sWanderlust: sWanderlust

In JinmiaoChenLab/uSORT: uSORT: A self-refining ordering pipeline for gene selection

Description

autoSPIN guided wanderlust. Specifically, we use autoSPIN to help find the starting point for wanderlust.

Usage

sWanderlust(data, data_type = c("linear", "cyclical"),
  SPIN_option = c("STS", "neighborhood"), alpha = 0.2, sigma_width = 1,
  diffusionmap_components = 4, l = 15, k = 15, num_waypoints = 150,
  flock_waypoints = 2, waypoints_seed = 2711)

Arguments

data	data Input data matrix.
data_type	The data type which guides the autoSPIN sorting, including linear, cyclical.
SPIN_option	SPIN contains two options including STS(default), neighborhood.
alpha	alpha parameter for autoSPIN, default is 0.2.
sigma_width	Sigma width parameter for SPIN, default is 1.
diffusionmap_components	Number of components from diffusion map used for wanderlust analysis, default is 4.
l	Number of nearest neighbors, default is 15.
k	Number of nearest neighbors for repeating graphs, default is 15, should be less than or equal to l.
num_waypoints	Number of waypoint used for wanderlust, default is 150.
flock_waypoints	The number of times for flocking the waypoints, default is 2.
waypoints_seed	The seed for reproducing the results.

Value

a vector of the sorted oder.

Author(s)

Hao Chen

Examples

set.seed(15)
shuffled_iris <- iris[sample(150, 150, replace = FALSE), ]
data <- shuffled_iris[,1:4]
data_label <- shuffled_iris[,5]
wishbone <- sWanderlust(data = data, num_waypoints = 100)

JinmiaoChenLab/uSORT documentation built on May 7, 2019, 10:53 a.m.