R/depricated_format_luminex_results.R

In rmsharp/snprcspf: SNPRC SPF Colony Screening Data Software Tool Package

## ## Returns Excel file name of file that has been formatted to highlight
## ## non-negative results in the sheet indicated.
## ##
## ## This highlights "I" and "P" results
## ## @param excel_file character vector with the name of the Excel file
## ## @param .df dataframe being used to guide highlighting. It is the same
## ## one as was used to make the worksheet.
## ## @param sheet_name name of the worksheet to highlight.
## ## @param low_positive_controls_df dataframe with the low positive controls
## ## @importFrom stats complete.cases
## ## @import XLConnect
## ## @export
## depricated_format_luminex_results <- function(excel_file, .df,
##                                    sheet_name = "final_result",
##                                    low_positive_controls_df) {
##   ## set-rows
##   ## format cells with highlighting, text wrapping, grey header, and column
##   ## specific borders
##   wb <- loadWorkbook(excel_file)
##   cs_positive <- createCellStyle(wb)
##   cs_indeterminate <- createCellStyle(wb)
##   cs_to_repeat <- createCellStyle(wb) # low positive control wells
##   cs_header <- createCellStyle(wb)
##   cs_border_header <- createCellStyle(wb)
##
##   ## set-wrap
##   setWrapText(cs_positive, wrap = TRUE)
##   setWrapText(cs_indeterminate, wrap = TRUE)
##   setWrapText(cs_to_repeat, wrap = TRUE)
##   setWrapText(cs_header, wrap = TRUE)
##   setWrapText(cs_border_header, wrap = TRUE)
##
##   ## set-fill
##   setFillPattern(cs_positive, fill = XLC$FILL.SOLID_FOREGROUND)
##   setFillForegroundColor(cs_positive, color = XLC$COLOR.ROSE)
##   setFillPattern(cs_indeterminate, fill = XLC$FILL.SOLID_FOREGROUND)
##   setFillForegroundColor(cs_indeterminate, color = XLC$COLOR.CORNFLOWER_BLUE)
##   setFillPattern(cs_to_repeat, fill = XLC$FILL.SOLID_FOREGROUND)
##   setFillForegroundColor(cs_to_repeat, color = XLC$COLOR.LEMON_CHIFFON)
##   setFillPattern(cs_header, fill = XLC$FILL.SOLID_FOREGROUND)
##   setFillPattern(cs_border_header, fill = XLC$FILL.SOLID_FOREGROUND)
##   setFillForegroundColor(cs_header, color = XLC$COLOR.GREY_25_PERCENT)
##   setFillForegroundColor(cs_border_header, color = XLC$COLOR.GREY_25_PERCENT)
##
##
##   ## make-matrices
##   ## Include row offset for column label in Excel sheets
##   positive_row <- matrix(data = rep(1:nrow(.df), each = ncol(.df)),
##                          nrow = nrow(.df),
##                          ncol = ncol(.df), byrow = TRUE) + 1L
##   positive_col <- matrix(data = rep(1:ncol(.df), each = nrow(.df)),
##                          nrow = nrow(.df),
##                          ncol = ncol(.df))
##   indeterminate_row <- positive_row
##   indeterminate_col <- positive_col
##   to_repeat_row <- positive_row
##   to_repeat_col <- positive_col
##
##   positive <- data.frame(row = positive_row[.df == "P"],
##                          col = positive_col[.df == "P"])
##   indeterminate <- data.frame(row = indeterminate_row[.df == "I"],
##                               col = indeterminate_col[.df == "I"])
##   ## Include row offset for column label in Excel sheets
##   well_rows <- ((1:nrow(.df)) + 1L)[.df[ , "wells"] %in%
##                                low_positive_controls_df$wells]
##   to_repeat <- data.frame(
##     row = rep(well_rows, ncol(.df)),
##     col = rep(1:ncol(.df), each = length(well_rows)))
##
##   positive <- positive[complete.cases(positive), ]
##   indeterminate <- indeterminate[complete.cases(indeterminate), ]
##
##   ## set-style
##   if (nrow(positive) > 0) {
##     setCellStyle(wb, sheet = sheet_name, row = positive$row, col = positive$col,
##                  cellstyle = cs_positive)
##   }
##   if (nrow(indeterminate) > 0) {
##     setCellStyle(wb, sheet = sheet_name, row = indeterminate$row,
##                col = indeterminate$col,
##                cellstyle = cs_indeterminate)
##   }
##   if (nrow(to_repeat) > 0) {
##     setCellStyle(wb, sheet = sheet_name, row = to_repeat$row,
##                  col = to_repeat$col,
##                  cellstyle = cs_to_repeat)
##   }
##   setCellStyle(wb, sheet = sheet_name, row = 1, col = seq_along(names(.df)),
##                cellstyle = cs_header)
##
##   ## setCellStyle(wb, sheet = sheet_name, row = positive$row,
##   ##              col = positive$col,
##   ##              cellstyle = cs_border_positive)
##   ## setCellStyle(wb, sheet = sheet_name, row = indeterminate$row,
##   ##              col = indeterminate$col,
##   ##              cellstyle = cs_border_indeterminate)
##   setCellStyle(wb, sheet = sheet_name, row = 1, col = seq_along(names(.df)),
##                cellstyle = cs_border_header)
##   ## save-wb
##   saveWorkbook(wb)
##   excel_file
## }