PlotXpress

PlotXpress is a shiny app that simplifies the analysis and plotting of data from a dual luciferase experiment in 96-well format.

Operation

The app is available online: https://huygens.science.uva.nl/PlotXpress/

The app can also run locally. To launch the app from R/Rstudio, paste this in the command line:

shiny::runGitHub('PlotXpress', 'ScienceParkStudyGroup')

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, ggplot2, dplyr, tidyr, readr, magrittr, readxl, DT, stringr) Run this command in R/Rstudio to download and install all the packages at once: -install.packages("shiny", "ggplot2", "dplyr", "tidyr", "magrittr", "readxl", "DT", "readr", "stringr")

Input data (expressed as arbitrary luminescence units)

Option 1

• Excel sheet containing 2 tables in 96-well lay-out (raw output from a Promega GloMax® Navigator). An unprocessed example output file is included: DualLuc_example_data.xlsx
• A CSV file in which conditions are listed for each well. An example file is available in this repo: Tidy_design.csv

Option 2

• A CSV in tidy format that contains the data and the condition. The minimal information that is required is a column with wells (in the format A01, B01, ..), a column with intensity data and a column with the conditions. An example file is available in this repo: plotXpress_Tidy-3.csv

Example output

Standard output generated with the example data and example design:

Credits

The plotXpress app is created as a team effort by Elias Brandorff, Marc Galland & Joachim Goedhart

Contact

Questions related to the shiny app can be addressed to: Joachim Goedhart (@joachimgoedhart)

License

The Apache-2.0 License (see the file LICENSE for full text) applies to the software and the CC-BY-4 license (see the file LICENSE-data for full text) applies to the datafiles (DualLuc_example_data.xlsx & Tidy_design.csv)

Contributors ✨

Thanks goes to these wonderful people (emoji key):

Joachim Goedhart 💻 🐛 💡 🔧 ⚠️

ebrando 🔣 💡 🤔 📆 📓

Marc Galland 🤔 📆 ⚠️

This project follows the all-contributors specification. Contributions of any kind welcome!