README.md

In JinmiaoChenLab/ClusterX: Fast clustering by automaticly search and find of density peaks

Fast clustering by automatic search and find of density peaks

ClusterX

This package implement the clustering algorithm described by Alex Rodriguez and Alessandro Laio (2014) [1] with improvements of automatic peak detection and parallel computing.

Installation

To install the latest version from the github repository, use:

if(!require(devtools)){
  install.packages("devtools") # If not already installed
}
devtools::install_github("JinmiaoChenLab/ClusterX")

Usage

After installing the package, use the following code to run a simple example (to install, see below).

dir <- system.file("extdata", package = "ClusterX")
r15 <- read.table(paste(dir, "R15.txt", sep = .Platform$file.sep), header = FALSE)
r15_c <- ClusterX(r15[,c(1,2)])
clusterPlot(r15_c)
peakPlot(r15_c)

d31 <- read.table(paste(dir, "D31.txt", sep = .Platform$file.sep), header = FALSE)
d31_c <- ClusterX(d31[,c(1,2)])
clusterPlot(d31_c)
densityPlot(d31_c)
peakPlot(d31_c)

Reference

[1] Rodriguez A, Laio A. Clustering by fast search and find of density peaks. Science. 2014;344: 1492–6. doi:10.1126/science.1242072

JinmiaoChenLab/ClusterX documentation built on May 7, 2019, 10:52 a.m.