README.md

In JRC-COMBINE/PlantPhysioSpace: Plant Stress Response Analysis by Mapping into Physiological Spaces

PlantPhysioSpace

Notice: This repository is missing raw files!

Due to file size restrictions of GitHub, we moved the full version of package to a GitLab repository, hosted by RWTH Aachen university.

For accessing raw files and scripts for generating included spaces, use the GitLab version here: https://git.rwth-aachen.de/jrc-combine/PlantPhysioSpace.

PlantPhysioSpace is a R data package which provides plant stress spaces to be used with the package PhysioSpaceMethods for in depth analysis of plant response to different types of stress.

Table of Contents

Installation Instructions License Usage Instructions Test Environments

Installation Instructions

It is recommended to install PhysioSpaceMethods before PlantPhysioSpace. More information about how to install PhysioSpaceMethods is provided in https://github.com/JRC-COMBINE/PhysioSpaceMethods.

Installing via Devtools (Recommended method):

Easiest way to install PlantPhysioSpace is via Devtools. After installing Devtools from cran, you can install PlantPhysioSpace by:

devtools::install_github(repo = "JRC-COMBINE/PlantPhysioSpace", build_vignettes = TRUE)

Alternative installation methods (Manual download):

In case you encountered any problem while installing PlantPhysioSpace, you can download the repository first and install the package from downloaded local files. In your terminal, first clone the repository in your desired repository:

cd [Your desired directory]
git clone https://github.com/JRC-COMBINE/PlantPhysioSpace.git

Then install the downloaded package using Devtools:

R -e "devtools::install_local('./PlantPhysioSpace/', build_vignettes = TRUE)"

License

Distributed under GNU General Public License v3.0. See the accompanying license file or the copy at https://www.gnu.org/licenses/gpl-3.0.html.

Usage Instructions

PlantPhysioSpace can map user samples inside a physiological space, calculated prior from a compendium of known samples. We demonstrated how to use this package in a vignette which you can access via:

browseVignettes(package = "PlantPhysioSpace")

Test Environments

The package was tested with R 3.4 on ~~Windows 10~~, Mac OS X and ~~Linux (CentOS 7.4)~~.

JRC-COMBINE/PlantPhysioSpace documentation built on Nov. 25, 2020, 8:01 a.m.