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<h1> <img src="http://www.combine.rwth-aachen.de/files/cbio/content/partner/PlantPhysiosSpace_Logo3small.png" width=100> PlantPhysioSpace</h1>
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PlantPhysioSpace is a R data package which provides plant stress spaces to be used with the package <a href="https://git.rwth-aachen.de/jrc-combine/physiospacemethods">PhysioSpaceMethods</a> for in depth analysis of plant response to different types of stress.
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#### Table of Contents
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**[Installation Instructions](#installation-instructions)**<br>
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**[License](#license)**<br>
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**[Usage Instructions](#usage-instructions)**<br>
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**[Test Environments](#test-environments)**<br>
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### Installation Instructions
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It is recommended to install [PhysioSpaceMethods](https://git.rwth-aachen.de/jrc-combine/physiospacemethods) before PlantPhysioSpace. More information about how to install PhysioSpaceMethods is provided in https://git.rwth-aachen.de/jrc-combine/physiospacemethods.
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#### Installing via Devtools (Recommended method):
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Easiest way to install PlantPhysioSpace is via <a href="https://cran.r-project.org/web/packages/devtools/">Devtools</a>.
After installing Devtools from cran, you can install PlantPhysioSpace by:
```r
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devtools::install_github(repo = "JRC-COMBINE/PlantPhysioSpace", build_vignettes = TRUE)
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```

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#### Alternative installation methods (Manual download):
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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:
```Shell
cd [Your desired directory]
git clone https://github.com/JRC-COMBINE/PlantPhysioSpace.git
```
Then install the downloaded package using <a href="https://cran.r-project.org/web/packages/devtools/">Devtools</a>:
```Shell
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R -e "devtools::install_local('./PlantPhysioSpace/', build_vignettes = TRUE)"
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```

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### License
Distributed under GNU General Public License v3.0. See the accompanying [license](https://github.com/JRC-COMBINE/PlantPhysioSpace/blob/master/LICENSE) file or the copy at https://www.gnu.org/licenses/gpl-3.0.html.

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### Usage Instructions
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PlantPhysioSpace can map user samples inside a physiological space, calculated prior from a compendium 
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of known samples. We demonstrated how to use this package in a vignette which you can access via:
```r
browseVignettes(package = "PlantPhysioSpace")
```
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### Test Environments
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The package was tested with R 3.4 on ~~Windows 10~~, Mac OS X and ~~Linux (CentOS 7.4)~~.