Hierarchial Meta-Storms: An R package for community ecologists —— popular ordination methods, ecological null models & diversity analysis

Introduction
System Requirement and dependency
Installation guide
Usage
Tools in this package

Introduction

Hierarchical Meta-Storms (HMS) comprehensively calculates the dissimilarities of microbiome functional profiles by considering multi-level metabolic pathway hierarchy. It contains two core components: i) a dissimilarity algorithm that comprehensively calculates the distances among microbiome functional profiles by considering their multi-level metabolic pathway hierarchy among functional gene families, and ii) a PCoA implementation optimized by multi-thread parallel computing to rapidly parse out the beta-diversity pattern for thousands of samples. It takes the microbiome functional profiles of KO and their relative abundance as input, and computes and outputs their pairwise distance matrix and then the principle coordinates of PCoA.

In addition, the standalone package is also developed by C++ (Github: hierarchical-meta-storms) for direct installation and use under Linux and MAC operating systems.

System Requirement and dependency

Hardware Requirements

Hierarchical Meta-Storms only requires a standard computer with sufficient RAM to support the operations defined by a user. For typical users, this would be a computer with about 2 GB of RAM. For optimal performance, we recommend a computer with the following specs:

RAM: 8+ GB
CPU: 4+ cores, 3.3+ GHz/core

Software Requirements

OpenMP library is the C/C++ parallel computing library. Most Linux releases have OpenMP already been installed in the system. In Mac OS X, to install the compiler that supports OpenMP, we recommend using the Homebrew package manager:

brew install gcc

The package depends C++ (>= 4.7), R (>= 2.10) and links to Rcpp, RcppArmadillo and RcppEigen package.

Installation guide

At present, Hierarchical Meta-Storms provides a fully automatic installer for easy installation.

a. Download the package

wget http://bioinfo.single-cell.cn/Released_Software/hierarchical-meta-storms/data/hrms_1.01.tar.gz

b. Install the package in R environment

install.packages("hrms_1.01.tar.gz")

The package should take less than 1 minute to install on a computer with the specifications recommended above.

Usage

a. Load the demo datasets

data(abd_matrix)
data(dist_matrix)

b. Compute the distance matrix

compfunc(abd_matrix, rev=0, dist_type=0, is_sim=0)

The method returns the pairwise distance or similarity matix.

c. Implement the PCoA

pcoa(dist_matrix, k=3)

The method returns the coordinates matrix of PCoA.

Methods in this package

a. compfunc

It calculates the hierarchical meta-storms distance matrix among microbiome functional profiles. Run:

?compfunc

in R environment for detailed parameters.

b. pcoa

It calculates the PCoA based the distance matrix. Run:

?pcoa