auranic / elpigraph.r

An R package to construct Elastic Principal Graphs

• Description
• Installation
• Usage

Description

This package provides an R implementation of the ElPiGraph algorithm. A self-contained description of the algorithm is available here

A native MATLAB implementation of the algorithm (coded by Andrei Zinovyev and Evgeny Mirkes) is also available

Installation

To improve the performance of the algorithm, a number of functions have been implemented as C++ functions. To simplify the maintenance and updating of the package, these functions have been implemented in the package distutils, which needs to be installed separately. The following command will check the presence of the devtools, and install it if necessary, after that it will install the distutils package. A working internet connection is required.

if(!require("devtools")){
  install.packages("devtools")
}
devtools::install_github("Albluca/distutils")  

Once distutils has been installed, ElPiGraph.R can be installed by typing

devtools::install_github("Albluca/ElPiGraph.R")

It is also possible to get the most recent developmental version (which will contains more feature, but is potentially more unstable) via:

devtools::install_github("Albluca/ElPiGraph.R", ref = "Development")

The package can then be loaded via the command

library("ElPiGraph.R")

Usage

Several guides are available to exemplify the behavior of ElPiGraph.R:

• Basic usage
• Derivation of graph substructures
• Derivation and visualization of pseudotime
• Usage of the trimming radius
• Advanced bootstrapping (Currently unavailable)
• Generation of synthetic data (Currently unavailable)
• Plotting (Currently unavailable)

Acknowledgements

Supported by the University of Leicester (UK), Institut Curie (FR), the Ministry of Education and Science of the Russian Federation, project № 14.Y26.31.0022, ITMO Cancer SysBio program (MOSAIC project), INCa PLBIO program (Calys project).