read_plate: Read a plater-formatted file and turn it into a tidy data...

In plater: Read, Tidy, and Display Data from Microtiter Plates

Description

Converts data from plater format to a data frame with one well per row identified by well name.

Usage

read_plate(file, well_ids_column = "Wells", sep = ",")

Arguments

file	The path of a .csv file formatted as described below.
well_ids_column	The name to give the column that will contain the well identifiers. Default "Wells".
sep	The character used to separate columns in the file (e.g. "," or ";"). Defaults to ",".

Value

Returns a data frame with each well as a row. One column will be named with well_ids_column and contain the well names (A01, A02..). There will be as many additional columns as layouts in file. Empty wells are omitted.

plater format

The .csv file should be formatted as a microtiter plate. The top-left most cell contains the name to use for the column representing that plate. For example, for a 96-well plate, the subsequent wells in the top row should be labeled 1-12. The subsequent cells in the first column should be labeled A-H. That is:

ColName	1	2	3	...
A	A01	A02	A03	...
B	B01	B02	B03	...
...	...	...	...	...

In this example, the cells within the plate contain the well IDs ("A01", "A02"), but they may contain arbitrary characters: numbers, letters, or punctuation. Any cell may also be blank.

Note that Microsoft Excel will sometimes include cells that appear to be blank in the .csv files it produces, so the files may have spurious columns or rows outside of the plate, causing errors. To solve this problem, copy and paste just the cells within the plate to a fresh worksheet and save it.

Multiple columns

Multiple columns of information about a plate can be included in a single file. After the first plate, leave one row blank, and then add another plate formatted as described above. (The "blank" row should appear as blank in a spreadsheet editor, but as a row of commas when viewed as plain text.) As many plates as necessary can be included in a single file (e.g. data measured, subject, treatment, replicate, etc.).

Examples

file_path <- system.file("extdata", "example-1.csv", package = "plater")

# Data are stored in plate-shaped form
data <- read_plate(
   file = file_path,
   well_ids_column = "Wells")

# Now data are tidy
head(data)

Example output

  Wells Drug Concentration Bacteria Killing
1   A01    A       100.000  E. coli      98
2   A02    A        20.000  E. coli      95
3   A03    A         4.000  E. coli      92
4   A04    A         0.800  E. coli      41
5   A05    A         0.160  E. coli      17
6   A06    A         0.032  E. coli       2

plater documentation built on Feb. 12, 2022, 1:07 a.m.