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)
@@ -18,3 +19,5 @@ import(readxl)
 import(stringr)
 import(utils)
 importFrom(R6,R6Class)
+importFrom(stats,IQR)
+importFrom(stats,quantile)

R/helpers.R

@@ -113,3 +113,15 @@ color_codes <-
     green_start = "\033[32m",
     green_end = "\033[39m"
   )
+
+
+#' Check if a value is an outlier
+#'
+#' @param x Vector of numeric values from which the outliers are to be detected.
+#'
+#' @return A logical vector indicating whether each value is an outlier.
+#'
+#' @importFrom stats IQR quantile
+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 +1,71 @@
+#' 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[["Median"]] %>%
+    dplyr::select(analyte) %>%
+    dplyr::rename("MFI" = analyte) %>%
+    dplyr::mutate(
+      SampleId = paste0("SampleId: ", seq_len(nrow(.))),
+      SampleType = plate$sample_types,
+    )
+
+  blanks_df <- df %>% dplyr::filter(SampleType == "BLANK")
+  blank_mean <- mean(blanks_df$MFI)
+  sc_df <- df %>% dplyr::filter(SampleType == "STANDARD CURVE")
+  test_df <- df %>% dplyr::filter(SampleType == "TEST")
+
+  p <- test_df %>%
+    dplyr::mutate(
+      outlier = ifelse(is_outlier(MFI), SampleId, as.character(NA))
+    ) %>%
+    ggplot2::ggplot(aes(x = SampleType, y = MFI)) +
+    main_geom(color = "blue") +
+    ggplot2::geom_text(aes(label = outlier), na.rm = TRUE, hjust = -0.1) +
+    ggplot2::geom_hline(
+      aes(yintercept = blank_mean, linetype = "BLANK MEAN"),
+      color = "dark grey", linewidth = 1
+    ) +
+    ggplot2::geom_point(data = sc_df, size = 3, color = "red") +
+    ggplot2::scale_linetype_manual(
+      name = "Boundries", values = c("BLANK MEAN" = "dashed")
+    ) +
+    ggplot2::guides(color = ggplot2::guide_legend(title = "Sample Type")) +
+    ggplot2::ggtitle(
+      paste0("MFI Boxplot of test sample coverage\n for analyte: ", analyte)
+    ) +
+    ggplot2::xlab("Sample Type") +
+    ggplot2::ylab("MFI (Median)") +
+    ggplot2::theme_minimal() +
+    ggplot2::theme(
+      plot.title = element_text(hjust = 0.5) # Center title
+    )
+  p
+}

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))
 })