Merge pull request #25 from plinders/main

Add 1536-well plate format

Author: jpquast

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ggplate
 Title: Create Layout Plots of Biological Culture Plates and Microplates
-Version: 0.1.4
+Version: 0.1.5
 Authors@R: person(given = "Jan-Philipp",
            family = "Quast",
            role = c("aut", "cre"),
@@ -11,7 +11,7 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Imports: 
     dplyr,
     ggplot2,

NEWS.md

@@ -1,3 +1,7 @@
+# ggplate 0.1.5
+
+* The package received the 1536-well format. Thanks to @plinders!
+
 # ggplate 0.1.4
 
 * Fix issue #23. If not all possible rows were part of the data, wells were shifted down to the bottom of the plate. This has been fixed and every well is in the correct position irrespective of the completeness of the data.

R/data.R

@@ -108,3 +108,12 @@
 #' @format A data frame with a `Value` and a `well` column.
 #' @source Drugs were chosen from a standard FDA approved drug library.
 "data_discrete_96"
+
+#' Continuous 1536-well plate dataset
+#'
+#' A dataset containing 1536 positive numeric values randomly generated using a normal distribution (`rnorm()`).
+#' Each value is assigned to a position in a 1536-well plate.
+#'
+#' @format A data frame with a `Value` and a `well` column.
+#' @source Randomly generated.
+"data_continuous_1536"

R/plate_plot.R

@@ -12,7 +12,7 @@
 #' @param label a character or numeric column in the `data` data frame that contains values that should be plotted as labels
 #' on the plate layout. Can be the same column as `value`.
 #' @param plate_size a numeric value that specifies the plate size (number of wells) used for the plot. Possible values
-#' are: 6, 12, 24, 48, 96 and 384.
+#' are: 6, 12, 24, 48, 96, 384 and 1536.
 #' @param plate_type a character value that specifies the well type. Possible values are "round" and "square". The default is
 #' "square".
 #' @param colour optional, a character vector that contains colours used for the plot. If the `value` argument is discrete
@@ -127,7 +127,7 @@ plate_plot <- function(data,
                        label_size,
                        silent = TRUE,
                        scale) {
-  if (!plate_size %in% c(6, 12, 24, 48, 96, 384)) {
+  if (!plate_size %in% c(6, 12, 24, 48, 96, 384, 1536)) {
     stop("Selected plate_size not available!")
   }
 
@@ -223,15 +223,17 @@ plate_plot <- function(data,
     nchar() |>
     max()
 
+  MORELETTERS <- c(LETTERS, "AA", "AB", "AC", "AD", "AE", "AF")
+
   data_prep <- data |>
     dplyr::ungroup() |>
     dplyr::mutate(
       row = stringr::str_extract({{ position }}, pattern = "[:upper:]+"),
       col = as.numeric(stringr::str_extract({{ position }}, pattern = "\\d+")),
-      row_num = as.numeric(match(.data$row, LETTERS)),
+      row_num = as.numeric(match(.data$row, MORELETTERS)),
       colours = data_colours,
       label_colours = label_col
-    ) 
+    )
 
   if (!is.numeric(dplyr::pull(data, {{ value }}))) {
     # Convert character values to factors
@@ -413,7 +415,26 @@ plate_plot <- function(data,
       size <- (4.4 - max((max_label_length - 13) * 0.07, 0)) * scale
     }
   }
-  
+
+  if (plate_size == 1536) {
+    n_cols <- 48
+    n_rows <- 32
+    size <- 1.8 * scale
+    min_x_axis <- 0.95
+    max_x_axis <- n_cols
+    min_y_axis <- 0.9
+    max_y_axis <- n_rows
+    text_size <- 4 * scale
+    legend_text_size <- text_size
+    legend_title_size <- text_size
+    title_size_preset <- 10 * scale
+    legend_size <- size
+    stroke_width <- 0.3 * scale
+    if (show_legend) {
+      size <- (2.2 - max((max_label_length - 13) * 0.07, 0)) * scale
+    }
+  }
+
   # Update row number to be reversed
   # This depends on the n_rows variable, which depends on the plate size
   data_prep <- data_prep |>
@@ -465,7 +486,7 @@ plate_plot <- function(data,
       xlim = c(min_x_axis, max_x_axis),
       ylim = c(min_y_axis, max_y_axis)
     ) +
-    ggplot2::scale_y_continuous(breaks = seq(1, n_rows), labels = rev(LETTERS[1:n_rows])) +
+    ggplot2::scale_y_continuous(breaks = seq(1, n_rows), labels = rev(MORELETTERS[1:n_rows])) +
     ggplot2::scale_x_continuous(breaks = seq(1, n_cols), position = "top") +
     {
       if (is.numeric(dplyr::pull(data, {{ value }}))) {
@@ -485,15 +506,15 @@ plate_plot <- function(data,
       y = ""
     ) +
     {
-      if (!missing(label)) ggplot2::geom_text(ggplot2::aes(x = col, 
-                                                           y = .data$row_num, 
+      if (!missing(label)) ggplot2::geom_text(ggplot2::aes(x = col,
+                                                           y = .data$row_num,
                                                            label = format(
-                                                             {{ label }}, 
+                                                             {{ label }},
                                                              drop0Trailing = FALSE, # does not drop trailing 0
                                                              justify = "none", # does not add white spaces for justification
                                                              trim = TRUE) # removes leading white spaces
-                                                             ), 
-                                              colour = data_prep$label_colours, 
+                                                             ),
+                                              colour = data_prep$label_colours,
                                               size = label_size_scaled)
     } +
     ggplot2::theme_bw() +

README.Rmd

@@ -31,6 +31,7 @@ Currently the package supports the following plate sizes:
 * 48-well plate
 * 96-well plate
 * 384-well plate
+* 1536-well plate
 
 
 ## Installation

data-raw/example_data.R

@@ -1,5 +1,6 @@
 library(dplyr)
 library(tidyr)
+library(stringr)
 
 set.seed(1234)
 
@@ -167,3 +168,18 @@ data_continuous_384 <- data.frame(matrix(round(abs(rnorm(384)), 2), nrow = 16, n
   distinct(well, Value)
 
 usethis::use_data(data_continuous_384, overwrite = TRUE)
+
+#1536-well plate
+
+MORELETTERS <- c(LETTERS, "AA", "AB", "AC", "AD", "AE", "AF")
+
+data_continuous_1536 <- data.frame(matrix(round(abs(rnorm(1536)), 2), nrow = 32, ncol = 48)) |>
+  mutate(rows = MORELETTERS[1:32]) |>
+  pivot_longer(cols = -rows, names_to = "cols", values_to = "Value") |>
+  mutate(
+    cols = as.numeric(str_remove(cols, pattern = "V|X")),
+    well = paste0(rows, cols)
+  ) |>
+  distinct(well, Value)
+
+usethis::use_data(data_continuous_1536, overwrite = TRUE)