easyplater

easyplater is a tool for generating microplate manifests while decoupling clinical data from plate location effects.

In short, easyplater is an easy to use algorithm for generating 96-well plate designs without confounding clinical variables with plate location effects. Simply input clinical data and user-assigned clinical variable weights, and easyplater outputs the most deconvolved plate design it finds in plain text and R Markdown formats.

Installation

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

# install.packages("pak")
pak::pak("IMCM-OX/easyplater")

Example usage

library(easyplater)

# easyplater comes with a built-in example plate manifest
example_manifest
#> # A tibble: 423 × 9
#>    SampleID Cohort Group   Sex   Age plate   column   row   well 
#>       <dbl> <chr>  <chr> <dbl> <dbl> <chr>   <chr>    <chr> <chr>
#>  1        0 C2     D5        2    43 plate 1 Column 1 A     A1   
#>  2        1 C1     D7        1    66 plate 1 Column 1 B     B1   
#>  3        2 C1     D7        1    68 plate 1 Column 1 C     C1   
#>  4        3 C2     D7        2    77 plate 1 Column 1 D     D1   
#>  5        4 C1     D1        2    54 plate 1 Column 1 E     E1   
#>  6        5 C1     D7        2    75 plate 1 Column 1 F     F1   
#>  7        6 C2     D1        2    65 plate 1 Column 1 G     G1   
#>  8        7 C2     D7        1    58 plate 1 Column 1 H     H1   
#>  9        8 C2     D1        2    67 plate 1 Column 2 A     A2   
#> 10        9 C2     D8        2    61 plate 1 Column 2 B     B2   
#> # ℹ 413 more rows

# Run easyplater in one step
easyplater_design <- make_easyplater_design(
  manifest_df = example_manifest,
  plateID = "plate 1",
  columns_for_scoring = c("Cohort","Group","Sex","AgeGroup"),
  column_weights = c(5, 5, 10, 4),
  cols_to_categorize = list(c("Age", 10, NULL, "AgeGroup")),
  imbalance_fixer = list(TRUE, "Group", list("D1", "HC1", "D7", "D8"), 3),
  plate_size = 96
)
#> [1] "Getting and formatting plate data fram from manifest."
#> [1] "Allocating similar samples to distal wells."
#> [1] "Performing sample switching search."
#> [1] "Store the easyPlateR plate design in a data frame."

# Use a function exported from the OlinkAnalyze package to display plate layout
olink_displayPlateLayout(data = easyplater_design, fill.color = "Group", include.label = TRUE)
#> Warning: Removed 16 rows containing missing values or values outside the scale range
#> (`geom_text()`).