index.Rmd

---
title: "Data analysis pipeline in Paterlini, Belevich *et al.*, 2020"
author: "created by Andrea Paterlini"
date: "*1st October 2019*"

---

<br>

Hello user!

Welcome to the online resources for the Paterlini, Belevich *et al.*, 2020 paper. 
The paper will be found at the journal website [here](http://www.plantphysiol.org/content/184/1/53).

These resources (in the form of plugins and scripts) have been developed to study Plasmodesmata, small channels that connect plant cells[^1]. Our goal was to extract information about their spatial distribution and cellular environment, as described in our paper.

However, in principle, both the plugins and the pipelines can be more broadly applied and we are happy for people to get ideas from them, tweak them or repurpose them to better suit their specific needs. Should people do so, we request the developers to provide the corresponding annotated code on some open source platform, in order for the community to benefit from it.

In this document, which was generated with R Markdown[^2], you will be guided through the specific data analysis steps performed in the paper. The raw files of this R Markdown are stored on my GitHub (AndreaPaterlini) at this [repository](https://github.com/AndreaPaterlini/Plasmodesmata_dist_wall). You don't need them for the analysis process but you are welcome to look at them if you are interested in the source code.

The aim is for you to apply this pipeline (or parts of the same) to your own data. We provide some sample datasets here just for you to familiarise yourself with the various steps and scripts employed. 

When you are ready please move to the [Preliminary steps section](preliminary.html)

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# Outline of the sections

<br>

* [Preliminary steps](preliminary.html) **details the required software, data and libraries**
* [Distributions](distributions.html) **looks for spatial patterns of how PDs are distributed over a cellular interface**
* [Clusters](clusters.html) **quantifies parameters of the detected PD clusters, such as their number per interface**
* [Surfaces](surfaces.html) **calculates what proportions of the cellular surface these clusters occupy**
* [Cell wall](wall.html) **looks for differences in thickness of the cell wall in proximity of plasmodesmata**
* [Alternatives](ripley.html) provides alternative approaches for the spatial analysis

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# Contacts 

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Please report issues concerning the R code present on this website by opening a new issue on our repository (alternatively, please e-mail andrea.paterlini@slcu.cam.ac.uk). Suggestions are also warmly welcomed.

For comments directly related to the workings of the plugins please contact ilya.belevich@helsinki.fi 
You can also check out [his GitHub](https://github.com/Ajaxels).

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# License and Citation 

<br>

The work is under a GNU AGPLv3 open access license[^3]. Please compile with its conditions.

When using or editing the resources developed here please reference the paper and the online resources on the github of [Andrea Paterlini](https://github.com/AndreaPaterlini).

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# Acknowledgements 

<br>

We thank [Hugo Tavares](https://github.com/tavareshugo) from [SLCU - University of Cambridge](https://www.slcu.cam.ac.uk/people/tavares-hugo) for his kind help in setting up this website and repository. Check out his github repositories and profile.

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[^1]: For a short review paper on Plasmodesmata with good illustrations we refer to 
https://jcs.biologists.org/content/131/11/jcs209346.long

[^2]: For more information about simple R Markdown websites, please read the documentation at 
https://bookdown.org/yihui/rmarkdown/rmarkdown-site.html.

[^3]: For more information on GNU AGPLv3 and other types of licenses, please read the documentation at 
https://choosealicense.com/licenses/