R/import_tecanendpoint.R

In FishParade/bfish:

import_tecanendpoint <- function(tecan_path = "./rawdata/uv-vis/", tecan_pattern = ".xlsx") {
  # Function for importing Tecan plate reader .xlsx files matching a particular filename suffix, e.g. "_test-assay.xlsx"

  file_list <- list.files(path = tecan_path, pattern = str_c("*", tecan_pattern))
  assay_rawdf <- list()
  assay_timelist <- list()
  assay_data <- list()


  for (i in seq_along(file_list)) {
    # Find the row at which tabular data beings before data import.
    assay_rawdf[[i]] <- read_xlsx(str_glue("{tecan_path}{file_list[[i]]}"), sheet = "Sheet2") %>% 
      clean_names()
    data_skip <- grep("<>", assay_rawdf[[i]]$application_tecan_i_control)
    
    # Find the wavelength of the dataset.
    assay_hv <- grep("Measurement Wavelength", assay_rawdf[[i]]$application_tecan_i_control)
    assay_hv <- assay_rawdf[[i]][[assay_hv, 5]] %>% as.numeric()
  
    # Find the time of the measurement.
    assay_time <- grep("Start Time:", assay_rawdf[[i]]$application_tecan_i_control)
    assay_time <- lubridate::mdy_hms(assay_rawdf[[i]][[assay_time, 2]])
    
    assay_rawdf[[i]] <- read_xlsx(str_glue("{tecan_path}{file_list[[i]]}"), sheet = "Sheet2", skip = data_skip, guess_max = 200) %>% 
      clean_names() %>%
      mutate_if(is.numeric, as.character) %>%
      drop_na()
  
    # Data without time, temp
    assay_data[[i]] <- assay_rawdf[[i]] %>%
      pivot_longer(-x) %>%
      rename(row = x, column = name, abs = value) %>%
      mutate(column = as.character(parse_number(column)),
             well = str_c(row, column),
             notebook = str_replace(file_list[[i]], tecan_pattern, ""),
             abs = as.numeric(case_when(abs == "OVER" ~ "4",
                                        TRUE ~ abs)),
             wavelength = assay_hv,
             assay_datetime = assay_time)
}
    
    # Bind rows of the data list
    assay_data %>% 
      bind_rows()
}