tidyplate

Microtiter plates or microplates have become a standard tool in analytical research and clinical diagnostic testing laboratories. They are convenient, high-throughput tools for organizing tissue culture, PCR tests (such as HIV/ COVID screening), or immunological assays such as ELISA, RIA and FIA. They offer many advantages over traditional assay formats including reduced sample and reagent volumes, increased throughput, and ease of automation. The goal of tidyplate is to help researchers convert different types of microplates into tidy dataframes which can be used in data analysis. tidyplate accepts xlsx and csv files formatted in a specific way as input. tidyplate supports all types of standard microplate formats namely: 6-well, 12-well, 24-well, 48-well, 96-well, 384-well, and 1536-well plates.

tidyplate has four functions:

tidy_plate: Transforms the input file (xlsx or csv) into a tidy dataframe.
check_plate: Checks whether the input file is valid for use with tidy_plate().
view_plate_names: Returns names/ id(s) of each plate in the input file.
build_plate: Generates a csv or xlsx template for each plate type.

Installation

To install tidyplate from CRAN:

install.packages("tidyplate")

You can install the development version of tidyplate from GitHub with:

devtools::install_github("shubhamdutta26/tidyplate")

Formating the input data file

The input excel or csv file should be formatted in a specific way:

Top left corner must hold the name for that plate.
Column names should be: 1, 2, 3, and so on and so forth.
Row names should be: A, B, C, and so on and so forth.
There must be an empty row between each plate.

Example

This is an example which shows you how to use the tidyplate. If the input file is an xlsx file it reads the first sheet by default. Users can specify sheet using the sheet argument for an xlsx file. Users can also specify the variable name of column where well ids will be stored (defaults to “well”). Please make sure that well_id argument does not match individual plate names in the input file.

First check if the input file is valid or not:

library(tidyplate)
file <- system.file("extdata", 
                    "example_12_well.xlsx", 
                    package = "tidyplate")
check_plate(file) # No error for valid file

example_12_well.xlsx: OK; Plate type: 12-well

incorrect_file <- system.file("extdata",
                              "incorrect_format.csv",
                              package = "tidyplate")
check_plate(incorrect_file) # Error type displayed

Error:
! Verify row and column ids in incorrect_format.csv.
ℹ Expected column ids: 1, 2, 3, and so on.
ℹ Expected row ids: A, B, C, and so on.
ℹ Use the `build_plate()` function to build an empty template.

As mentioned above, the formatting of the input file is very important. A csv or excel template for each plate type can be created using the build_plate function:

build_plate(plate_type = 96, 
            n_plates = 2, 
            file_type = "xlsx") # default is csv

If you want to retrieve the names of individual plates:

view_plate_names(file)

[1] "drug"             "cell_line"        "percent_survived"

Read and import the file as a tibble:

data <- tidy_plate(file)

Plate type: 12-well

head(data)

# A tibble: 6 × 4
  well  drug      cell_line percent_survived
  <chr> <chr>     <chr>                <int>
1 A01   Neomycin  HEK293                  60
2 A02   Puromycin HEK293                  NA
3 A03   Neomycin  Hela                    52
4 A04   Puromycin Hela                    18
5 B01   Neomycin  HEK293                  62
6 B02   Puromycin HEK293                  23

Import multiple csv files into separate tibbles:

csv_files <- list.files(path = file, 
                        pattern = "*.csv",
                        full.names = TRUE)

names <- tools::file_path_sans_ext(basename(csv_files))

# Loop through the filenames and assign data
for(i in seq_along(csv_files)) {
  assign(names[i], tidy_plate(csv_files[i]))
}

Import multiple csv files as a list of tibbles:

# Initialize an empty list to store tibbles for each file
tb_csv_list <- list()

# Loop through the filenames and assign data
for(i in seq_along(csv_files)) {
  tb_csv_list[[i]] <- tidy_plate(csv_files[i])
}

For multiple excel sheets in the same excel file:

# as individual tibbles
xl_file <- system.file("extdata", 
                       "multisheet_example.xlsx", 
                       package = "tidyplate")

sheets <- readxl::excel_sheets(xl_file)

for (sheet in sheets) {
  tb <- tidy_plate(xl_file, sheet = sheet)
  name <- paste0("tb_", sheet)
  assign(name, tb)
}

Plate type: 6-well
Plate type: 12-well
Plate type: 12-well

# as elements of a list
# Initialize an empty list to store tibbles for each sheet
tb_xl_list <- list()

for (sheet in sheets) {
  tb_xl_list[[sheet]] <- tidy_plate(xl_file, sheet = sheet)
}

Plate type: 6-well
Plate type: 12-well
Plate type: 12-well

References

Dutta, Shubham. 2024. Tidyplate: Transform Microplate Data into Tidy Dataframes. https://CRAN.R-project.org/package=tidyplate.