calc_principal_graph: Function to automatically learn the structure of data by...

In cole-trapnell-lab/monocle3: Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq

Function to automatically learn the structure of data by either using L1-graph or the spanning-tree formulization

Description

Function to automatically learn the structure of data by either using L1-graph or the spanning-tree formulization

Usage

calc_principal_graph(
  X,
  C0,
  maxiter = 10,
  eps = 1e-05,
  L1.gamma = 0.5,
  L1.sigma = 0.01,
  verbose = TRUE
)

Arguments

X	the input data DxN
C0	the initialization of centroids
maxiter	maximum number of iteration
eps	relative objective difference
L1.gamma	regularization parameter for k-means (the prefix of 'param' is used to avoid name collision with gamma)
L1.sigma	bandwidth parameter
verbose	emit results from iteration

Value

a list of X, C, W, P, objs X is the input data C is the centers for principal graph W is the principal graph matrix P is the cluster assignment matrix objs is the objective value for the function

cole-trapnell-lab/monocle3 documentation built on April 7, 2024, 9:24 p.m.