README.md

In MartinBanchero/mpxtractor: Process microplate reader output files into a tidy dataframe

mpxtractor

mpxtractor: A flexible R package to process data from different plate reader machines.

The main function of mpxtractor is to provide a simple method that can process raw data from microplate readers like SpectraMax, FluorStar, and MultiscanGO and apply different methods to it. This package generates tidy tibble objects, this data can be combined with layout files, and then growth rates are calculated and plot over a microplate frame. This is a critical point in several research lines performing experiments using microplate reader machines mainly due to the time that takes to clean and sort the raw data into a tidy format. Also, the features of this package allow detecting which wells present faulty data e.g wells not filled correctly. Another feature of mpxtractor is that it allows plotting the layout file over a microplate frame, this is very useful because it is easy to visualize the layout, this is handy in the lab to set the experiment. This package main contribution is orientated to save time and get fast into data analysis. For the reasons mentioned above is why mpxtractor can help to reduce the time to process the raw data into tidy data frames, combine layout files with tidy data. Also, mpxtractor provides features to visualize growth curves and layout files over a microplate frame. The latter can be printed to be used in the lab during the set up of experiments. ## Features of `mpxtractor` This package is divided by two sets of functions: **1.** Function to wrangling the data in raw files, this functions are explained in detail in vignette `wrangling_and_layout_functions` along side with some examples. **2.** Functions to plot layout files and growth rates, the vignette `plotting_functions` explain how they work and some details. ## Installation wzxhzdk:0 ## Usage ### Example #### Layout design file and visualization Lets suppose we want to perform an experiment to measure growth rates under different type of sugars. The first step is to design the layout. Using `mpxtractor` we can load the layout file into a tidy data frame. wzxhzdk:1 Now we want to set the microplates and run the experiment in the lab, for this we can use the `plot_layout_file()` function that provide a visualization of our experimental design. For example, to avoid edge effects due to temperature, evaporation, etc. the wells around the perimeter of the plate might be more sensitive to this effects, visualizing the layout design over the microplate give an easy way to check whether the control or the samples are well positioned in the plate. In **Fig.1** is shown the `basic` and the `Medium` conditions over the microplate. wzxhzdk:2

**Figure 1:** Representation over a microplate mimic of the design file. In this case the medium was chosen to be colored. to be coloured.

### Data wrangling Once all the experimental design is complete we are ready to use the microplate reader machines. In this example we are using a fluorStar to measure our growth rates. Within `mpxtractor` we can find one wrangling function for each machine, in this case we going to use `read_fluorstar_data()` (see vignette `wrangling_and_layout_functions`) to store the raw data into a tidy dataframe. wzxhzdk:3 Now let’s suppose we want to repeat the experiment but this time we want to measure absorbance under the same conditions. In this case we have two raw data files to be analyzed. Using the function `read_multiple_data_files()` we can store both files into a tidy dataframe. There many options that can be used to gather files with this function, for more information check vignette `wrangling_and_layout_functions` . wzxhzdk:4 At this point we have two measurements under the same layout design. Now we want to add the layout information to our tidy data frame with both files. To do this we can use the function `combine_data_with_layout()` and store all the information in one tidy data frame. wzxhzdk:5 ### Visualization of growth rates The last step is to calculate and plot the growth curves for each well. wzxhzdk:6 wzxhzdk:7

**Figure 2:** Representation of growth rate curves per well mimicking a plate-shaped format. Note that in this case the attribute *Medium* was chosen to be coloured.

## Learn more To get started, first read `vignette("Introduction_to_mpxtractor")`. Then read more about the specific package components that you want to apply. - For data wrangling and layout files, read `vignette("wrangling_and_layout_functions")`. - For plotting functions, read `vignette("plotting_functions")` - For auxiliary functions read `vignette("Auxiliary_functions")`

MartinBanchero/mpxtractor documentation built on March 30, 2022, 10:56 p.m.