The Well-Plate Maker (WPM) is a shiny application deployed as an R package. Functions for a command-line/script use are also available. The WPM allows users to generate well plate maps to carry out their experiments while improving the handling of batch effects. In particular, it helps controlling the “plate effect” thanks to its ability to randomize samples over multiple well plates. The algorithm for placing the samples is inspired by the backtracking algorithm: the samples are placed at random while respecting specific spatial constraints. The use of WPM as well as the definition of configurable spatial constraints are described in the following sections.
This tutorial explains how to use the Well Plate Maker package.
To generate plate maps, the WPM uses an algorithm inspired from the backtracking algorithm. More precisely, WPM loops on the following actions until all of the samples are given a correct location:
This process allows for an experimental design by block randomization.
There are two ways to use the
Important: Even in case of command line use, we strongly recommend to read the section about the shiny app section, as this is where all terms and concepts are detailed.
|Input Format||Command line||WPM app|
Make sure you are using a recent version of R (\(\geq 4.0.0\)). For Windows users who do not have the Edge browser, we recommend using the Chrome browser rather than Internet Explorer.
From GitHub (consider it a devel version):
From Bioconductor (release, stable version):
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("wpm")
Instructions can also be found on the Bioconductor page
Whether you use RStudio or simply work in an R console, the procedure remains the same to launch the shiny app:
If everything is in order, a new window will open in your default browser.
If not, find the line written in the R console that looks like
Listening on http://127.0.0.1:8000, and paste the URL in your web browser.
WPM has 4 main tabs: Home, Parameters, Results and Help.
This tab briefly presents the aim of the app, shows the last package version, explains how to support our work by citing the associated article and gives contact information.