Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/JoachimGoedhart/PlotsOfData

Shiny App for comparison of samples
https://github.com/JoachimGoedhart/PlotsOfData

boxplot confidence-interval datavisualization ggplot2 median shiny shiny-apps spreadsheet statistics

Last synced: 3 months ago
JSON representation

Shiny App for comparison of samples

Awesome Lists containing this project

README 

        
# PlotsOfData

A Shiny App for comparison of samples



[![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/JoachimGoedhart/Plotsofdata/master?urlpath=shiny)



### About PlotsOfData



PlotsOfData visualizes data and statistics to enable the comparison of (experimental) conditions. The philosophy of the approach is that plotting the raw data (instead of a summary) improves transparency and interpretation (see also [this blog](http://thenode.biologists.com/leaving-bar-five-steps/)). To further facilitate the comparison, summary statistics (mean, median, boxplot) and inferential statistics (confidence intervals) can be added. The user has full control over the visibility of the raw data and statistics by adjustment of the transparency (alpha). Details are described in a [publication](https://doi.org/10.1371/journal.pbio.3000202)



Bootstrapping is used to calculate the (asymmetric) 95% CI of medians. More information in [this blog](http://thenode.biologists.com/a-better-bar/education/)



The data can be supplied in spreadsheet/long format (e.g. by copy-pasting from excel) or in tidy format. For more information on the conversion of spreadsheet data to tidy data see [this blog](http://thenode.biologists.com/converting-excellent-spreadsheets-tidy-data/education/).



The plot can be saved as a PDF file, which can be opened and edited with Adobe Illustrator to allow for fine adjustments of the lay-out.



### Running the App



The app is available online: [https://huygens.science.uva.nl/PlotsOfData/](https://huygens.science.uva.nl/PlotsOfData/) or [https://amsterdamstudygroup.shinyapps.io/PlotsOfData/](https://amsterdamstudygroup.shinyapps.io/PlotsOfData/)



But you can also run it offline in R/Rstudio. In the command line (in R or Rstudio) type

shiny::runGitHub('PlotsOfData', 'JoachimGoedhart')



Or download it to use it offline:



-download the app.R and csv files with example data.



-Run RStudio and load app.R



-Select 'Run All' (shortcut is command-option-R on a Mac) or click on "Run App" (upper right button on the window)



This should launch a web browser with the Shiny app.

Note that the app depends on several R packages that need to be installed (shiny, tidyverse, dplyr, ggbeeswarm, RCurl)

Run this command in R/Rstudio to download and install all the packages at once:

-install.packages("shiny", "tidyverse", "DT", "ggbeeswarm", "RCurl")



### Background info



Videos that highlight several of the features of PlotsOfData are [available on YouTube](https://bit.ly/2FteV34)



Some aspects of the app are explained in [blogs at The Node](http://thenode.biologists.com/author/joachimg/)



### Credits



PlotsOfData is inspired on [BoxPlotR](http://shiny.chemgrid.org/boxplotr/). See [this link](https://www.nature.com/articles/nmeth.2813) for background information on boxplots.  

The code for the shiny app is partially derived from [ggplotGUI](https://github.com/gertstulp/ggplotgui) by [Gert Stulp](https://www.gertstulp.com)  

The colorblind safe palettes were developed by [Paul Tol](https://personal.sron.nl/~pault/).



PlotsOfData is created and maintained by Joachim Goedhart ([@joachimgoedhart](https://twitter.com/joachimgoedhart))and Marten Postma



### Example output



![alt text](https://github.com/JoachimGoedhart/Plotsofdata/blob/master/ComparisonPlot_example1.png "Output")