Implement boxplot for MFI

NAMESPACE

@@ -4,6 +4,7 @@ export(PlateBuilder)
 export(create_standard_curve_model_analyte)
 export(is_valid_data_type)
 export(is_valid_sample_type)
+export(plot_mfi_for_analyte)
 export(plot_standard_curve_analyte)
 export(plot_standard_curve_analyte_with_model)
 export(predict_dilutions)

R/helpers.R

@@ -113,3 +113,8 @@ color_codes <-
     green_start = "\033[32m",
     green_end = "\033[39m"
   )
+
+
+is_outlier <- function(x) {
+  return(x < quantile(x, 0.25) - 1.5 * IQR(x) | x > quantile(x, 0.75) + 1.5 * IQR(x))
+}

R/plots-mfi.R

@@ -0,0 +1,57 @@
+#' Plot MFI value distribution for a given analyte
+#'
+#' @param plate A plate object
+#' @param analyte The analyte to plot
+#' @param data_type The type of data to plot. Default is "Median"
+#' @param plot_type The type of plot to generate. Default is "boxplot".
+#' Available options are "boxplot" and "violin".
+#'
+#' @return A ggplot object
+#'
+#' @import dplyr
+#' @import ggplot2
+#'
+#' @export
+plot_mfi_for_analyte <- function(plate, analyte,
+                                 data_type = "Median", plot_type = "boxplot") {
+  if (!(analyte %in% plate$analyte_names)) {
+    stop("Analyte not found in the plate")
+  }
+  if (!is_valid_data_type(data_type)) {
+    stop("Datatype not supported.")
+  }
+
+  main_geom <- switch(plot_type,
+    "boxplot" = ggplot2::geom_boxplot,
+    "violin" = ggplot2::geom_violin,
+    {
+      stop("Plot type not supported. Use either 'boxplot' or 'violin'")
+    }
+  )
+
+  df <- plate$data[[data_type]]
+  df %>%
+    dplyr::select(analyte) %>%
+    dplyr::rename("MFI" = analyte) %>%
+    dplyr::mutate(
+      SampleId = paste0("SampleId: ", seq_len(nrow(.))),
+      SampleTypes = plate$sample_types,
+    ) %>%
+    dplyr::group_by(SampleTypes) %>%
+    dplyr::mutate(
+      outlier = ifelse(is_outlier(MFI), SampleId, as.character(NA))
+    ) %>%
+    ggplot2::ggplot(aes(x = SampleTypes, y = MFI)) +
+    main_geom() +
+    ggplot2::geom_text(aes(label = outlier), na.rm = TRUE, hjust = -0.1) +
+    ggplot2::xlab("Sample Types") +
+    ggplot2::ylab("MFI (Median)") +
+    ggplot2::ggtitle(
+      paste0("Boxplot of MFI per sample type for analyte: ", analyte)
+    ) +
+    ggplot2::theme_minimal() +
+    ggplot2::theme(
+      plot.title = element_text(hjust = 0.5), # Center title
+      axis.title.x = element_text(margin = margin(t = 10)) # Adjust x-axis title
+    )
+}

R/standard_curves.R

@@ -260,6 +260,4 @@ plot_standard_curve_analyte_with_model <- function(plate, analyte_name, model, d
         yintercept = bottom_asymptote, linetype = "dashed", color = "gray"
       )
   }
-
-  print(p)
 }

tests/testthat/test-integration.R

@@ -3,12 +3,16 @@ library(testthat)
 test_that("Fully Parse CovidOISExPONTENT.csv plate data", {
   path <- system.file("extdata", "CovidOISExPONTENT.csv", package = "PvSTATEM", mustWork = TRUE)
   expect_no_error(plate <- read_luminex_data(path, format = "xPONENT"))
+
+  expect_no_error(p <- plot_mfi_for_analyte(plate, "S2"))
+  expect_true(inherits(p, "ggplot"))
+
   expect_warning(plate <- plate$blank_adjustment(in_place = FALSE))
   expect_equal(plate$blank_adjusted, TRUE)
 })
 
 test_that("Fully Parse CovidOISExPONTENT_CO.csv plate data with layout", {
   path <- system.file("extdata", "CovidOISExPONTENT_CO.csv", package = "PvSTATEM", mustWork = TRUE)
   layout_path <- system.file("extdata", "CovidOISExPONTENT_CO_layout.xlsx", package = "PvSTATEM", mustWork = TRUE)
-  expect_no_error(read_luminex_data(path, format = "xPONENT", layout_filepath = layout_path))
+  expect_no_error(plate <- read_luminex_data(path, format = "xPONENT", layout_filepath = layout_path))
 })