runWanderlust: Run the wanderlust algorithm

In kbrulois/MATLABfuncs: R interface for the MATLAB implementation of the tSpace and wanderlust algorithms

Description

This is an interface to the wanderlust algorithm described in Bendall et al.

Usage

runWanderlust(
  data,
  s,
  k = c(20, 30, 50, 100),
  l = "auto",
  metric = "euclidean",
  graphs = 20,
  landmarks = 20,
  voting_scheme = "exponential",
  matlab_version = "auto",
  matlab_path = "~/Documents/MATLAB"
)

Arguments

data	A matrix-like object where cells correspond to rows and features correspond to columns.
k	Number of nearest neighbors. If a vector of integers is provided (recommended), the wanderlust calculation will be attempted on the smallest value in the vector and then reattempted on successively higher values of k should the algorithm fail. Wanderlust caclualtions that require an excessively high k value suggest the presence of outlier data points that should be removed from the input data for better performance.
l	Number of nearest neighbors. If set to 'auto' (default), l will be 2/3 of k (rounded to the nearest integer). If k is a vector, l must be a vector the same length and all corresponding values must be less than k.
metric	A distance metric accepted by the dist function in matlab: euclidean, correlation, cityblock, chebyshev, minkowski, hamming, mahalanobis, jaccard, cosine or spearman.
graphs	Number of graphs over which to average trajectories.
landmarks	Number of landmarks.
voting_scheme	Arugment passed to wanderlust.
matlab_version	A character string specifying the active matlab version (e.g. "R2019a"). If set to "auto," the latest version of matlab will be used. Only works for mac users.
matlab_path	The path to the MATLAB folder containing cyt and tSpace scripts.

Value

A data.frame containing the cell labels and the wanderlust trajectory.

Author(s)

Kevin Brulois

kbrulois/MATLABfuncs documentation built on Sept. 14, 2021, 2:02 p.m.