How to use Well Plate Maker

Helene Borges

Abstract

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.

1 Introduction

This tutorial explains how to use the Well Plate Maker package.

1.1 General principle

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:

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.

1.2 Uses and associated input formats

There are two ways to use the WPM:

• Command line with appropriate R functions: for users who want to work with scripts or want to integrate the WPM into a pre-existing pipeline.
• Through a graphical interface (GUI): for users who do not necessarily have advanced R programming skills.

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
CSV	yes	yes
ExpressionSet	yes	no
SummarizedExperiment	yes	no
MSnSet	yes	no

2 Getting started

2.1 Prerequisites

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.

2.2 How to install

From GitHub (consider it a devel version):

devtools::install_github("HelBor/wpm", build_vignettes=TRUE)

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

3 How to use the WPM shiny application

3.1 Load the WPM package

library(wpm)

3.2 Launch the shiny application

Whether you use RStudio or simply work in 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 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.

3.3 The Home tab

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.