How to use Well Plate Maker

Helene Borges

Abstract

WPM is a shiny application deployed in the form of an R package. Its objective is to allow the user to create one (or more) randomized plate maps in order to perform his experiments by controlling batch effects without programming skills. However, R functions are available for users who want to work with their own R scripts.

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))
    install.packages("BiocManager")

BiocManager::install("wpm")

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:

library(wpm)
wpm()

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 http://127.0.0.1:8000, 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.