), no penalization will be used.

AdjustElasticMatrix.Initial

a penalization function to adjust the elastic matrices of the initial configuration (e.g., AdjustByConstant). If NULL (the default), no penalization will be used.

Lambda.Initial

real, the lambda parameter used the construct the elastic matrix associted with ther initial configuration if needed. If NULL, the value of Lambda will be used.

Mu.Initial

real, the mu parameter used the construct the elastic matrix associted with ther initial configuration if needed. If NULL, the value of Mu will be used.

...

optional parameter that will be passed to the AdjustElasticMatrix function

Value

A list of principal graph strucutures containing the curves constructed during the different replica of the algorithm. If the number of replicas is larger than 1. The the final element of the list is the "average curve", which is constructed by fitting the coordinates of the nodes of the reconstructed curves

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
Elastic curve with different parameters
PG <- computeElasticPrincipalCurve(X = tree_data, NumNodes = 30, InitNodes = 2, verbose = TRUE)
PG <- computeElasticPrincipalCurve(X = circle_data, NumNodes = 30, InitNodes = 2, verbose = TRUE)

PG <- computeElasticPrincipalCurve(X = tree_data, NumNodes = 30, InitNodes = 2, verbose = TRUE, Mu = 1, Lambda = .001)
PG <- computeElasticPrincipalCurve(X = circle_data, NumNodes = 30, InitNodes = 2, verbose = TRUE, Mu = 1, Lambda = .001)


Bootstrapping the construction of the curve
PG <- computeElasticPrincipalCurve(X = tree_data, NumNodes = 40, InitNodes = 2,
drawAccuracyComplexity = FALSE, drawPCAView = FALSE, drawEnergy = FALSE,
verbose = FALSE, nReps = 50, ProbPoint = .8)

PlotPG(X = tree_data, TargetPG = PG[[length(PG)]], BootPG = PG[1:(length(PG)-1)])

Albluca/ElPiGraph.R documentation built on June 10, 2018, 5:22 p.m.