#' Form an Excel workbook and worksheet similar in format to those being
#' made by Luis Giavedoni's laboratory.
#'
#' The Excel file ``Report plate 62 08-15-2014.xlsx'' was used as a guide.
#' @param file character vector of length one with name of file to create
#' @param w_raw_mfi_df dataframe with raw results from Luminex machine
#' @param w_mfi_df dataframe with background substracted from raw results
#' @param w_d_mfi_df dataframe with normalized values where divisors were
#' used on background subtracted results
#' @param w_r_mfi_df dataframe where each antigen result is called as N, I, or
#' P based on is values relative to a fraction of the low control value.
#' @param w_combined_df dataframe with the antigen calls combined into agent
#' (virus) calls. (See get_combined() for algorithm).
#' @param low_positive_controls_df dataframe with \code{sample}, \code{name},
#' \code{wells}, and \code{val} columns that identify the well with low
#' positive control values (<5000 for Human or Goat IgG).
#'
#' @importFrom rmsutilityr create_wkbk
#' @export
make_excel_wkbk <- function(file, w_raw_mfi_df, w_mfi_df, w_d_mfi_df,
w_r_mfi_df, w_combined_df,
low_positive_controls_df) {
w_raw_mfi_df$file <- basename(w_raw_mfi_df$file)
w_mfi_df$file <- basename(w_mfi_df$file)
w_d_mfi_df$file <- basename(w_d_mfi_df$file)
w_r_mfi_df$file <- basename(w_r_mfi_df$file)
w_combined_df$file_name <- basename(w_combined_df$file_name)
if (nrow(low_positive_controls_df) > 0) {
df_list <- list(
w_raw_mfi_df,
w_mfi_df,
w_d_mfi_df,
w_r_mfi_df,
w_combined_df,
low_positive_controls_df)
sheetnames <- c(
"raw_mfi",
"minus_background",
"normalized",
"antigen_called",
"final_result",
"low_positive_controls")
} else {
df_list <- list(
w_raw_mfi_df,
w_mfi_df,
w_d_mfi_df,
w_r_mfi_df,
w_combined_df)
sheetnames <- c(
"raw_mfi",
"minus_background",
"normalized",
"antigen_called",
"final_result")
}
create_wkbk(file, df_list, sheetnames)
sheets_index <- c(3, 4, 5)
for (i in seq_along(sheets_index)) {
df_index <- c(4, 4, 5) # normalized sheet gets same format as antigen sheet
fmt_luminex_results(
excel_file = file,
df_list = df_list,
fmtIndexNum = df_index[i],
wrkSheetIndex = sheets_index[i],
sheet_name = sheetnames[sheets_index[i]],
low_positive_controls_df = low_positive_controls_df
)
}
file
}
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