1 Introduction

To generate plate maps, 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:

  1. randomly choose a well on the plate
  2. Randomly selects a sample;
  3. Check whether all the specified location constraints are met. If yes, place the sample accordingly.

This process allows for an experimental design by block randomization.

There are two ways using the wpm package:

  • through a shiny application for users who do not have sufficient R programming skills.
  • using R commands for users who want to work with their own R scripts.

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 explained in detail.

1.1 Supported input formats

Input Format Command line WPM app
CSV yes yes
ExpressionSet yes no
SummarizedExperiment yes no
MSnSet yes no

2 Getting started

2.1 Prerequisites

This tutorial explains how to use the Well Plate Maker package. Make sure you are using a recent R version (\(\geq 4.0.0\)). For Windows users who do not have the Edge browser, we recommend using the Chrome browser rather than Internet Explorer.

2.2 Installation from BioConductor:

if (!requireNamespace("BiocManager", quietly = TRUE))


3 How to use the WPM shiny application

3.1 Launch the shiny application

Whether you use RStudio or simply work with 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: Listening on, and paste the URL in your web browser.

WPM has 4 main tabs: Home, Parameters, Results ans Help.

3.2 The Home tab

Briefly presents the aim of the app, shows the last package version, explains how to cite us to support our work and gives the contact information.