diff --git a/README.md b/README.md index 1f05641..e971cc0 100644 --- a/README.md +++ b/README.md @@ -13,13 +13,41 @@ 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/](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: + +```r +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` -* An excel file or CSV file in which conditions are indicated in a 96-well lay-out. The conditions are seperated by underscores (see the example design that is included in this repo: `Design_example.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 +## Example output -Standard output generated with the example data: +Standard output generated with the example data and example design: ![alt text](https://github.com/ScienceParkStudyGroup/PlotXpress/blob/master/plotXpress_example.png "Output")