---
title: How to use Well Plate Maker
author:
- name: Helene Borges
affiliation: Universite Grenoble Alpes
email: borges.helene.sophie@gmail.com
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.
vignette: >
    %\VignetteIndexEntry{How to use Well Plate Maker}
    %\VignetteEngine{knitr::rmarkdown}
    %\VignetteEncoding{UTF-8}
output: 
    BiocStyle::html_document:
        toc: yes
        toc_float: true

---


# 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](#shiny_app) for users who do not have sufficient  R programming skills.
* using [R commands](#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](#shiny_app), as this is where all terms and concepts are 
explained in detail.


## Supported input formats

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


# Getting started

## 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.

## Installation from __BioConductor__:
```{r install from BioConductor, eval=FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("wpm")
```

# How to use the WPM shiny application {#shiny_app}

## 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:

```{r launch wpm, eval = FALSE}
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__.

## 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.

![The Home page when wpm is started](images/home.PNG)

## The __Parameters__ tab

Overall the page is organized in two sections.

The one on the left contains all the configuration steps. It is divided into 6 main steps, detailed below. It is of the utmost importance to correctly specify all the constraints for generating the desired plate maps.

The one on the right summarizes the input parameters (tuned along the 6 steps of the left panel)
as well as the chosen (empty) plate layout. The right section is 
automatically updated each time a parameter is changed in the left section.

![Parameters Panel](images/parametersPanel.PNG)


### Upload dataset

First, you must upload a *__Comma-separated values__* (.CSV) or a text (.txt) file. 
This file contains at least one kind of information: the sample names.
```{r, echo=FALSE}
knitr::kable(data.frame("Sample" = c("s1","s2","s3","s4")))
```
It is also possible to provide a file containing several variables describing
the data, as in the example below:
```{r, echo=FALSE}
knitr::kable(
    data.frame("Sample" = c("s1","s2","s3","s4"), "Type" = c("A","A","B","C"),
               "Treatment" = c("trt1","tr1","Ctrl","Ctrl"))
)
```

__IMPORTANT__ Please respect this ORDER of columns for the data in the CSV file:
Sample names in the __first__ column, and other variables in the other columns, 
like the example below (if there are rownames, then the Samples' Column must be 
the second in the file.):

    Sample;Type;Treatment
    s1;A;trt1
    s2;A;trt1
    s3;B;Ctrl
    s4;C;Ctrl

Second, you have to specify if there are quotes in your file or not. 
The Default is none, meaning that there is no __*"*__ or __*'*__ characters in your file.
If you select the appropriate quote, then you will be able to:

* check if your file does have a __header__ and __row names__.
* select the appropriate __separator__ field. Default is semicolon (__*";"*__)

Then you can select one of the variables that you want to use as the grouping
factor for WPM.  
This column will be renamed "Group" in the final dataset.

![Choose the grouping factor](images/groupVariable.PNG)

The names you give to columns in your CSV do not matter, because WPM will create
a new dataset having 3 fields: _"Sample"_ , _"Group"_ and _"ID"_.

You will see your dataset on the right side of the window, and another dataset 
which will be used by WPM to generate the map(s).   
Each sample is assigned a unique ID, which will be used to name the samples
onto the plate maps (for more details on the ID see the [Results section](#results_panel) ).

![Dataset vizualisation](images/toy2rightpanel.PNG)

__IMPORTANT__ Please ensure that the dataset is correctly displayed in the right window and that the number of samples / groups is correct.    
If you see that the total number of samples is wrong, this means that you have
not chosen the appropriate options among those described above and you need to
set the correct ones.

### Choose a Project name
This step is optional. If you provide one, it will be used in the plots titles 
and in the name of the final dataset.


### Plate(s) dimensions {#plate-dims}

Here you have to specify the plate dimensions and their number. Currently, WPM 
supports plate dimensions of 6,24, 48, 96, 386, 1534 wells and a custom option 
(where you specify the number of lines and columns by hand).

To the right of step 2 you can see an information box, warning you that WPM 
will distribute the samples in a balanced manner within the plates (if there 
are several).

![balanced way message](images/balanceInfobox.PNG)

If you select a plate size compatible with the total number of samples, you 
will see two blues boxes and a plate plan appear on the right summarizing all 
of your configuration.
In the example below, we selected the pre-defined dimension of 96 wells and only
one plate:

![plate dimensions example](images/platedimensions.PNG)

The right side of the panel will summarize all these parameters:

![parameters summary](images/parametersCheck.PNG)

This plot updates with each modification of the parameters, thus making it 
possible to see if one has made an error.

__IMPORTANT__: If WPM detects a problem or incompatibility between parameters, 
you will see an error message instead of the plate map, explaining you what 
could be the problem.

![Example of error message](images/exErrorMsg.PNG)


### Forbidden wells {#forbidden_wells}

In this step are listed the __Forbidden wells__ if any (optional): 

> A __Forbidden well__ will not be filled with any kind of sample. 
We simply do not want to fill them (*e.g.* the coins of the plate), or in 
case of dirty wells, broken pipettes, etc.

You fill the text input with the coordinates of the wells (a combination of letters and numbers like in the example below):

![Example of forbidden wells listed in the text input](images/forbiddenEx1.PNG)

You will see the plot updated in the right section:

![Updated plot with forbidden wells](images/forbiddenEx2.PNG)

The wells filled with forbidden wells will have the *"forbidden"* ID in the 
final dataset.


### Buffers {#buffers}
At this stage you can specify the wells which correspond to buffers, if there 
are any. 

> A __buffer well__ corresponds to wells filled in with solution but without 
biological material (*e.g.* to avoid cross-contamination).

Five patterns are available for placing the buffers:

**1)** *no buffers*: there will be no buffer on the plate(s).

**2)** *Per line*: Automatically places buffers every other line. 
You can choose to start placing in even or odd line.

![Per line mode example with even option](images/bufferLine.PNG)

**3)** *Per column*: Automatically places buffers every other column. 
You can choose to start placing in even or odd column.

![Per Column mode example with even option](images/bufferColumn.PNG)

**4)** *Checkerboard*: Automatically places buffers like a checkerboard.

![Checkerboard mode](images/bufferCheckerboard.PNG)

**5)** *Choose by hand*: It is the same procedure as for specifying forbidden 
wells.

#### Specify the neighborhood constraints {#neighborhood}

These are the spatial constraints that WPM needs to create the plates.
Currently, 4 types of them are proposed. Note that the patterns are available only 
if they are compatible with the chosen buffer pattern.
The question here is: Should samples from the same group be found side by side?

Schematically, the spatial constraints can be summarized as follows (the blue
well is the current well evaluated by WPM; The wells in green are those 
assessed for compliance with the chosen constraint. The blue well therefore has 
the possibility (but not the obligation since the filling of the plate is done 
randomly) to be filled with a sample belonging to the same group as the samples 
in the wells evaluated.

![No constraint](images/NCnone.PNG)

![North-South constraint](images/NCns.PNG) 

![East-West constraint](images/NCew.PNG)

![North-South-East-West constraint](images/NCnsew.PNG)

The wells filled with buffer wells will have the *"buffer"* ID in the 
final dataset.

### Fixed wells {#fixed_wells}

At this stage you can specify the wells which correspond to fixed 
wells, if there are any. 

> A __fixed well__ corresponds to quality control samples or standards,
the precise location of which must be controlled by the experimenter.

This step works in exactly the same way as the 
[forbidden well](#forbidden_wells) step. The only difference is that the fixed 
will appear in **black** on the plot.

The wells filled with fixed wells will have the *"fixed"* ID in 
the final dataset.

### Number of iterations

Here you choose a maximum number of iterations that WPM is authorized to find a 
solution (the default value is 20, but if your configuration is somewhat complex, then 
it is advisable to increase this number).
Afterwards, start WPM by clicking the **"start WPM"** button.
An *iteration* corresponds to an attempt by WPM to find a solution. The 
algorithm used is not "fully" backtracked: WPM stops as soon as there are no 
more possibilities to finalize the current solution, and starts from scratch 
the plate map, until providing a solution that complements all the constraints.
With this approach, not all possible combinations are explored, but it does 
reduce execution time.

When you start WPM, a progress bar shows which iteration WPM is at.

If WPM finds a solution, you will see this pop in the browser, inviting you to 
go to the [Result Panel](#results_panel):

![WPM succeeded](images/wpmSuccess.PNG)

If WPM fails, an error message will appear, prompting you to try again: 

![WPM failed](images/wpmFailed.PNG)


__IMPORTANT__ If after launching WPM and generating the results, you realize that one or more parameters do not work, you can always return to the "Parameters" tab and modify them. The data displayed in the "Results" tab will not be automatically changed, you will have to click again on the "start WPM" button to take into account the new changes.

__NOTE__ If you want to create a new plate plan for another project, press `ctrl + f5`, this will reset the application.

---

## The __Results__ tab {#results_panel}

This tab allows you to look after the final dataset containing the wells 
chosen for each sample:

![Final dataframe](images/final_dataset.PNG)

The dataset contains 7 columns giving all the information needed to run the 
experiment: The sample name with its corresponding group; its ID for the plot; 
the well chosen; the row and the column to which the well corresponds and the 
number of the plate on which the sample must be placed during the experiment.

This tab also shows you the generated plot(s) of your final well-plate map(s).
One color corresponds to one group level. The numbers are the IDs used in 
place of the sample names which could be too long and make the plot unreadable.

Below is an example of 80 samples distributed in 10 groups and placed on a 
96 well-plate, with the North-South-East-West neighborhood constraint:

![Plate map](images/plot1.png)

Dataset and plots are downloadable separately.

# How to use WPM using command lines {#R_commands}

As explained before, WPM can also be used through R command lines by following these steps:

1. Create the dataset for WPM
2. Run WPM
3. Visualize the final plate plan(s)

## Prepare the dataset
The user can work with CSV files, `ExpressionSet`, `MSnSet` or 
`SummarizedExperiment`objects.
The first step is to create a dataframe containing all the data needed by wpm 
to work properly. To do so:

### Starting from a CSV file, then run:
```{r convert CSV file, eval = FALSE}
imported_csv <- wpm::convertCSV("path-to-CSV-file")
```
### Starting from an `ExpressionSet` or `MSnSet` object
```{r create an MSnSet object}
sample_names <- c("s1","s2","s3","s4", "s5")
M <- matrix(NA, nrow = 4, ncol = 5)
colnames(M) <- sample_names
rownames(M) <- paste0("id", LETTERS[1:4])
pd <- data.frame(Environment = rep_len(LETTERS[1:3], 5),
                 Category = rep_len(1:2, 5), row.names = sample_names)
rownames(pd) <- colnames(M)
my_MSnSet_object <- MSnbase::MSnSet(exprs = M,pData =  pd)
```

then run `convertESet` by specifying the object and the variable to use as 
grouping factor for samples:
```{r convert ESet/MSnSet object}
df <- wpm::convertESet(my_MSnSet_object, "Environment")
```

### Starting from a `SummarizedExperiment`

```{r convert SummarizedExperiment object}
nrows <- 200
ncols <- 6
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
colData <- data.frame(Treatment=rep(c("ChIP", "Input"), 3),
                      row.names=LETTERS[1:6])
se <- SummarizedExperiment::SummarizedExperiment(assays=list(counts=counts),
                                                 colData=colData)
df <- wpm::convertSE(se, "Treatment")
```

## Run WPM

The next step is to run the wpm wrapper function by giving it all the parameters
needed. For more details on the parameters, please see the sections about
[plate dimensions](#plate-dims), [forbidden wells](#forbidden_wells), 
[buffers](#buffers), [Quality Control wells](#fixed_wells) and 
[Spatial constraints](#neighborhood).

In this toy example, we do not specify any buffer well.

### After importing a CSV file

```{r run wpm with a CSV file, eval=FALSE}
wpm_result <- wpm::wrapperWPM(user_df = imported_csv$df_wpm,
            plate_dims = list(8,12),
            nb_plates = 1,
            forbidden_wells = "A1,A2,A3",
            fixed_wells = "B1,B2",
            spatial_constraint = "NS")
```

### after importing an `ExpressionSet`, `MSnSet` or `SummarizedExperiment`
```{r run wpm}
wpm_result <- wpm::wrapperWPM(user_df = df,
            plate_dims = list(8,12),
            nb_plates = 1,
            forbidden_wells = "A1,A2,A3",
            fixed_wells = "B1,B2",
            spatial_constraint = "NS")
```

## Plate map visualization
The last step is to plot the plate map(s) using:
```{r visualize plate map}
drawned_map <- wpm::drawMap(df = wpm_result,
        sample_gps = length(levels(as.factor(colData$Treatment))),
        gp_levels = gp_lvl <- levels(as.factor(colData$Treatment)),
        plate_lines = 8,
        plate_cols = 12,
        project_title = "my Project Title")
```

```{r see the map}
drawned_map
```


Plots can be saved with:
```{r save map plot, eval=FALSE}
ggplot2::ggsave(
    filename = "my file name",
    plot = drawned_map,
    width = 10,
    height = 7,
    units = "in"
)
```

__IMPORTANT__ If multiple plates where specified, then `wpm_result` will be a 
list containing a dataset **for each generated plate**. Concretely, if 2 plates 
are generated, each of them can be accessed with `wpm_result[[numberOfThePlate]]`:
```{r, eval = FALSE}
numberOfThePlate <- 1
drawned_map <- wpm::drawMap(df = wpm_result[[numberOfThePlate]],
        sample_gps = length(levels(as.factor(pd$Environment))),
        gp_levels = gp_lvl <- levels(as.factor(pd$Environment)),
        plate_lines = 8,
        plate_cols = 12,
        project_title = "my Project Title")
```



# Citing Our work
> The published article of the project will be linked here.

# SessionInfo
```{r SessionInfo}
sessionInfo()
```